diff --git a/TEST_FLU/config.yaml b/TEST_FLU/config.yaml deleted file mode 100644 index 8c7ae34..0000000 --- a/TEST_FLU/config.yaml +++ /dev/null @@ -1,34 +0,0 @@ -Submission: - NCBI: - Username: username - Password: password - Submission_Position: 2 - Description: - Title: flu_test_submission - Comment: This is a test submission - Organization: - '@role': owner - '@type': institute - Name: CDC - Address: - Affil: Centers for Disease Control and Prevention - Div: Respiratory Viruses Branch, Division of Viral Diseases - Street: 1600 Clifton Rd - City: Atlanta - Sub: GA - Postal_code: 30329 - Country: USA - Email: email@myemail.com - Phone: "" - Submitter: - '@email': email@myemail.com - '@alt_email': "" - Name: - First: Jane - Last: Doe - GISAID: - Client-Id: TEST-EA76875B00C3 - Username: username - Password: password - Submission_Position: 1 - diff --git a/TEST_FLU/metadata.csv b/TEST_FLU/metadata.csv deleted file mode 100755 index 084104f..0000000 --- a/TEST_FLU/metadata.csv +++ /dev/null @@ -1,17 +0,0 @@ -sequence_name,organism, collection_date,authors,ncbi-spuid,ncbi-spuid_namespace,ncbi-bioproject,bs-description,bs-package,bs-collected_by,bs-geo_loc_name, bs-host, bs-host_disease,bs-isolate,bs-isolation_source,bs-lat_lon,bs-host_sex,bs-host_age,bs-serotype,sra-file_location,sra-file_name,sra-library_name,sra-instrument_model,sra-library_strategy,sra-library_source,sra-library_selection,sra-library_layout,sra-library_construction_protocol,sra-sra_loader,gb-seq_id,gb-subm_lab,gb-subm_lab_division,gb-subm_lab_addr,gb-publication_status,gb-publication_title,src-strain,src-country,src-host,src-serotype,src-isolation_source,src-note,cmt-StructuredCommentPrefix,cmt-Assembly-Method,cmt-Coverage,cmt-Sequencing-Technology,cmt-Adamantane_resistance,cmt-Patient_symptoms,cmt-EPI_ISOLATE_ID,cmt-TYPE,cmt-Segment_name,cmt-HOST_AGE,cmt-HOST_GENDER,cmt-PASSAGE,cmt-StructuredCommentSuffix,gs-Isolate_Name,gs-seq_id,gs-segment,gs-Subtype,gs-Lineage,gs-Passage_History,gs-Location,gs-province,gs-sub_province,gs-Location_Additional_info,gs-Host,gs-Host_Additional_info,gs-Submitting_Sample_Id,gs-Originating_Lab_Id,gs-Originating_Sample_Id,gs-Antigen_Character,gs-Adamantanes_Resistance_geno,gs-Oseltamivir_Resistance_geno,gs-Zanamivir_Resistance_geno,gs-Peramivir_Resistance_geno,gs-Other_Resistance_geno,gs-Adamantanes_Resistance_pheno,gs-Oseltamivir_Resistance_pheno,gs-Zanamivir_Resistance_pheno,gs-Peramivir_Resistance_pheno,gs-Other_Resistance_pheno,gs-Host_Age,gs-Collection_Month,gs-Collection_Year,gs-Host_Age_Unit,gs-Host_Gender,gs-Health_Status,gs-Note,gs-PMID -XX-566912_PB2,Influenza A virus,12/28/2016,"Doe, John; Doe, Jane;",XX-566912,CDC-OAMD,PRJNA217342,CDC Influenza Sequencing Baseline Constellation,Pathogen.cl.1.0,Helix,USA: California,Homo sapiens,Influenza A viruses,A/California/566912/2016,Nasal Wash,36.78 N 119.42 W,female,92,H3N2,local,"fastq_1_R1.fastq.gz,fastq_1_R2.fastq.gz",Helix COVID-19 and Flu Test,Illumina NovaSeq 6000,AMPLICON,VIRAL RNA,RT-PCR,PAIRED,Helix Hybrid-Capture Test,latf-load,CDC-XX-566912.1,NIH,NCBI,"10 Center Dr, Bethesda, MD, USA 20895",unpublished,Test_Submission,A/California/566912/2016,USA: California,Homo sapiens; gender F; age 92,H3N2,Nasal Wash,passage: PMK1,FluData,Newbler v. 2.3,100x,Illumina ,resistant,ILI,EPI_ISL_8289,H3N2,PB2,92,F,PMK1 (2017-01-03),FluData,A/California/566912/2016,A/California/566912/2016_PB2,PB2,H3N2,,Original,United States,California,,,Human,,,3080,,,,,,,,,,,,,92,,,Y,F,,, -XX-566912_PB1,Influenza A virus,12/28/2016,"Doe, John; Doe, Jane;",XX-566912,CDC-OAMD,PRJNA217342,CDC Influenza Sequencing Baseline Constellation,Pathogen.cl.1.0,Helix,USA: California,Homo sapiens,Influenza A viruses,A/California/566912/2016,Nasal Wash,36.78 N 119.42 W,female,92,H3N2,local,"fastq_1_R1.fastq.gz,fastq_1_R2.fastq.gz",Helix COVID-19 and Flu Test,Illumina NovaSeq 6000,AMPLICON,VIRAL RNA,RT-PCR,PAIRED,Helix Hybrid-Capture Test,latf-load,CDC-XX-566912.2,NIH,NCBI,"10 Center Dr, Bethesda, MD, USA 20895",unpublished,Test_Submission,A/California/566912/2016,USA: California,Homo sapiens; gender F; age 92,H3N2,Nasal Wash,passage: PMK1,FluData,Newbler v. 2.3,100x,Illumina ,resistant,ILI,EPI_ISL_8289,H3N2,PB1,92,F,PMK1 (2017-01-03),FluData,A/California/566912/2016,A/California/566912/2016_PB1,PB1,H3N2,,Original,United States,California,,,Human,,,3080,,,,,,,,,,,,,92,,,Y,F,,, -XX-566912_PA,Influenza A virus,12/28/2016,"Doe, John; Doe, Jane;",XX-566912,CDC-OAMD,PRJNA217342,CDC Influenza Sequencing Baseline Constellation,Pathogen.cl.1.0,Helix,USA: California,Homo sapiens,Influenza A viruses,A/California/566912/2016,Nasal Wash,36.78 N 119.42 W,female,92,H3N2,local,"fastq_1_R1.fastq.gz,fastq_1_R2.fastq.gz",Helix COVID-19 and Flu Test,Illumina NovaSeq 6000,AMPLICON,VIRAL RNA,RT-PCR,PAIRED,Helix Hybrid-Capture Test,latf-load,CDC-XX-566912.3,NIH,NCBI,"10 Center Dr, Bethesda, MD, USA 20895",unpublished,Test_Submission,A/California/566912/2016,USA: California,Homo sapiens; gender F; age 92,H3N2,Nasal Wash,passage: PMK1,FluData,Newbler v. 2.3,100x,Illumina ,resistant,ILI,EPI_ISL_8289,H3N2,PA,92,F,PMK1 (2017-01-03),FluData,A/California/566912/2016,A/California/566912/2016_PA,PA,H3N2,,Original,United States,California,,,Human,,,3080,,,,,,,,,,,,,92,,,Y,F,,, -XX-566912_HA,Influenza A virus,12/28/2016,"Doe, John; Doe, Jane;",XX-566912,CDC-OAMD,PRJNA217342,CDC Influenza Sequencing Baseline Constellation,Pathogen.cl.1.0,Helix,USA: California,Homo sapiens,Influenza A viruses,A/California/566912/2016,Nasal Wash,36.78 N 119.42 W,female,92,H3N2,local,"fastq_1_R1.fastq.gz,fastq_1_R2.fastq.gz",Helix COVID-19 and Flu Test,Illumina NovaSeq 6000,AMPLICON,VIRAL RNA,RT-PCR,PAIRED,Helix Hybrid-Capture Test,latf-load,CDC-XX-566912.4,NIH,NCBI,"10 Center Dr, Bethesda, MD, USA 20895",unpublished,Test_Submission,A/California/566912/2016,USA: California,Homo sapiens; gender F; age 92,H3N2,Nasal Wash,passage: PMK1,FluData,Newbler v. 2.3,100x,Illumina ,resistant,ILI,EPI_ISL_8289,H3N2,HA,92,F,PMK1 (2017-01-03),FluData,A/California/566912/2016,A/California/566912/2016_HA,HA,H3N2,,Original,United States,California,,,Human,,,3080,,,,,,,,,,,,,92,,,Y,F,,, -XX-566912_NP,Influenza A virus,12/28/2016,"Doe, John; Doe, Jane;",XX-566912,CDC-OAMD,PRJNA217342,CDC Influenza Sequencing Baseline Constellation,Pathogen.cl.1.0,Helix,USA: California,Homo sapiens,Influenza A viruses,A/California/566912/2016,Nasal Wash,36.78 N 119.42 W,female,92,H3N2,local,"fastq_1_R1.fastq.gz,fastq_1_R2.fastq.gz",Helix COVID-19 and Flu Test,Illumina NovaSeq 6000,AMPLICON,VIRAL RNA,RT-PCR,PAIRED,Helix Hybrid-Capture Test,latf-load,CDC-XX-566912.5,NIH,NCBI,"10 Center Dr, Bethesda, MD, USA 20895",unpublished,Test_Submission,A/California/566912/2016,USA: California,Homo sapiens; gender F; age 92,H3N2,Nasal Wash,passage: PMK1,FluData,Newbler v. 2.3,100x,Illumina ,resistant,ILI,EPI_ISL_8289,H3N2,NP,92,F,PMK1 (2017-01-03),FluData,A/California/566912/2016,A/California/566912/2016_NP,NP,H3N2,,Original,United States,California,,,Human,,,3080,,,,,,,,,,,,,92,,,Y,F,,, -XX-566912_NA,Influenza A virus,12/28/2016,"Doe, John; Doe, Jane;",XX-566912,CDC-OAMD,PRJNA217342,CDC Influenza Sequencing Baseline Constellation,Pathogen.cl.1.0,Helix,USA: California,Homo sapiens,Influenza A viruses,A/California/566912/2016,Nasal Wash,36.78 N 119.42 W,female,92,H3N2,local,"fastq_1_R1.fastq.gz,fastq_1_R2.fastq.gz",Helix COVID-19 and Flu Test,Illumina NovaSeq 6000,AMPLICON,VIRAL RNA,RT-PCR,PAIRED,Helix Hybrid-Capture Test,latf-load,CDC-XX-566912.6,NIH,NCBI,"10 Center Dr, Bethesda, MD, USA 20895",unpublished,Test_Submission,A/California/566912/2016,USA: California,Homo sapiens; gender F; age 92,H3N2,Nasal Wash,passage: PMK1,FluData,Newbler v. 2.3,100x,Illumina ,resistant,ILI,EPI_ISL_8289,H3N2,NA,92,F,PMK1 (2017-01-03),FluData,A/California/566912/2016,A/California/566912/2016_NA,NA,H3N2,,Original,United States,California,,,Human,,,3080,,,,,,,,,,,,,92,,,Y,F,,, -XX-566912_M,Influenza A virus,12/28/2016,"Doe, John; Doe, Jane;",XX-566912,CDC-OAMD,PRJNA217342,CDC Influenza Sequencing Baseline Constellation,Pathogen.cl.1.0,Helix,USA: California,Homo sapiens,Influenza A viruses,A/California/566912/2016,Nasal Wash,36.78 N 119.42 W,female,92,H3N2,local,"fastq_1_R1.fastq.gz,fastq_1_R2.fastq.gz",Helix COVID-19 and Flu Test,Illumina NovaSeq 6000,AMPLICON,VIRAL RNA,RT-PCR,PAIRED,Helix Hybrid-Capture Test,latf-load,CDC-XX-566912.7,NIH,NCBI,"10 Center Dr, Bethesda, MD, USA 20895",unpublished,Test_Submission,A/California/566912/2016,USA: California,Homo sapiens; gender F; age 92,H3N2,Nasal Wash,passage: PMK1,FluData,Newbler v. 2.3,100x,Illumina ,resistant,ILI,EPI_ISL_8289,H3N2,M,92,F,PMK1 (2017-01-03),FluData,A/California/566912/2016,A/California/566912/2016_MP,MP,H3N2,,Original,United States,California,,,Human,,,3080,,,,,,,,,,,,,92,,,Y,F,,, -XX-566912_NS,Influenza A virus,12/28/2016,"Doe, John; Doe, Jane;",XX-566912,CDC-OAMD,PRJNA217342,CDC Influenza Sequencing Baseline Constellation,Pathogen.cl.1.0,Helix,USA: California,Homo sapiens,Influenza A viruses,A/California/566912/2016,Nasal Wash,36.78 N 119.42 W,female,92,H3N2,local,"fastq_1_R1.fastq.gz,fastq_1_R2.fastq.gz",Helix COVID-19 and Flu Test,Illumina NovaSeq 6000,AMPLICON,VIRAL RNA,RT-PCR,PAIRED,Helix Hybrid-Capture Test,latf-load,CDC-XX-566912.8,NIH,NCBI,"10 Center Dr, Bethesda, MD, USA 20895",unpublished,Test_Submission,A/California/566912/2016,USA: California,Homo sapiens; gender F; age 92,H3N2,Nasal Wash,passage: PMK1,FluData,Newbler v. 2.3,100x,Illumina ,resistant,ILI,EPI_ISL_8289,H3N2,NS,92,F,PMK1 (2017-01-03),FluData,A/California/566912/2016,A/California/566912/2016_NS,NS,H3N2,,Original,United States,California,,,Human,,,3080,,,,,,,,,,,,,92,,,Y,F,,, -XX-566913_PB2,Influenza A virus,11/10/2016,"Doe, John; Doe, Jane;",XX-566913,CDC-OAMD,PRJNA217342,CDC Influenza Sequencing Baseline Constellation,Pathogen.cl.1.0,Helix,USA: Texas,Homo sapiens,Influenza A viruses,A/Texas/566913/2016,Nasal Wash,29.42 N 98.49 W,male,21,H3N2,local,"fastq_2_R1.fastq.gz,fastq_2_R2.fastq.gz",Helix COVID-19 and Flu Test,Illumina NovaSeq 6000,AMPLICON,VIRAL RNA,RT-PCR,PAIRED,Helix Hybrid-Capture Test,latf-load,CDC-XX-566913.1,NIH,NCBI,"10 Center Dr, Bethesda, MD, USA 20895",unpublished,Test_Submission,A/Texas/566913/2016,USA: Texas,Homo sapiens; gender M; age 21,H3N2,Nasal Wash,passage: PMK1,FluData,Newbler v. 2.3,100x,Illumina ,resistant,ILI,EPI_ISL_8290,H3N2,PB2,21,M,PMK1 (2017-01-03),FluData,A/Texas/566913/2016,A/Texas/566913/2016_PB2,PB2,H3N2,,Original,United States,Texas,,,Human,,,3081,,,,,,,,,,,,,21,,,Y,M,,, -XX-566913_PB1,Influenza A virus,11/10/2016,"Doe, John; Doe, Jane;",XX-566913,CDC-OAMD,PRJNA217342,CDC Influenza Sequencing Baseline Constellation,Pathogen.cl.1.0,Helix,USA: Texas,Homo sapiens,Influenza A viruses,A/Texas/566913/2016,Nasal Wash,29.42 N 98.49 W,male,21,H3N2,local,"fastq_2_R1.fastq.gz,fastq_2_R2.fastq.gz",Helix COVID-19 and Flu Test,Illumina NovaSeq 6000,AMPLICON,VIRAL RNA,RT-PCR,PAIRED,Helix Hybrid-Capture Test,latf-load,CDC-XX-566913.2,NIH,NCBI,"10 Center Dr, Bethesda, MD, USA 20895",unpublished,Test_Submission,A/Texas/566913/2016,USA: Texas,Homo sapiens; gender M; age 21,H3N2,Nasal Wash,passage: PMK1,FluData,Newbler v. 2.3,100x,Illumina ,resistant,ILI,EPI_ISL_8290,H3N2,PB1,21,M,PMK1 (2017-01-03),FluData,A/Texas/566913/2016,A/Texas/566913/2016_PB1,PB1,H3N2,,Original,United States,Texas,,,Human,,,3081,,,,,,,,,,,,,21,,,Y,M,,, -XX-566913_PA,Influenza A virus,11/10/2016,"Doe, John; Doe, Jane;",XX-566913,CDC-OAMD,PRJNA217342,CDC Influenza Sequencing Baseline Constellation,Pathogen.cl.1.0,Helix,USA: Texas,Homo sapiens,Influenza A viruses,A/Texas/566913/2016,Nasal Wash,29.42 N 98.49 W,male,21,H3N2,local,"fastq_2_R1.fastq.gz,fastq_2_R2.fastq.gz",Helix COVID-19 and Flu Test,Illumina NovaSeq 6000,AMPLICON,VIRAL RNA,RT-PCR,PAIRED,Helix Hybrid-Capture Test,latf-load,CDC-XX-566913.3,NIH,NCBI,"10 Center Dr, Bethesda, MD, USA 20895",unpublished,Test_Submission,A/Texas/566913/2016,USA: Texas,Homo sapiens; gender M; age 21,H3N2,Nasal Wash,passage: PMK1,FluData,Newbler v. 2.3,100x,Illumina ,resistant,ILI,EPI_ISL_8290,H3N2,PA,21,M,PMK1 (2017-01-03),FluData,A/Texas/566913/2016,A/Texas/566913/2016_PA,PA,H3N2,,Original,United States,Texas,,,Human,,,3081,,,,,,,,,,,,,21,,,Y,M,,, -XX-566913_HA,Influenza A virus,11/10/2016,"Doe, John; Doe, Jane;",XX-566913,CDC-OAMD,PRJNA217342,CDC Influenza Sequencing Baseline Constellation,Pathogen.cl.1.0,Helix,USA: Texas,Homo sapiens,Influenza A viruses,A/Texas/566913/2016,Nasal Wash,29.42 N 98.49 W,male,21,H3N2,local,"fastq_2_R1.fastq.gz,fastq_2_R2.fastq.gz",Helix COVID-19 and Flu Test,Illumina NovaSeq 6000,AMPLICON,VIRAL RNA,RT-PCR,PAIRED,Helix Hybrid-Capture Test,latf-load,CDC-XX-566913.4,NIH,NCBI,"10 Center Dr, Bethesda, MD, USA 20895",unpublished,Test_Submission,A/Texas/566913/2016,USA: Texas,Homo sapiens; gender M; age 21,H3N2,Nasal Wash,passage: PMK1,FluData,Newbler v. 2.3,100x,Illumina ,resistant,ILI,EPI_ISL_8290,H3N2,HA,21,M,PMK1 (2017-01-03),FluData,A/Texas/566913/2016,A/Texas/566913/2016_HA,HA,H3N2,,Original,United States,Texas,,,Human,,,3081,,,,,,,,,,,,,21,,,Y,M,,, -XX-566913_NP,Influenza A virus,11/10/2016,"Doe, John; Doe, Jane;",XX-566913,CDC-OAMD,PRJNA217342,CDC Influenza Sequencing Baseline Constellation,Pathogen.cl.1.0,Helix,USA: Texas,Homo sapiens,Influenza A viruses,A/Texas/566913/2016,Nasal Wash,29.42 N 98.49 W,male,21,H3N2,local,"fastq_2_R1.fastq.gz,fastq_2_R2.fastq.gz",Helix COVID-19 and Flu Test,Illumina NovaSeq 6000,AMPLICON,VIRAL RNA,RT-PCR,PAIRED,Helix Hybrid-Capture Test,latf-load,CDC-XX-566913.5,NIH,NCBI,"10 Center Dr, Bethesda, MD, USA 20895",unpublished,Test_Submission,A/Texas/566913/2016,USA: Texas,Homo sapiens; gender M; age 21,H3N2,Nasal Wash,passage: PMK1,FluData,Newbler v. 2.3,100x,Illumina ,resistant,ILI,EPI_ISL_8290,H3N2,NP,21,M,PMK1 (2017-01-03),FluData,A/Texas/566913/2016,A/Texas/566913/2016_NP,NP,H3N2,,Original,United States,Texas,,,Human,,,3081,,,,,,,,,,,,,21,,,Y,M,,, -XX-566913_NA,Influenza A virus,11/10/2016,"Doe, John; Doe, Jane;",XX-566913,CDC-OAMD,PRJNA217342,CDC Influenza Sequencing Baseline Constellation,Pathogen.cl.1.0,Helix,USA: Texas,Homo sapiens,Influenza A viruses,A/Texas/566913/2016,Nasal Wash,29.42 N 98.49 W,male,21,H3N2,local,"fastq_2_R1.fastq.gz,fastq_2_R2.fastq.gz",Helix COVID-19 and Flu Test,Illumina NovaSeq 6000,AMPLICON,VIRAL RNA,RT-PCR,PAIRED,Helix Hybrid-Capture Test,latf-load,CDC-XX-566913.6,NIH,NCBI,"10 Center Dr, Bethesda, MD, USA 20895",unpublished,Test_Submission,A/Texas/566913/2016,USA: Texas,Homo sapiens; gender M; age 21,H3N2,Nasal Wash,passage: PMK1,FluData,Newbler v. 2.3,100x,Illumina ,resistant,ILI,EPI_ISL_8290,H3N2,NA,21,M,PMK1 (2017-01-03),FluData,A/Texas/566913/2016,A/Texas/566913/2016_NA,NA,H3N2,,Original,United States,Texas,,,Human,,,3081,,,,,,,,,,,,,21,,,Y,M,,, -XX-566913_M,Influenza A virus,11/10/2016,"Doe, John; Doe, Jane;",XX-566913,CDC-OAMD,PRJNA217342,CDC Influenza Sequencing Baseline Constellation,Pathogen.cl.1.0,Helix,USA: Texas,Homo sapiens,Influenza A viruses,A/Texas/566913/2016,Nasal Wash,29.42 N 98.49 W,male,21,H3N2,local,"fastq_2_R1.fastq.gz,fastq_2_R2.fastq.gz",Helix COVID-19 and Flu Test,Illumina NovaSeq 6000,AMPLICON,VIRAL RNA,RT-PCR,PAIRED,Helix Hybrid-Capture Test,latf-load,CDC-XX-566913.7,NIH,NCBI,"10 Center Dr, Bethesda, MD, USA 20895",unpublished,Test_Submission,A/Texas/566913/2016,USA: Texas,Homo sapiens; gender M; age 21,H3N2,Nasal Wash,passage: PMK1,FluData,Newbler v. 2.3,100x,Illumina ,resistant,ILI,EPI_ISL_8290,H3N2,M,21,M,PMK1 (2017-01-03),FluData,A/Texas/566913/2016,A/Texas/566913/2016_MP,MP,H3N2,,Original,United States,Texas,,,Human,,,3081,,,,,,,,,,,,,21,,,Y,M,,, -XX-566913_NS,Influenza A virus,11/10/2016,"Doe, John; Doe, Jane;",XX-566913,CDC-OAMD,PRJNA217342,CDC Influenza Sequencing Baseline Constellation,Pathogen.cl.1.0,Helix,USA: Texas,Homo sapiens,Influenza A viruses,A/Texas/566913/2016,Nasal Wash,29.42 N 98.49 W,male,21,H3N2,local,"fastq_2_R1.fastq.gz,fastq_2_R2.fastq.gz",Helix COVID-19 and Flu Test,Illumina NovaSeq 6000,AMPLICON,VIRAL RNA,RT-PCR,PAIRED,Helix Hybrid-Capture Test,latf-load,CDC-XX-566913.8,NIH,NCBI,"10 Center Dr, Bethesda, MD, USA 20895",unpublished,Test_Submission,A/Texas/566913/2016,USA: Texas,Homo sapiens; gender M; age 21,H3N2,Nasal Wash,passage: PMK1,FluData,Newbler v. 2.3,100x,Illumina ,resistant,ILI,EPI_ISL_8290,H3N2,NS,21,M,PMK1 (2017-01-03),FluData,A/Texas/566913/2016,A/Texas/566913/2016_NS,NS,H3N2,,Original,United States,Texas,,,Human,,,3081,,,,,,,,,,,,,21,,,Y,M,,, diff --git a/TEST_FLU/raw_reads/fastq_1_R1.fastq.gz b/TEST_FLU/raw_reads/fastq_1_R1.fastq.gz deleted file mode 100644 index 4f1c470..0000000 Binary files a/TEST_FLU/raw_reads/fastq_1_R1.fastq.gz and /dev/null differ diff --git a/TEST_FLU/raw_reads/fastq_1_R2.fastq.gz b/TEST_FLU/raw_reads/fastq_1_R2.fastq.gz deleted file mode 100644 index 76cb481..0000000 Binary files a/TEST_FLU/raw_reads/fastq_1_R2.fastq.gz and /dev/null differ diff --git a/TEST_FLU/raw_reads/fastq_2_R1.fastq.gz b/TEST_FLU/raw_reads/fastq_2_R1.fastq.gz deleted file mode 100644 index 0e69847..0000000 Binary files a/TEST_FLU/raw_reads/fastq_2_R1.fastq.gz and /dev/null differ diff --git a/TEST_FLU/raw_reads/fastq_2_R2.fastq.gz b/TEST_FLU/raw_reads/fastq_2_R2.fastq.gz deleted file mode 100644 index 231e47a..0000000 Binary files a/TEST_FLU/raw_reads/fastq_2_R2.fastq.gz and /dev/null differ diff --git a/TEST_FLU/sequence.fasta b/TEST_FLU/sequence.fasta deleted file mode 100644 index 1bbe657..0000000 --- a/TEST_FLU/sequence.fasta +++ /dev/null @@ -1,482 +0,0 @@ ->XX-566912_NP -atgtccaacatggatatcgacggtatgaacactggaacaattaacaaaacaccggaagaa -ataacttctggaaccagtgggacaaccagaccaatcattagaccagcaacccttgcccca -ccaagcaacaaacgaacccgtaacccatctccggaaagagcaaccacaagcagtgaagat -gatgtcggaaggaaagcccaaaagaagcagaccccgacagagataaagaagagcgtctac -aacatggtggtgaaactgggcgaattctacaaccagatgatggttaaagctggactcaat -gatgacatggagagaaatctaatccaaaatgcacatgccgtggagagaattttattggct -gccactgatgacaagaaaaccgagttccagaagaaaaagaatgccagagatgtcaaagaa -gggaaggaagaaatagatcacaacaagacaggaggcaccttttacaagatggtaagagat -gataaaaccatctatttcagccctataagaattacctttttaaaagaagaggtgaaaaca -atgtacaaaaccaccatggggagtgatggtttcagtggattaaatcacataatgattggg -cattcgcagatgaatgatgtctgtttccaaagatcaaaggcactaaaaagagttggactt -gatccttcattaatcagtacctttgcgggaagcacagtccccagaagatcaggtgcgact -ggtgttgcaatcaagggaggtggaaccttagtggctgaagccattcgatttataggaaga -gcaatggcagacagagggctattgagagacattaaagccaagactgcctatgaaaagatt -cttctgaatctaaagaacaaatgctctgcgccccaacaaaaggctctagttgatcaagtg -atcggaagcagaaatccggggattgcagacattgaagatctaaccctgcttgctcgtagt -atggtcgttgttaggccctctgtggcaagcaaagtggtgcttcccataagcatttacgcc -aaaatacctcaactagggttcaatgttgaagagtactctatggttgggtacgaagccatg -gctctttacaatatggcaacacctgtttccatattaagaatgggagatgatgcaaaggat -aaatcgcaattattcttcatgtcttgcttcggagctgcctatgaagacctgagagttttg -tctgcattaacaggcacagaattcaagcctagatcagcattaaaatgtaagggtttccat -gttccagcaaaggaacaggtagaaggaatgggagcagctctgatgtccatcaagctccag -ttttgggctcctatgaccagatctggggggaacgaggcaggtggagacggagggtctggc -caaataagctgcagcccagtgtttgcagtggagagacctattgctttaagcaagcaagct -gtaagaagaatgctgtcaatgaatattgaggggcgtgatgcagatgtcaaaggaaatcta -ctcaagatgatgaatgactcaatggctaagaaaaccagtggaaatgctttcattgggaag -aaaatgttccaaatatcagacaaaaacaaaaccaatcccattgaaattccaattaagcag -accatccccaatttcttctttgggagggacacagcagaggattatgatgacctcgattat -taa ->XX-566913_NP -atgtccaacatggatatcgacggtatgaacactgggacaattgacaaaacaccggaagaa -ataacttctggaaccagtgggacaaccagaccaatcattagaccagcaacccttgcccca -ccaagcaacaaacgaacccgtaacccatctccggaaagagcaaccacaagcagtgaagat -gatgtcggaaggaaagcccaaaagaagcagaccccgacagagataaagaagagcgtctac -aacatggtggtgaaactgggcgaattctacaaccagatgatggttaaagctggactcaat -gatgacatggagagaaatctaatccaaaatgcacatgccgtggagagaattttattggct -gccactgatgacaagaaaaccgagttccagaagaaaaagaatgccagagatgtcaaagaa -gggaaggaagaaatagatcacaacaaaacaggaggcaccttttacaagatggtaagagat -gataaaaccatctatttcagccctataagaattacctttttaaaagaagaggtgaaaaca -atgtacaaaaccaccatggggagtgatggcttcagtggattaaatcacataatgattggg -cattcgcagatgaatgatgtctgtttccaaagatcaaaggcactaaaaagagttggactt -gatccttcattaatcagtacctttgcgggaagcacagtccccagaagatcaggtgcgact -ggtgttgcaatcaagggaggtggaaccttagtggctgaagccattcgatttataggaaga -gcaatggcagacagagggctattgagagacattaaaaccaagactgcctatgaaaagatt -cttctgaatctaaagaacaaatgctctgcgccccaacaaaaggctctagttgatcaagtg -atcggaagcagaaatccggggattgcagacattgaagatctaaccctgcttgctcgtagt -atggtcgttgttaggccctctgtggcaagcaaagtggtgcttcccataagcatttacgcc -aaaatacctcaactagggttcaatgttgaagagtactctatggttgggtacgaagccatg -gctctttacaatatggcaacacctgtttccatattaagaatgggagatgatgcaaaggat -aaatcgcaattattcttcatgtcttgcttcggagctgcctatgaagacctgagagttttg -tctgcattaacaggcacagaattcaagcctagatcagcattaaaatgtaagggtttccat -gttccagcaaaggaacaggtagaaggaatgggagcagctctgatgtccatcaagctccag -ttttgggctccgatgaccagatctggggggaacgaagcaggtggagacggagggtctggc -caaataagctgcagcccagtgtttgcagtggagagacctattgctttaagcaagcaagct -gtaagaagaatgctgtcaatgaatattgaggggcgtgatgcagatgtcaaaggaaatcta -ctcaagatgatgaatgactcaatggctaagaaaaccagtggaaatgctttcattgggaag -aaaatgttccaaatatcagacaaaaacaaaaccaatcccattgaaattccaattaagcag -accatccccaatttcttctttgggagggacacagcagaggattatgatgacctcgattat -taa ->XX-566912_PB2 -atgacattagccaaaattgaattgttaaaacaactgctaagggacaatgaagccaaaaca -gtcctgaagcaaacaacagtagaccaatataacataataagaaaattcaatacatcaagg -attgaaaagaatccttcactaaggatgaagtgggccatgtgttctaactttcccttggct -ctcaccaagggcgatatggcaaacagaatccccttggaatacaaagggatacaactcaaa -acaaatgctgaagacataggaaccaaaggccaaatgtgctcaatagcagcagttacatgg -tggaatacatatggaccaataggagacactgaaggttttgaaagggtctacgaaagcttt -tttctcagaaaaatgagacttgacaacgccacttggggccggataacttttggcccagtt -gaaagagtgagaaaaagagtactactaaaccctctcaccaaggaaatgcctccggatgag -gcgagcaatgtgataatggaaatattatttcctaaagaagcaggaataccaagagaatcc -acttggatacatagggaactgataaaagaaaagagagaaaaattgaaagggacaatgata -actccaatcgtactggcatacatgcttgaaagagaactggttgctcgaagaagattcttg -ccagtggcaggagcaacatcagctgagttcatagaaatgctgcactgcttacaaggtgaa -aattggagacaaatatatcacccaggagggaataaattaactgagtccaggtctcaatca -atgatagtagcttgtaggaaaataatcagaagatcaatagtcgcttcaaacccactggag -ctagctgtagaaattgcaaacaagactgtgatagatactgaacctttaaagtcatgtctg -gcagccatagacggaggtgatgtagcttgtgacataataagagctgcattaggactaaag -atcagacaaagacaaagatttgggcggcttgagctaaaaagaatatcaggaagaggattc -aaaaatgatgaagaaatattaatagggaacggaacaatacagaagattggaatatgggat -ggggaagaggagttccacgtaagatgtggtgaatgcaggggaatattaaaaaagagtaaa -atgaaactggaaaaattactgataaattcagccaaaaaggaggatatgagagatttaata -atcttatgcatggtattttctcaagacactaggatgttccaaggggtgagaggagaaata -aattttcttaatcgagcaggccaacttttatctccaatgtaccaactccaacgatatttt -ttgaatagaagcaatgacctttttgatcaatgggggtatgaggaatcacccaaagcaagt -gaactacatgggataaatgaatcaatgaatgcatctgactatacattgaaagggattgta -gtgacaagaaatgtaattgacgactttagctctactgaaacagagaaagtatccataaca -aaaaatcttagcttaataaaaaggactggagaagtcataatgggagctaatgacgtgagt -gaattagaatcacaagcacagctgatgataacatatgatacacctaaaatgtgggaaatg -ggaacaaccaaagaactggtgcaaaacacttatcaatgggtgctaaaaaacttggtgaca -ctgaaggctcagtttcttctaggaaaagaggatatgttccaatgggatgcatttgaagca -tttgagagcataattcctcaaaaaatggctggtcagtacagtggatttgcaagagcagtg -ctcaaacaaatgagagaccaggaggttatgaaaactgatcagttcataaagttgctgcct -ttttgtttctcaccaccaaaattaagaagcaatggggagccttatcaattcttaaaactt -gtattgaaaggaggaggggaaaatttcattgaagtaaggaaagggtctcctctattttcc -tataatccacaaacagaagtcttaactatatgcggcagaatgatgtcattaaaagggaaa -attgaagatgaagaaaggaatagatcaatggggaatgcagtattagcaggctttctcgtt -agtggcaagtatgaccctgatcttggagatttcaaaactattgaagaacttgaaaagcta -aaaccaggggaaaaggcaaacatcttgctttatcaaggaaaaccagttaaagtagtgaaa -aggaaaaggtatagtgctttgtccaatgacatttcacaaggaattaaaagacaaagaatg -acagttgagtccatggggtgggccttgagctaa ->XX-566913_PB2 -atgacattagccaaaattgaattgttaaaacaactgctaagggacaatgaggccaaaaca -gtcctgaagcaaacaacagtagaccaatataacataataagaaaattcaatacatcaagg -attgaaaagaatccttcactaaggatgaagtgggccatgtgttctaactttcccttggct -ctcaccaagggcgatatggcaaacagaatccccttggaatacaaagggatacaactcaaa -acaaatgctgaagacataggaaccaaaggccaaatgtgctcaatagcagcagttacatgg -tggaatacatatggaccaataggagacactgaaggttttgaaagggtctacgaaagcttt -tttctcagaaaaatgagacttgacaacgccacttggggccggataacttttggcccagtt -gaaagagtgagaaaaagagtactactaaaccctctcaccaaggaaatgcctccggatgag -gcgagcaatgtgataatggaaatattatttcctaaagaagcaggaataccaagagaatcc -acttggatacatagggaactgataaaagaaaagagagaaaaattgaaagggacaatgata -actcccatcgtactggcatacatgcttgaaagagaactggttgctcgaagaagattcttg -ccagtggcaggagcaacatcagctgagttcatagaaatgctgcactgcttacaaggtgaa -aattggagacaaatatatcacccaggagggaataaattaactgagtccaggtctcaatca -atgatagtagcttgtaggaaaataatcagaagatcaatagtcgcttcaaacccactggag -ctagctgtagaaattgcaaacaagactgtgatagatactgaacctttaaagtcatgtctg -gcagccatagacggaggtgatgtagcttgtgacataataagagctgcattaggactaaag -atcagacaaagacaaagatttgggcggcttgagctaaaaagaatatcaggaagaggattc -aaaaatgatgaagaaatattaatagggaacggaacaatacagaagattggaatatgggat -ggggaagaggagttccacgtaagatgtggtgaatgcaggggaatattaaaaaagagtaaa -atgaaactggaaaaattactgataaattcagccaaaaaggaggatatgagagatttaata -atcttatgcatggtattttctcaagacactaggatgttccaaggggtgagaggagaaata -aattttcttaatcgagcaggccaacttttatctccaatgtaccaactccaacgatatttt -ttgaatagaagcaacgacctttttgatcaatgggggtatgaggaatcacccaaagcaagt -gaactacatgggataaatgaatcaatgaatgcatctgactatacattgaaagggattgta -gtgacaagaaatgtaattgacgactttagctctactgaaacagagaaagtatccataaca -aaaaatcttagcttaataaaaaggactggagaagtcataatgggagctaatgacgtgagt -gaattagaatcacaagcacagctgatgataacatatgatacacctaaaatgtgggaaatg -ggaacaaccaaagaactggtgcaaaacacttatcaatgggtgctaaaaaacttggtgaca -ctgaaggctcagtttcttctaggaaaagaggatatgttccaatgggatgcatttgaagca -tttgagagcataattcctcaaaaaatggctggtcagtacagtggatttgcaagagcagtg -ctcaaacaaatgagagaccaggaggttatgaaaactgatcagttcataaagttgctgcct -ttttgtttctcaccaccaaaattaagaagcaatggggagccttatcaattcttaaaactt -gtattgaaaggaggaggggaaaatttcattgaagtaaggaaagggtctcctctattttcc -tataatccacaaacagaagtcttaactatatgcggcagaatgatgtcattaaaagggaaa -attgaagatgaagaaaggaatagatcaatggggaatgcagtattagcaggctttctcgtt -agtggcaagtatgaccctgatcttggagatttcaaaactattgaagaacttgaaaagctg -aaaccaggggaaaaggcaaacatcttgctttatcaaggaaaaccagttaaagtagtgaaa -aggaaaaggtatagtgctttgtccaatgacatttcacaaggaattaaaagacaaagaatg -acagttgagtccatggggtgggccttgagctaa ->XX-566912_HA -atgaaggcaataattgtactactcatggtagtaacatccaatgcagatcgaatctgcact -gggataacatcgtcaaactcaccacatgtcgtcaaaactgctactcaaggggaggtcaat -gtgactggtgtaataccactgacaacaacacccaccaaatctcattttgcaaatctcaaa -ggaacagaaaccagggggaaactatgcccaaaatgcctaaactgcacagatctggatgta -gccttgggcagaccaaaatgcacagggaaaataccctctgcaagggtttcaatactccat -gaagtcagacctgttacgtctgggtgctttcctataatgcatgatagaacaaaaattaga -cagctgcctaaccttctccgaggatacgaacatgtcagattatcaactcacaacgttatc -aatacagaagatgcaccaggaggaccctacgaaattggaacctcagggtcttgcctcaac -attaccaatggaaaaggattcttcgcaacaatggcttgggccgtcccaaaaaacaaaaca -gcaacaaatccattaacaatagaagtaccatacatttgtacagaagaagaagaccaaatt -accgtttgggggttccactctgatgaagagacccaaatggcaagactctatggggattca -aagccccagaagttcacctcatctgccaacggagtgaccacacactacgtctcacagatt -ggtggcttcccaaatcaaacagaagacggaggactaccacaaagtggcagaattgttgtt -gattacatggtgcaaaaatctggaaaaacaggaacaattacctatcaaagaggtatttta -ttgcctcaaaaggtgtggtgcgcaagtggcaagagcaaggtaataaaaggatccttgccc -ttaattggagaagcagattgcctccatgaaaaatacggtggattaaacaaaagcaagcct -tactacacaggggaacatgcaaaggccataggaaattgcccaatatgggtgaaaacaccc -ttgaagctggccaatggaaccaaatatagacctcctgcaaaactgttaaaggaaagaggt -ttcttcggagccattgctggtttcttagaaggaggatgggaaggaatgattgcaggttgg -cacggatacacatcccatggggcacatggagtagcagtggcagctgaccttaagagcact -caagaggccataaacaagataacaaaaaatctcaactctttgagtgagctggaagtaaag -aatcttcaaagactaagcggtgccatggatgaactccacaacgaaatactagaactagat -gagaaagtggatgatctcagagctgatacaataagctcacagatagaactcgcagtcctg -ctttccaatgaaggaataataaacagtgaagatgaacatctcttggcgcttgaaagaaag -ctgaagaaaatgctgggcccctctgctgtagagataggaaatggatgctttgaaaccaaa -cacaagtgcaaccagacctgtctcgacagaatagctgctggtacctttgatgcaggagaa -ttttctctccccacctttgattcactgaatattactgctgcatctttaaatgacgatgga -ttggacaatcatactatactgctttactactcaactgctgcctccagtttggctgtaaca -ctgatgatagctatctttgttgtttatatggtctccagagacaatgtttcttgctccatt -tgtctataa ->XX-566913_HA -atgaaggcaataattgtactactcatggtagtaacatccaatgcagatcgaatctgcact -gggataacatcgtcaaactcaccacatgtcgtcaaaactgctactcaaggggaggtcaat -gtgactggtgtaataccactgacaacaacacccaccaaatctcattttgcaaatctcaaa -ggaacagaaaccagggggaaactatgcccaaaatgcctaaactgcacagatctggatgta -gccttgggcagaccaaaatgcacagggaaaataccctctgcaagggtttcaatactccat -gaagtcagacctgttacgtctgggtgctttcctataatgcatgatagaacaaaaattaga -cagctgcctaaccttctccgaggatacgaacatgtcaggttatcaactcacaacgttatc -aatacagaagatgcaccaggaggaccctatgaaattggaacctcagggtcttgcctcaac -attaccaatggaaaaggattcttcgcaacaatggcttgggccgtcccaaaaaacaaaaca -gcaacaaatccattaacaatagaagtaccatacatttgtacagaagaagaagaccaaatt -accgtttgggggttccactctgacgaagagacccaaatggcaagactctatggggattca -aagccccagaagttcacctcatctgccaacggagtgaccacacactacgtctcacagatt -ggtggcttcccaaatcaaacagaagacggaggactaccacaaagtggcagaattgttgtt -gattacatggtgcaaaaatctggaaaaacaggaacaattacctatcaaagaggtatttta -ttgcctcaaaaggtgtggtgcgcaagtggcaagagcaaggtaataaaaggatccttgccc -ttaattggagaagcagattgcctccatgaaaaatacggtggattaaacaaaagcaagcct -tactacacaggggaacatgcaaaggccataggaaattgcccaatatgggtgaaaacaccc -ttgaagctggccaatggaaccaaatatagacctcctgcaaaactgttaaaggaaagaggt -ttcttcggagccattgctggtttcttagaaggaggatgggaaggaatgattgcaggttgg -cacggatacacatcccatggggcacatggagtagcagtggcagctgaccttaagagcact -caagaggccataaacaagataacaaaaaatctcaactctttgagtgagctggaagtaaag -aatcttcaaagactaagcggtgccatggatgaactccacaacgaaatactagaactagat -gagaaagtggatgatctcagagctgatacaataagctcacagatagaactcgcagtcctg -ctttccaatgaaggaataataaacagtgaagatgaacatctcttggcgcttgaaagaaag -ctgaagaaaatgctgggcccctctgctgtagagataggaaatggatgctttgaaaccaaa -cacaagtgcaaccaaacctgtctcgacagaatagctgctggtacctttgatgcaggagaa -ttttctctccccacctttgattcactgaatattactgctgcatctttaaatgacgatgga -ttggacaatcatactatactgctttactactcaactgctgcctccagtttggctgtaaca -ctgatgatagctatctttgttgtttatatggtctccagagacaatgtttcttgctccatt -tgtctataa ->XX-566912_M -atgtcgctgtttggagacacaattgcctacttgctttcattgatagaagatggagaaggc -aaagcagaactagcagaaaagttacactgttggtttggtgggaaagaatttgacctagac -tcagccttggaatggataaaaaacaaaagatgcttaactgatatacaaaaagcactaatt -ggtgcctctatatgctttttaaaacccaaagaccaggaaagaaaaagaagattcatcaca -gagcccttatcaggaatgggaacaacagcaacaaaaaagaaaggcctgattctggctgag -agaaaaatgagaaaatgtgtgagctttcatgaagcatttgaaatagcagaaggccatgaa -agctcagcgctactatactgtctcatggtcatgtacctgaatcctggaaattattcgatg -caagtaaaactaggaacgctctgtgctttatgcgagaaacaagcatcacattcacacaga -gctcatagcagagcagctagatcttcagtgcctggagtaagacgagaaatgcaaatggtc -tcagctatgaacacagcaaaaacgatgaatggaatgggaaaaggagaagacgtccaaaag -ctggcagaagagttgcaaagcaacattggagtgctgagatctcttggggcaagtcaaaag -aatggggaagggattgcaaaggatgtaatggaagtgctaaagcagagctccatgggaaat -tcagctcttgtgaagaaatatctataatgctcgaaccatttcagattcttacaatttgtt -cttttatcttatcagctctccatttcatggcttggacaatagggcatttgaatcaaataa -aaagaggaataaacatgaaaatacgaataaaaggtccaaacaaagagacaataaacagag -aggtatcaattttgaggcacagttaccaaaaagaaatccaggccaaagaaacaatgaagg -aagtgctctctgacaacatggaggtattgaatgaccacataataattgaggggctttctg -ccgaagagataataaaaatgggtgaaacagttttggagatagaagaattgcattaa ->XX-566913_M -atgtcgctgtttggagacacaattgcctacttgctttcattgatagaagatggagaaggc -aaagcagaactagcagaaaagttacactgttggtttggtgggaaagaatttgacctagac -tcagccttggaatggataaaaaacaaaagatgcttaactgatatacaaaaagcactaatt -ggtgcctctatatgctttttaaaacccaaagaccaggaaagaaaaagaagattcatcaca -gagcccttatcaggaatgggaacaacagcaacaaaaaagaaaggcctgattctggctgag -agaaaaatgagaaaatgtgtgagctttcatgaagcatttgaaatagcagaaggccatgaa -agctcagcgctactatactgtctcatggtcatgtacctgaatcctggaaattattcgatg -caagtaaaactaggaacgctctgtgctttatgcgagaaacaagcatcacattcacacaga -gctcatagcagagcagctagatcttcagtgcctggagtaagacgagaaatgcaaatggtc -tcagctatgaacacagcaaaaacgatgaatggaatgggaaaaggagaagacgtccaaaag -ctggcagaagagttgcaaagcaacattggagtgctgagatctcttggggcaagtcaaaag -aatggggaagggattgcaaaggatgtaatggaagtgctaaagcagagctccatgggaaat -tcagctcttgtgaagaaatatctataatgctcgaaccatttcagattcttacaatttgtt -cttttatcttatcagctctccatttcatggcttggacaatagggcatttgaatcaaataa -aaagaggaataaacatgaaaatacgaataaaaggtccaaacaaagagacaataaacagag -aggtatcaattttgaggcacagttaccaaaaagaaatccaggccaaagaaacaatgaagg -aagtgctctctgacaacatggaggtattgaatgaccacataataattgaggggctttctg -ccgaagagataataaaaatgggtgaaacagttttggagatagaagaattgcattaa ->XX-566912_NA -atgaacaatgttaccctcaactatacaaacgttaaccctatttctcacatcagggggagt -attattatcactatatgtgtcagcctcattatcatacttactatattcggatatattgct -aaaattctcacaaacagaagtaactgcaccaacaatgccattggattgtgcaaacgcatc -aaatgttcaggctgtgaaccgttctgcaacaaaaggggcgacacttcttctcccagaacc -ggagtggacatacccgcgtttatcttgcccgggctcaacctttcagaaagcactcctaat -tagccctcatagattcggagaaaccaaaggaaactcagctcccttgataataagggaacc -ttttgttgcttgtggaccaaatgaatgcaaacactttgctttaactcattatgcagccca -accagggggatactacaatggaacaagaggagacagaaacaagctgaggcatctaatttc -agtcaaattgggcaaaatcccaacagtagagaactccattttccatatggcagcatggag -cgggtccgcgtgccatgatggtaaggaatggacatatatcggagttgatggccctgacaa -taatgcattgctcaaagtaaaatatggagaagcatatactgacacataccattcctatgc -aaacaacatcctaagaacacaagaaagtgcctgcaattgcatcgggggaaattgttatct -aatgataactgatggctcagcttcaggtgttagtgaatgcagatttcttaagattcgaga -gggccgaataataaaagaaatatttccaacaggaagagtaaaacacactgaggaatgcac -atgcggatttgccagtaataaaaccatagaatgtgcctgtagagacaacaggtacacagc -caaaagaccttttgtcaaattaaacgtggagactgatacagcagaaataagattgatgtg -tacagatacttatttggacacccccagaccaaatgatggaagcataacaggcccttgtga -atctgatggggaagaggggagtggaggcatcaaaggaggatttgttcatcaaagaatgaa -atccaagattggaaggtggtactctcgaacgatgtctaaaactgaaaggatggggatgga -actgtatgtcaagtatggtggagacccatgggctgacagtgatgccctagtttttagtgg -agtaatgatttcaatgaaagaacctggttggtattcctttggcttcgaaatcaaagataa -gaaatgcgatgtcccctgtattgggatagagatggtacatgatggtggaaaagagacttg -gcactcagcagcaacagccatttactgtttaatgggctcaggacagctgctgtgggacac -tgtcacaggtgttgatatggctctgtaa ->XX-566913_NA -atgaacaatgttaccctcaactatacaaacgttaaccctatttctcacatcagggggagt -attattatcactatatgtgtcagcttcattatcatacttactatattcggatatattgct -aaaattctcacaaacagaaataactgcaccaacaatgccattggattgtgcaaacgcatc -aaatgttcaggctgtgaaccgttctgcaacaaaaggggcgacacttcttctcccagaacc -ggagtggacatacccgcgtttatcttgcccgggctcaacctttcagaaagcactcctaat -tagccctcatagattcggagaaaccaaaggaaactcagctcccttgataataagggaacc -ttttgttgcttgtggaccaaatgaatgcaaacactttgctttaactcattatgcagccca -accagggggatactacaatggaacaagaggagacagaaacaagctgaggcatctaatttc -agtcaaattgggcaaaatcccaacagtagagaactccattttccatatggcagcatggag -cgggtccgcgtgccatgatggtaaggaatggacatatatcggagttgatggccctgacaa -taatgcattgctcaaagtaaaatatggagaagcatatactgacacataccattcctatgc -aaacaacatcctaagaacacaagaaagtgcctgcaattgcatcgggggaaattgttatct -aatgataactgatggctcagcttcaggtgttagtgaatgcagatttcttaagattcgaga -gggccgaataataaaagaaatatttccaacaggaagagtaaaacacactgaggaatgcac -atgcggatttgccagtaataaaaccatagaatgtgcctgtagagacaacaggtacacagc -caaaagaccttttgtcaaattaaacgtggagactgatacagcagaaataagattgatgtg -tacagatacttatttggacacccccagaccaaatgatggaagcataacaggcccttgtga -atctgatggggaagaggggagtggaggcatcaaaggaggattcgttcatcaaagaatgaa -atccaagattggaaggtggtactctcgaacgatgtctaaaactgaaaggatggggatgga -actgtatgtcaagtatggtggagacccatgggctgacagtgatgccctagtttttagtgg -agtaatgatttcaatgaaagaacctggttggtattcctttggcttcgaaatcaaagataa -gaaatgcgatgtcccctgtattgggatagagatggtacatgatggtggaaaagagacttg -gcactcagcagcaacagccatttactgtttaatgggctcaggacagctgctgtgggacac -tgtcacaggtgttgatatggctctgtaa ->XX-566912_NS -atggcgaacaacaacatgaccacaacacaaattgaggtgggtccgggagcaaccaatgcc -accataaactttgaagcaggaattctggagtgctatgaaaggctttcatggcaaagagcc -cttgactaccccggtcaagaccgcctaaacagactaaaaagaaaattagagtcaagaata -aagactcacaacaaaagtgagcctgaaagtaaaaggatgtcccttgaagagagaaaagca -attggagtaaaaatgatgaaagtactcctatttatgaatccgtctgctggaattgaaggg -tttgagccacactgtatgaacagttcctcaaatagcaactgtacgaaatacaattggacc -gattacccttcaacaccagagagatgctttgatgacatagaggaagaaccagaggatgtt -gatggcccaactgaaataatattaagggacatgaacaacaaagatgcaaggcaaaagata -aaggaggaagtaaacactcagaaagaagggaagttccgtttgacaataaaaagggatatg -cgtaatgtattgtccttgagagtgttggtaaatggaactttcctcaaacaccccaatgga -tacaagtccttatcaactctgcatagattaaatgcatatgaccagagtggaaggcttgtt -gctaaacttgttgccactgatgatcttacagtggaggatgaagaagatggccatcggatc -ctcaactcactcttcgagcgtctcaatgaaggacattcaaagccaattcgagcagctgaa -actgcggtgggagtcttatcccaatttggtcaagagcaccgattatcaccagaagaggga -gacaattagattggtcacggaagaactttatcttttaagtaaaagaattgatgataacat -actattccacaaaacagtgatagctaacagccccataatagctgacatggttgtatcatt -atcattattagaaacattgtatgaaatgaaggatgtggttgaagtgtacagcaggcagtg -cttgtga ->XX-566913_NS -atggcgaacaacaacatgaccacaacacaaattgaggtgggtccgggagcaaccaatgcc -accataaactttgaagcaggaattctggagtgctatgaaaggctttcatggcaaagagcc -cttgactaccccggtcaagaccgcctaaacagactaaaaagaaaattagagtcaagaata -aagactcacaacaaaagtgagcctgaaagtaaaaggatgtcccttgaagagagaaaagca -attggagtaaaaatgatgaaagtactcctatttatgaatccgtctgctggaattgaaggg -tttgagccacactgtatgaacagttcctcaaatagcaactgtacgaaatacaattggacc -gattacccttcaacaccagagaggtgctttgatgacatagaggaagaaccagaggatgtt -gatggcccaactgaaatagtattaagggacatgaacaacaaagatgcaaggcaaaagata -aaggaggaagtaaacactcagaaagaagggaagttccgtttgacaataaaaagggatatg -cgtaatgtattgtccttgagagtgttggtaaatggaactttcctcaaacaccccaatgga -tacaagtccttatcaactctgcatagattaaatgcatatgaccagagtggaaggcttgtt -gctaaacttgttgccactgatgatcttacagtggaggatgaagaagatggccatcggatc -ctcaactcactcttcgagcgtctcaatgaaggacattcaaagccaattcgagcagctgaa -actgcggtgggagtcttatcccaatttggtcaagagcaccgattatcaccagaagaggga -tacaattagattggtcacggaagaactttatcttttaagtaaaagaattgatgataacat -actattccacaaaacagtgatagctaacagccccataatagctgacatggttgtatcatt -atcattattagaaacattgtatgaaatgaaggatgtggttgaagtgtacagcaggcagtg -cttgtga ->XX-566912_PA -atggatacttttattacaagaaacttccagactacaataatacaaaaggccaaaaacaca -atggcagaatttagtgaagatcctgaattgcaaccagcaatgctattcaacatctgtgtc -catctagaggtttgctatgtaataagtgacatgaattttcttgacgaagaaggaaaagca -tatacagcattagaaggacaagggaaagaacaaaacttgagaccacaatatgaagtaatt -gagggaatgccaagaaccatagcatggatggtccagagatccttagctcaagagcatgga -atagagactcccaagtatctggctgatttgtttgattacaaaaccaaaagatttatagaa -gttggaataacaaagggattggctgatgattacttttggaaaaagaaagaaaaattggga -aacagcatggaactgatgatattcagctacaatcaagactactcgttaagtaatgaatcc -tcattggatgaggaagggaaagggagagtgctaagcagactcacagaacttcaggctgaa -ttaagtctaaaaaatttatggcaagttctcataggagaagaagatgttgaaaagggaatt -gattttaaacttggacagacaatatctagactaagggatatatctgttccagccggtttc -tccaattttgaaggaatgaggagctacatagacaatatagacccaaaaggagcaatagag -agaaatctagcaaggatgtctcccttagtatcagtcacacctaaaaagttgacatgggag -gacctaagaccaatagggcctcacatttacgatcatgagctaccagaagttccatataat -gcctttcttctaatgtctgatgaactaggattggccaatatgactgagggaaagtctaaa -aaaccgaagacattagccaaagaatgtttagaaagatactcaacactacgggatcaaact -gacccaatattaataatgaaaagcgagaaagctaacgaaaatttcttatggaagctttgg -agagactgtgtaaatacaataagtaatgaggaagcaagtaacgaattacagaaaaccaat -tatgccaaatgggccacaggggatggattaacataccagaaaataatgaaagaagtagca -atagatgacgagacaatgtgccaagaagagcctaaaatccctaacaaatgtagagtggct -gcttgggttcaaacagagatgaatctattgagcactctgacaagtaaaagagctctggac -ctaccagaaatagggccagacatagcgcctgtagagcatgtaggaagtgaaagaaggaaa -tactttgttaacgaaatcaactactgtaaggcctctacagttatgatgaagtatgtgctt -tttcatacttcattgttgaatgaaagcaatgccagcatgggaaaatacaaagtaatacca -ataaccaacagagtagtaaatgaaaaaggagaaagtttcgacatgctttacggtttggcg -gttaaaggacaatctcatctgaggggagatactgatgttgtaacagttgtaacttttgaa -tttagtagtacagatcccagggtggacacaggaaagtggccaaaatatactgtgtttagg -attggctccctatttgtgagtgggagggaaaaatctgtgtacttgtattgcagagtgaat -ggcacaaataagatccaaatgaaatggggaatggaagctagaagatgtttgcttcaatca -atgcaacaaatggaggcaattgttgaacaggaatcatcaatacaaggatatgacatgacc -aaagcctgtttcaagggagacagagtaaatagccccaaaactttcagtattggaactcaa -gaaggaaaactagtaaaaggatcctttggaaaagcactaagagtaatatttactaaatgc -ttgatgcactatgtatttgggaatgctcaattggaggggtttagtgctgagtctaggaga -cttctattgttgattcaagcattaaaggacagaaagggtccttgggtgttcgacttagag -ggaatgtattctggaatagaagaatgtattagcaacaacccttgggtgatacagagtgta -tactggttcaatgaatggttggccgttgaaaaggaggggagcaaagtgttggaatcagtg -gatgaagtaatggatgaataa ->XX-566913_PA -atggatacttttattacaagaaacttccagactacaataatacaaaaggccaaaaacaca -atggcagaatttagtgaagatcctgaattgcaaccagcaatgctattcaacatctgtgtc -catctagaggtttgctatgtaataagtgacatgaattttcttgacgaagaaggaaaagca -tatacagcattagaaggacaagggaaagaacaaaacttgagaccacaatatgaagtaatt -gagggaatgccaagaaccatagcatggatggtccagagatccttagctcaagagcatgga -atagagactcccaagtatctggctgatttgtttgattacaaaaccaaaagatttatagaa -gttggaataacaaagggattggctgatgattacttttggaaaaagaaagaaaaattggga -aacagcatggaactgatgatattcagctacaatcaagactactcgttaagtaatgaatcc -tcattggatgaggaagggaaagggagagtgctaagcagactcacagaacttcaggctgaa -ttaagtctaaaaaatttatggcaagttctcataggagaagaagatgttgaaaagggaatt -gattttaaacttggacagacaatatctagactaagggatatatctgttccagccggtttc -tccaattttgaaggaatgaggagctacatagacaatatagacccaaaaggagcaatagag -agaaatctagcaaggatgtctcccttagtatcagtcacacctaaaaagttgacatgggag -gacctaagaccaatagggcctcacatttacgatcatgagctaccagaagttccatataat -gcctttcttctaatgtctgatgaactaggattggccaatatgactgagggaaagtctaaa -aaaccgaagacattagccaaagaatgtttagaaagatactcaacactacgggatcaaact -gacccaatattaataatgaaaagcgagaaagctaacgaaaatttcttatggaagctttgg -agagactgtgtaaatacaataagtaatgaggaagcaagtaacgaattacagaaaaccaat -tatgccaaatgggccacaggggatggattaacataccagaaaataatgaaagaagtagca -atagatgacgagacaatgtgccaagaagagcctaaaatccctaacaaatgtagagtggct -gcttgggttcaaacagagatgaatctattgagcactctgacaagtaaaagagctctggac -ctaccagaaatagggccagacatagcgcctgtagagcatgtaggaagtgaaagaaggaaa -tactttgttaacgaaatcaactactgtaaggcctctacagttatgatgaagtatgtgctt -tttcatacttcattgttgaatgaaagcaatgccagcatgggaaaatacaaagtaatacca -ataaccaacagagtagtaaatgaaaaaggagaaagtttcgacatgctttacggtttggcg -gttaaaggacaatctcatctgaggggagatactgatgttgtaacagttgtaacttttgaa -tttagtagtacagatcccagggtggacacaggaaagtggccaaaatatactgtgtttagg -attggctccctatttgtgagtgggagggaaaaatctgtgtacttgtattgcagagtgaat -ggcacaaataagatccaaatgaaatggggaatggaagctagaagatgtttgcttcaatca -atgcaacaaatggaggcaattgttgaacaggaatcatcaatacaaggatatgacatgacc -aaagcctgtttcaagggagacagagtaaatagccccaaaactttcagtattggaactcaa -gaaggaaaactagtaaaaggatcctttggaaaagcactaagagtaatatttactaaatgc -ttgatgcactatgtatttgggaatgctcaattggaggggtttagtgctgagtctaggaga -cttctattgttgattcaagcattaaaggacagaaagggtccttgggtgttcgacttagag -ggaatgtattctggaatagaagaatgtattagcaacaacccttgggtgatacagagtgta -tactggttcaatgaatggttggccgttgaaaaggaggggagcaaagtgttggaatcagtg -gatgaagtaatggatgaataa ->XX-566912_PB1 -atgaatataaatccttattttctcttcatagatgtgcccgtacaggcagcaatttcaaca -acattcccatacactggtgttcccccttattcccatggaacaggaacaggttacacaata -gacaccgtgatcagaacgcatgagtactcaaacaaggggaaacagtacatttctgatgtt -acaggatgcacaatagtggatccaacaaatggaccattacccgaagataatgagccgagt -gcctatgcgcaattagattgcgttttagaggctttggatagaatggatgaagaacaccca -ggtctttttcaagcagcctcacagaatgctatggaggccctaatggtcacaactgtagac -aaattaacccaggggagacaaacttttgattggacagtatgcagaaaccaacctgctgca -acggcactgaacacaacaataacctcttttaggttgaatgatttaaatggagccgacaaa -ggtggattaatacctttttgccaggatatcattgattcactagacagacctgaaatgact -ttcttctcagtaaagaatataaagaaaaaattgcctgccaaaaacagaaagggtttcctc -ataaagaggataccaatgaaggtaaaagacaaaataaccaaagtggaatacatcaaaaga -gcattatcattaaacacaatgacaaaagacgctgaaagaggcaaactgaaaagaagagcg -attgccactgctggaatacaaataagagggtttgtattagtagttgaaaacttggctaaa -aatatatgtgaaaatctagaacaaagtggtttaccagtaggtggaaacgagaagaaagcc -aaactgtcaaatgcagtggccaaaatgctcagtaactgcccaccaggagggattagcatg -acagtaacaggagacaatacaaaatggaatgaatgtttaaacccaagggtctttttggcc -atgaccgaaagaataaccagagacagcccagtttggttcagggatttttgtagtatagca -ccggtcctgttctccaataagatagcaagattggggaaaggatttatgataacaagcaaa -acaaaaagactaaaggcccaaataccttgtcctgatctgtttagtataccattagaaaga -tataatgaagaaacaagggcaaaattgaagaaactaaaaccattcttcaatgaagaagga -actgcatctctgtcacctgggatgatgatgggaatgtttaacatgctatctaccgtgttg -ggagtagctgcactaggtatcaagaacattggaaacaaagaatacctatgggatggactg -caatcttctgatgattttgctctatttgttaatgcaaaggatgaagaaacatgtatggaa -ggaataaacgacttttaccgaacgtgtaaactattgggaataaacatgagcaaaaagaaa -agttactgtaatgagactggaatgtttgaatttacaagcatgttctacagagatggattt -gtatctaattttgcaatggaactcccttcgtttggagttgctggagtaaatgaatcagca -gatatggcaataggaatgacaataataaagaacaacatgatcaacaatggaatgggtcca -gcaacagcacaaacagccatacagctattcatagctgattatagatacacctacaaatgc -cacaggggagattccaaagtagaaggaaagagaatgaaaatcataaaggagttatgggaa -aacactaaagggagagatggtctattagtagcagatggtgggcccaacatttacaatttg -agaaacttgcatatcccagaaatagtattgaagtataatctaatggaccctgaatacaaa -gggcgattacttcatcctcaaaatccctttgtgggacatttgtctattgagggcatcaaa -gaggcagacataactccagcacatggtccagtaaagaaaatggactacgatgcagtgtct -ggaactcatagttggagaaccaaaagaaacagatctatactaaacactgatcagaggaac -atgattcttgaggaacaatgctacgctaaatgttgcaacctatttgaggcctgttttaac -agtgcatcatacaggaagccagtgggtcaacatagcatgcttgaggctatggcccacaga -ttaagaatggatgcacgattagattatgaatcagggagaatgtcaaaagatgattttgag -aaagcaatggctcatcttggtgagattgggtacatataa ->XX-566913_PB1 -atgaatataaatccttattttctcttcatagatgtgcccgtacaggcagcaatttcaaca -acattcccatacactggtgttcccccttattcccatggaacaggaacaggttacacaata -gacaccgtgatcagaacgcatgagtactcaaacaaggggaaacagtacatttctgatgtt -acaggatgcacaatagtggatccaacaaatggaccattacccgaagataatgagccgagt -gcctatgcgcaattagattgcgttttagaggctttggatagaatggatgaagaacaccca -ggtctttttcaagcagcctcacagaatgctatggaggccctaatggtcacaactgtagac -aaattaacccaggggagacaaacttttgattggacagtatgcagaaaccaacctgctgca -acggcactgaacacaacaataacctcttttaggttgaatgatttaaatggagctgacaaa -ggtggattaatacctttttgccaggatatcattgattcactggacagacctgaaatgact -ttcttctcagtaaagaatataaagaaaaaattgcctgccaaaaacagaaagggtttcctc -ataaagaggataccaatgaaggtaaaagacaaaataaccaaagtggaatacatcaaaaga -gcattatcattaaacacaatgacaaaagacgctgaaagaggcaaactgaaaagaagagcg -attgccactgctggaatacaaataagagggtttgtattagtagttgaaaacttggctaaa -aatatatgtgaaaatctagaacaaagtggtttaccagtaggtggaaacgagaagaaagcc -aaactgtcaaatgcagtggccaaaatgctcagtaactgcccaccaggagggattagcatg -acagtaacaggagacaatacaaaatggaatgaatgtttaaacccaagggtctttttggcc -atgaccgaaagaataaccagagacagcccagtttggttcagggatttttgtagtatagca -ccggtcctgttctccaataagatagcaagattggggaaaggatttatgataacaagcaaa -acaaaaagactaaaggcccaaataccttgtcctgatctgtttagtataccattagaaaga -tataatgaagaaacaagggcaaaattgaagaaactaaaaccattcttcaatgaagaagga -actgcatctctgtcacctgggatgatgatgggaatgtttaatatgctatctaccgtgttg -ggagtagctgcactaggtatcaagaacattggaaacaaagaatacctatgggatggactg -caatcttctgatgattttgctctatttgttaatgcaaaggatgaagaaacatgtatggaa -ggaataaacgacttttaccgaacgtgtaaactattgggaataaacatgagcaaaaagaaa -agttactgtaatgagactggaatgtttgaatttacaagcatgttctacagagatggattt -gtatctaattttgcaatggaactcccttcgtttggagttgctggagtaaatgaatcagca -gatatggcaataggaatgacaataataaagaacaacatgatcaacaatggaatgggtcca -gcaacagcacaaacagccatacagctattcatagctgattatagatacacctacaaatgc -cacaggggagattccaaagtagaaggaaagagaatgaaaatcataaaggagttatgggaa -aacactaaagggagagatggtctattagtagcagatggtgggcccaacatttacaatttg -agaaacttgcatatcccagaaatagtattgaagtataatctaatggaccctgaatacaaa -gggcgattacttcatcctcaaaatccctttgtgggacatttgtctattgagggcatcaaa -gaggcagacataactccagcacatggtccagtgaagaaaatggactacgatgcagtgtct -ggaactcatagttggagaaccaaaagaaacagatctatactaaacactgatcagaggaac -atgattcttgaggaacaatgctacgctaaatgttgcaacctatttgaggcctgttttaac -agtgcatcatacaggaagccagtgggtcaacatagcatgcttgaggctatggcccacaga -ttaagaatggatgcacgattagactatgaatcagggagaatgtcaaaagatgattttgag -aaagcaatggctcatcttggtgagattgggtacatataa diff --git a/TEST_FLU/submission_files/BIOSAMPLE/submission.xml b/TEST_FLU/submission_files/BIOSAMPLE/submission.xml deleted file mode 100644 index 0ee7148..0000000 --- a/TEST_FLU/submission_files/BIOSAMPLE/submission.xml +++ /dev/null @@ -1,94 +0,0 @@ - - - - flu_test_submission - This is a test submission - - CDC - - - Jane - Doe - - - - - - - - - - - XX-566912 - - - CDC Influenza Sequencing Baseline Constellation - - - Influenza A virus - - - PRJNA217342 - - Pathogen.cl.1.0 - - Helix - USA: California - Homo sapiens - Influenza A viruses - A/California/566912/2016 - Nasal Wash - 36.78 N 119.42 W - female - 92 - H3N2 - 2016-12-28 - - - - - - XX-566912 - - - - - - - - - - XX-566913 - - - CDC Influenza Sequencing Baseline Constellation - - - Influenza A virus - - - PRJNA217342 - - Pathogen.cl.1.0 - - Helix - USA: Texas - Homo sapiens - Influenza A viruses - A/Texas/566913/2016 - Nasal Wash - 29.42 N 98.49 W - male - 21 - H3N2 - 2016-11-10 - - - - - - XX-566913 - - - - diff --git a/TEST_FLU/submission_files/GENBANK/TEST_FLU.zip b/TEST_FLU/submission_files/GENBANK/TEST_FLU.zip deleted file mode 100644 index 9bff6bf..0000000 Binary files a/TEST_FLU/submission_files/GENBANK/TEST_FLU.zip and /dev/null differ diff --git a/TEST_FLU/submission_files/GENBANK/authorset.sbt b/TEST_FLU/submission_files/GENBANK/authorset.sbt deleted file mode 100644 index 2f926a7..0000000 --- a/TEST_FLU/submission_files/GENBANK/authorset.sbt +++ /dev/null @@ -1,86 +0,0 @@ -Submit-block ::= { - contact { - contact { - name name { - last "Doe", - first "Jane", - middle "", - initials "", - suffix "", - title "" - }, - affil std { - affil "Centers for Disease Control and Prevention", - div "Respiratory Viruses Branch, Division of Viral Diseases", - city "Atlanta", - sub "GA", - country "USA", - street "1600 Clifton Rd", - email "email@myemail.com", - phone "", - postal-code "30329" - } - } - }, - cit { - authors { - names std { - { - name name { - last "Doe", - first "John" - } - }, - { - name name { - last "Doe", - first "Jane" - } - } - }, - affil std { - affil "Centers for Disease Control and Prevention", - div "Respiratory Viruses Branch, Division of Viral Diseases", - city "Atlanta", - sub "GA", - country "USA", - street "1600 Clifton Rd", - postal-code "30329" - } - } - }, - subtype new -} -Seqdesc ::= pub { - pub { - gen { - cit "unpublished", - authors { - names std { - { - name name { - last "Doe", - first "John" - } - }, - { - name name { - last "Doe", - first "Jane" - } - } - } - }, - title "Test_Submission" - } - } -} -Seqdesc ::= user { - type str "Submission", - data { - { - label str "AdditionalComment", - data str "Submission Title: TEST_FLU" - } - } -} diff --git a/TEST_FLU/submission_files/GENBANK/comment.cmt b/TEST_FLU/submission_files/GENBANK/comment.cmt deleted file mode 100644 index 15aa122..0000000 --- a/TEST_FLU/submission_files/GENBANK/comment.cmt +++ /dev/null @@ -1,17 +0,0 @@ -SeqID StructuredCommentPrefix organism collection_date Assembly-Method Coverage Sequencing-Technology Adamantane_resistance Patient_symptoms EPI_ISOLATE_ID TYPE Segment_name HOST_AGE HOST_GENDER PASSAGE StructuredCommentSuffix -CDC-XX-566912.1 FluData Influenza A virus 2016-12-28 Newbler v. 2.3 100x Illumina resistant ILI EPI_ISL_8289 H3N2 PB2 92 F PMK1 (2017-01-03) FluData -CDC-XX-566912.2 FluData Influenza A virus 2016-12-28 Newbler v. 2.3 100x Illumina resistant ILI EPI_ISL_8289 H3N2 PB1 92 F PMK1 (2017-01-03) FluData -CDC-XX-566912.3 FluData Influenza A virus 2016-12-28 Newbler v. 2.3 100x Illumina resistant ILI EPI_ISL_8289 H3N2 PA 92 F PMK1 (2017-01-03) FluData -CDC-XX-566912.4 FluData Influenza A virus 2016-12-28 Newbler v. 2.3 100x Illumina resistant ILI EPI_ISL_8289 H3N2 HA 92 F PMK1 (2017-01-03) FluData -CDC-XX-566912.5 FluData Influenza A virus 2016-12-28 Newbler v. 2.3 100x Illumina resistant ILI EPI_ISL_8289 H3N2 NP 92 F PMK1 (2017-01-03) FluData -CDC-XX-566912.6 FluData Influenza A virus 2016-12-28 Newbler v. 2.3 100x Illumina resistant ILI EPI_ISL_8289 H3N2 NA 92 F PMK1 (2017-01-03) FluData -CDC-XX-566912.7 FluData Influenza A virus 2016-12-28 Newbler v. 2.3 100x Illumina resistant ILI EPI_ISL_8289 H3N2 M 92 F PMK1 (2017-01-03) FluData -CDC-XX-566912.8 FluData Influenza A virus 2016-12-28 Newbler v. 2.3 100x Illumina resistant ILI EPI_ISL_8289 H3N2 NS 92 F PMK1 (2017-01-03) FluData -CDC-XX-566913.1 FluData Influenza A virus 2016-11-10 Newbler v. 2.3 100x Illumina resistant ILI EPI_ISL_8290 H3N2 PB2 21 M PMK1 (2017-01-03) FluData -CDC-XX-566913.2 FluData Influenza A virus 2016-11-10 Newbler v. 2.3 100x Illumina resistant ILI EPI_ISL_8290 H3N2 PB1 21 M PMK1 (2017-01-03) FluData -CDC-XX-566913.3 FluData Influenza A virus 2016-11-10 Newbler v. 2.3 100x Illumina resistant ILI EPI_ISL_8290 H3N2 PA 21 M PMK1 (2017-01-03) FluData -CDC-XX-566913.4 FluData Influenza A virus 2016-11-10 Newbler v. 2.3 100x Illumina resistant ILI EPI_ISL_8290 H3N2 HA 21 M PMK1 (2017-01-03) FluData -CDC-XX-566913.5 FluData Influenza A virus 2016-11-10 Newbler v. 2.3 100x Illumina resistant ILI EPI_ISL_8290 H3N2 NP 21 M PMK1 (2017-01-03) FluData -CDC-XX-566913.6 FluData Influenza A virus 2016-11-10 Newbler v. 2.3 100x Illumina resistant ILI EPI_ISL_8290 H3N2 NA 21 M PMK1 (2017-01-03) FluData -CDC-XX-566913.7 FluData Influenza A virus 2016-11-10 Newbler v. 2.3 100x Illumina resistant ILI EPI_ISL_8290 H3N2 M 21 M PMK1 (2017-01-03) FluData -CDC-XX-566913.8 FluData Influenza A virus 2016-11-10 Newbler v. 2.3 100x Illumina resistant ILI EPI_ISL_8290 H3N2 NS 21 M PMK1 (2017-01-03) FluData diff --git a/TEST_FLU/submission_files/GENBANK/sequence.fsa b/TEST_FLU/submission_files/GENBANK/sequence.fsa deleted file mode 100644 index 41a27f5..0000000 --- a/TEST_FLU/submission_files/GENBANK/sequence.fsa +++ /dev/null @@ -1,482 +0,0 @@ ->A/California/566912/2016_PB2 -atgacattagccaaaattgaattgttaaaacaactgctaagggacaatgaagccaaaaca -gtcctgaagcaaacaacagtagaccaatataacataataagaaaattcaatacatcaagg -attgaaaagaatccttcactaaggatgaagtgggccatgtgttctaactttcccttggct -ctcaccaagggcgatatggcaaacagaatccccttggaatacaaagggatacaactcaaa -acaaatgctgaagacataggaaccaaaggccaaatgtgctcaatagcagcagttacatgg -tggaatacatatggaccaataggagacactgaaggttttgaaagggtctacgaaagcttt -tttctcagaaaaatgagacttgacaacgccacttggggccggataacttttggcccagtt -gaaagagtgagaaaaagagtactactaaaccctctcaccaaggaaatgcctccggatgag -gcgagcaatgtgataatggaaatattatttcctaaagaagcaggaataccaagagaatcc -acttggatacatagggaactgataaaagaaaagagagaaaaattgaaagggacaatgata -actccaatcgtactggcatacatgcttgaaagagaactggttgctcgaagaagattcttg 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-actgcatctctgtcacctgggatgatgatgggaatgtttaacatgctatctaccgtgttg -ggagtagctgcactaggtatcaagaacattggaaacaaagaatacctatgggatggactg -caatcttctgatgattttgctctatttgttaatgcaaaggatgaagaaacatgtatggaa -ggaataaacgacttttaccgaacgtgtaaactattgggaataaacatgagcaaaaagaaa -agttactgtaatgagactggaatgtttgaatttacaagcatgttctacagagatggattt -gtatctaattttgcaatggaactcccttcgtttggagttgctggagtaaatgaatcagca -gatatggcaataggaatgacaataataaagaacaacatgatcaacaatggaatgggtcca -gcaacagcacaaacagccatacagctattcatagctgattatagatacacctacaaatgc -cacaggggagattccaaagtagaaggaaagagaatgaaaatcataaaggagttatgggaa -aacactaaagggagagatggtctattagtagcagatggtgggcccaacatttacaatttg -agaaacttgcatatcccagaaatagtattgaagtataatctaatggaccctgaatacaaa -gggcgattacttcatcctcaaaatccctttgtgggacatttgtctattgagggcatcaaa -gaggcagacataactccagcacatggtccagtaaagaaaatggactacgatgcagtgtct -ggaactcatagttggagaaccaaaagaaacagatctatactaaacactgatcagaggaac -atgattcttgaggaacaatgctacgctaaatgttgcaacctatttgaggcctgttttaac -agtgcatcatacaggaagccagtgggtcaacatagcatgcttgaggctatggcccacaga -ttaagaatggatgcacgattagattatgaatcagggagaatgtcaaaagatgattttgag -aaagcaatggctcatcttggtgagattgggtacatataa ->A/California/566912/2016_PA -atggatacttttattacaagaaacttccagactacaataatacaaaaggccaaaaacaca -atggcagaatttagtgaagatcctgaattgcaaccagcaatgctattcaacatctgtgtc -catctagaggtttgctatgtaataagtgacatgaattttcttgacgaagaaggaaaagca -tatacagcattagaaggacaagggaaagaacaaaacttgagaccacaatatgaagtaatt -gagggaatgccaagaaccatagcatggatggtccagagatccttagctcaagagcatgga -atagagactcccaagtatctggctgatttgtttgattacaaaaccaaaagatttatagaa -gttggaataacaaagggattggctgatgattacttttggaaaaagaaagaaaaattggga -aacagcatggaactgatgatattcagctacaatcaagactactcgttaagtaatgaatcc -tcattggatgaggaagggaaagggagagtgctaagcagactcacagaacttcaggctgaa -ttaagtctaaaaaatttatggcaagttctcataggagaagaagatgttgaaaagggaatt -gattttaaacttggacagacaatatctagactaagggatatatctgttccagccggtttc -tccaattttgaaggaatgaggagctacatagacaatatagacccaaaaggagcaatagag -agaaatctagcaaggatgtctcccttagtatcagtcacacctaaaaagttgacatgggag -gacctaagaccaatagggcctcacatttacgatcatgagctaccagaagttccatataat -gcctttcttctaatgtctgatgaactaggattggccaatatgactgagggaaagtctaaa -aaaccgaagacattagccaaagaatgtttagaaagatactcaacactacgggatcaaact -gacccaatattaataatgaaaagcgagaaagctaacgaaaatttcttatggaagctttgg -agagactgtgtaaatacaataagtaatgaggaagcaagtaacgaattacagaaaaccaat -tatgccaaatgggccacaggggatggattaacataccagaaaataatgaaagaagtagca -atagatgacgagacaatgtgccaagaagagcctaaaatccctaacaaatgtagagtggct -gcttgggttcaaacagagatgaatctattgagcactctgacaagtaaaagagctctggac -ctaccagaaatagggccagacatagcgcctgtagagcatgtaggaagtgaaagaaggaaa -tactttgttaacgaaatcaactactgtaaggcctctacagttatgatgaagtatgtgctt -tttcatacttcattgttgaatgaaagcaatgccagcatgggaaaatacaaagtaatacca -ataaccaacagagtagtaaatgaaaaaggagaaagtttcgacatgctttacggtttggcg -gttaaaggacaatctcatctgaggggagatactgatgttgtaacagttgtaacttttgaa -tttagtagtacagatcccagggtggacacaggaaagtggccaaaatatactgtgtttagg -attggctccctatttgtgagtgggagggaaaaatctgtgtacttgtattgcagagtgaat -ggcacaaataagatccaaatgaaatggggaatggaagctagaagatgtttgcttcaatca -atgcaacaaatggaggcaattgttgaacaggaatcatcaatacaaggatatgacatgacc 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-gatccttcattaatcagtacctttgcgggaagcacagtccccagaagatcaggtgcgact -ggtgttgcaatcaagggaggtggaaccttagtggctgaagccattcgatttataggaaga -gcaatggcagacagagggctattgagagacattaaagccaagactgcctatgaaaagatt -cttctgaatctaaagaacaaatgctctgcgccccaacaaaaggctctagttgatcaagtg -atcggaagcagaaatccggggattgcagacattgaagatctaaccctgcttgctcgtagt -atggtcgttgttaggccctctgtggcaagcaaagtggtgcttcccataagcatttacgcc -aaaatacctcaactagggttcaatgttgaagagtactctatggttgggtacgaagccatg -gctctttacaatatggcaacacctgtttccatattaagaatgggagatgatgcaaaggat -aaatcgcaattattcttcatgtcttgcttcggagctgcctatgaagacctgagagttttg -tctgcattaacaggcacagaattcaagcctagatcagcattaaaatgtaagggtttccat -gttccagcaaaggaacaggtagaaggaatgggagcagctctgatgtccatcaagctccag -ttttgggctcctatgaccagatctggggggaacgaggcaggtggagacggagggtctggc -caaataagctgcagcccagtgtttgcagtggagagacctattgctttaagcaagcaagct -gtaagaagaatgctgtcaatgaatattgaggggcgtgatgcagatgtcaaaggaaatcta -ctcaagatgatgaatgactcaatggctaagaaaaccagtggaaatgctttcattgggaag -aaaatgttccaaatatcagacaaaaacaaaaccaatcccattgaaattccaattaagcag -accatccccaatttcttctttgggagggacacagcagaggattatgatgacctcgattat -taa ->A/California/566912/2016_NA -atgaacaatgttaccctcaactatacaaacgttaaccctatttctcacatcagggggagt -attattatcactatatgtgtcagcctcattatcatacttactatattcggatatattgct -aaaattctcacaaacagaagtaactgcaccaacaatgccattggattgtgcaaacgcatc -aaatgttcaggctgtgaaccgttctgcaacaaaaggggcgacacttcttctcccagaacc -ggagtggacatacccgcgtttatcttgcccgggctcaacctttcagaaagcactcctaat -tagccctcatagattcggagaaaccaaaggaaactcagctcccttgataataagggaacc -ttttgttgcttgtggaccaaatgaatgcaaacactttgctttaactcattatgcagccca -accagggggatactacaatggaacaagaggagacagaaacaagctgaggcatctaatttc -agtcaaattgggcaaaatcccaacagtagagaactccattttccatatggcagcatggag -cgggtccgcgtgccatgatggtaaggaatggacatatatcggagttgatggccctgacaa -taatgcattgctcaaagtaaaatatggagaagcatatactgacacataccattcctatgc -aaacaacatcctaagaacacaagaaagtgcctgcaattgcatcgggggaaattgttatct -aatgataactgatggctcagcttcaggtgttagtgaatgcagatttcttaagattcgaga -gggccgaataataaaagaaatatttccaacaggaagagtaaaacacactgaggaatgcac -atgcggatttgccagtaataaaaccatagaatgtgcctgtagagacaacaggtacacagc -caaaagaccttttgtcaaattaaacgtggagactgatacagcagaaataagattgatgtg -tacagatacttatttggacacccccagaccaaatgatggaagcataacaggcccttgtga -atctgatggggaagaggggagtggaggcatcaaaggaggatttgttcatcaaagaatgaa -atccaagattggaaggtggtactctcgaacgatgtctaaaactgaaaggatggggatgga -actgtatgtcaagtatggtggagacccatgggctgacagtgatgccctagtttttagtgg -agtaatgatttcaatgaaagaacctggttggtattcctttggcttcgaaatcaaagataa -gaaatgcgatgtcccctgtattgggatagagatggtacatgatggtggaaaagagacttg -gcactcagcagcaacagccatttactgtttaatgggctcaggacagctgctgtgggacac -tgtcacaggtgttgatatggctctgtaa ->A/California/566912/2016_MP -atgtcgctgtttggagacacaattgcctacttgctttcattgatagaagatggagaaggc -aaagcagaactagcagaaaagttacactgttggtttggtgggaaagaatttgacctagac -tcagccttggaatggataaaaaacaaaagatgcttaactgatatacaaaaagcactaatt -ggtgcctctatatgctttttaaaacccaaagaccaggaaagaaaaagaagattcatcaca -gagcccttatcaggaatgggaacaacagcaacaaaaaagaaaggcctgattctggctgag -agaaaaatgagaaaatgtgtgagctttcatgaagcatttgaaatagcagaaggccatgaa -agctcagcgctactatactgtctcatggtcatgtacctgaatcctggaaattattcgatg -caagtaaaactaggaacgctctgtgctttatgcgagaaacaagcatcacattcacacaga -gctcatagcagagcagctagatcttcagtgcctggagtaagacgagaaatgcaaatggtc -tcagctatgaacacagcaaaaacgatgaatggaatgggaaaaggagaagacgtccaaaag -ctggcagaagagttgcaaagcaacattggagtgctgagatctcttggggcaagtcaaaag -aatggggaagggattgcaaaggatgtaatggaagtgctaaagcagagctccatgggaaat -tcagctcttgtgaagaaatatctataatgctcgaaccatttcagattcttacaatttgtt -cttttatcttatcagctctccatttcatggcttggacaatagggcatttgaatcaaataa -aaagaggaataaacatgaaaatacgaataaaaggtccaaacaaagagacaataaacagag -aggtatcaattttgaggcacagttaccaaaaagaaatccaggccaaagaaacaatgaagg -aagtgctctctgacaacatggaggtattgaatgaccacataataattgaggggctttctg -ccgaagagataataaaaatgggtgaaacagttttggagatagaagaattgcattaa ->A/California/566912/2016_NS -atggcgaacaacaacatgaccacaacacaaattgaggtgggtccgggagcaaccaatgcc -accataaactttgaagcaggaattctggagtgctatgaaaggctttcatggcaaagagcc -cttgactaccccggtcaagaccgcctaaacagactaaaaagaaaattagagtcaagaata -aagactcacaacaaaagtgagcctgaaagtaaaaggatgtcccttgaagagagaaaagca -attggagtaaaaatgatgaaagtactcctatttatgaatccgtctgctggaattgaaggg -tttgagccacactgtatgaacagttcctcaaatagcaactgtacgaaatacaattggacc -gattacccttcaacaccagagagatgctttgatgacatagaggaagaaccagaggatgtt -gatggcccaactgaaataatattaagggacatgaacaacaaagatgcaaggcaaaagata -aaggaggaagtaaacactcagaaagaagggaagttccgtttgacaataaaaagggatatg -cgtaatgtattgtccttgagagtgttggtaaatggaactttcctcaaacaccccaatgga -tacaagtccttatcaactctgcatagattaaatgcatatgaccagagtggaaggcttgtt -gctaaacttgttgccactgatgatcttacagtggaggatgaagaagatggccatcggatc -ctcaactcactcttcgagcgtctcaatgaaggacattcaaagccaattcgagcagctgaa -actgcggtgggagtcttatcccaatttggtcaagagcaccgattatcaccagaagaggga -gacaattagattggtcacggaagaactttatcttttaagtaaaagaattgatgataacat -actattccacaaaacagtgatagctaacagccccataatagctgacatggttgtatcatt -atcattattagaaacattgtatgaaatgaaggatgtggttgaagtgtacagcaggcagtg -cttgtga ->A/Texas/566913/2016_PB2 -atgacattagccaaaattgaattgttaaaacaactgctaagggacaatgaggccaaaaca -gtcctgaagcaaacaacagtagaccaatataacataataagaaaattcaatacatcaagg -attgaaaagaatccttcactaaggatgaagtgggccatgtgttctaactttcccttggct -ctcaccaagggcgatatggcaaacagaatccccttggaatacaaagggatacaactcaaa -acaaatgctgaagacataggaaccaaaggccaaatgtgctcaatagcagcagttacatgg -tggaatacatatggaccaataggagacactgaaggttttgaaagggtctacgaaagcttt -tttctcagaaaaatgagacttgacaacgccacttggggccggataacttttggcccagtt -gaaagagtgagaaaaagagtactactaaaccctctcaccaaggaaatgcctccggatgag -gcgagcaatgtgataatggaaatattatttcctaaagaagcaggaataccaagagaatcc -acttggatacatagggaactgataaaagaaaagagagaaaaattgaaagggacaatgata -actcccatcgtactggcatacatgcttgaaagagaactggttgctcgaagaagattcttg -ccagtggcaggagcaacatcagctgagttcatagaaatgctgcactgcttacaaggtgaa -aattggagacaaatatatcacccaggagggaataaattaactgagtccaggtctcaatca -atgatagtagcttgtaggaaaataatcagaagatcaatagtcgcttcaaacccactggag -ctagctgtagaaattgcaaacaagactgtgatagatactgaacctttaaagtcatgtctg -gcagccatagacggaggtgatgtagcttgtgacataataagagctgcattaggactaaag -atcagacaaagacaaagatttgggcggcttgagctaaaaagaatatcaggaagaggattc -aaaaatgatgaagaaatattaatagggaacggaacaatacagaagattggaatatgggat -ggggaagaggagttccacgtaagatgtggtgaatgcaggggaatattaaaaaagagtaaa -atgaaactggaaaaattactgataaattcagccaaaaaggaggatatgagagatttaata -atcttatgcatggtattttctcaagacactaggatgttccaaggggtgagaggagaaata -aattttcttaatcgagcaggccaacttttatctccaatgtaccaactccaacgatatttt -ttgaatagaagcaacgacctttttgatcaatgggggtatgaggaatcacccaaagcaagt -gaactacatgggataaatgaatcaatgaatgcatctgactatacattgaaagggattgta -gtgacaagaaatgtaattgacgactttagctctactgaaacagagaaagtatccataaca -aaaaatcttagcttaataaaaaggactggagaagtcataatgggagctaatgacgtgagt -gaattagaatcacaagcacagctgatgataacatatgatacacctaaaatgtgggaaatg -ggaacaaccaaagaactggtgcaaaacacttatcaatgggtgctaaaaaacttggtgaca -ctgaaggctcagtttcttctaggaaaagaggatatgttccaatgggatgcatttgaagca -tttgagagcataattcctcaaaaaatggctggtcagtacagtggatttgcaagagcagtg -ctcaaacaaatgagagaccaggaggttatgaaaactgatcagttcataaagttgctgcct -ttttgtttctcaccaccaaaattaagaagcaatggggagccttatcaattcttaaaactt -gtattgaaaggaggaggggaaaatttcattgaagtaaggaaagggtctcctctattttcc -tataatccacaaacagaagtcttaactatatgcggcagaatgatgtcattaaaagggaaa -attgaagatgaagaaaggaatagatcaatggggaatgcagtattagcaggctttctcgtt -agtggcaagtatgaccctgatcttggagatttcaaaactattgaagaacttgaaaagctg -aaaccaggggaaaaggcaaacatcttgctttatcaaggaaaaccagttaaagtagtgaaa -aggaaaaggtatagtgctttgtccaatgacatttcacaaggaattaaaagacaaagaatg -acagttgagtccatggggtgggccttgagctaa ->A/Texas/566913/2016_PB1 -atgaatataaatccttattttctcttcatagatgtgcccgtacaggcagcaatttcaaca -acattcccatacactggtgttcccccttattcccatggaacaggaacaggttacacaata -gacaccgtgatcagaacgcatgagtactcaaacaaggggaaacagtacatttctgatgtt -acaggatgcacaatagtggatccaacaaatggaccattacccgaagataatgagccgagt -gcctatgcgcaattagattgcgttttagaggctttggatagaatggatgaagaacaccca -ggtctttttcaagcagcctcacagaatgctatggaggccctaatggtcacaactgtagac -aaattaacccaggggagacaaacttttgattggacagtatgcagaaaccaacctgctgca -acggcactgaacacaacaataacctcttttaggttgaatgatttaaatggagctgacaaa -ggtggattaatacctttttgccaggatatcattgattcactggacagacctgaaatgact -ttcttctcagtaaagaatataaagaaaaaattgcctgccaaaaacagaaagggtttcctc -ataaagaggataccaatgaaggtaaaagacaaaataaccaaagtggaatacatcaaaaga -gcattatcattaaacacaatgacaaaagacgctgaaagaggcaaactgaaaagaagagcg -attgccactgctggaatacaaataagagggtttgtattagtagttgaaaacttggctaaa -aatatatgtgaaaatctagaacaaagtggtttaccagtaggtggaaacgagaagaaagcc -aaactgtcaaatgcagtggccaaaatgctcagtaactgcccaccaggagggattagcatg -acagtaacaggagacaatacaaaatggaatgaatgtttaaacccaagggtctttttggcc -atgaccgaaagaataaccagagacagcccagtttggttcagggatttttgtagtatagca -ccggtcctgttctccaataagatagcaagattggggaaaggatttatgataacaagcaaa -acaaaaagactaaaggcccaaataccttgtcctgatctgtttagtataccattagaaaga -tataatgaagaaacaagggcaaaattgaagaaactaaaaccattcttcaatgaagaagga -actgcatctctgtcacctgggatgatgatgggaatgtttaatatgctatctaccgtgttg -ggagtagctgcactaggtatcaagaacattggaaacaaagaatacctatgggatggactg -caatcttctgatgattttgctctatttgttaatgcaaaggatgaagaaacatgtatggaa -ggaataaacgacttttaccgaacgtgtaaactattgggaataaacatgagcaaaaagaaa -agttactgtaatgagactggaatgtttgaatttacaagcatgttctacagagatggattt -gtatctaattttgcaatggaactcccttcgtttggagttgctggagtaaatgaatcagca -gatatggcaataggaatgacaataataaagaacaacatgatcaacaatggaatgggtcca -gcaacagcacaaacagccatacagctattcatagctgattatagatacacctacaaatgc -cacaggggagattccaaagtagaaggaaagagaatgaaaatcataaaggagttatgggaa -aacactaaagggagagatggtctattagtagcagatggtgggcccaacatttacaatttg -agaaacttgcatatcccagaaatagtattgaagtataatctaatggaccctgaatacaaa -gggcgattacttcatcctcaaaatccctttgtgggacatttgtctattgagggcatcaaa -gaggcagacataactccagcacatggtccagtgaagaaaatggactacgatgcagtgtct -ggaactcatagttggagaaccaaaagaaacagatctatactaaacactgatcagaggaac -atgattcttgaggaacaatgctacgctaaatgttgcaacctatttgaggcctgttttaac -agtgcatcatacaggaagccagtgggtcaacatagcatgcttgaggctatggcccacaga -ttaagaatggatgcacgattagactatgaatcagggagaatgtcaaaagatgattttgag -aaagcaatggctcatcttggtgagattgggtacatataa ->A/Texas/566913/2016_PA -atggatacttttattacaagaaacttccagactacaataatacaaaaggccaaaaacaca -atggcagaatttagtgaagatcctgaattgcaaccagcaatgctattcaacatctgtgtc -catctagaggtttgctatgtaataagtgacatgaattttcttgacgaagaaggaaaagca -tatacagcattagaaggacaagggaaagaacaaaacttgagaccacaatatgaagtaatt -gagggaatgccaagaaccatagcatggatggtccagagatccttagctcaagagcatgga -atagagactcccaagtatctggctgatttgtttgattacaaaaccaaaagatttatagaa -gttggaataacaaagggattggctgatgattacttttggaaaaagaaagaaaaattggga -aacagcatggaactgatgatattcagctacaatcaagactactcgttaagtaatgaatcc -tcattggatgaggaagggaaagggagagtgctaagcagactcacagaacttcaggctgaa -ttaagtctaaaaaatttatggcaagttctcataggagaagaagatgttgaaaagggaatt -gattttaaacttggacagacaatatctagactaagggatatatctgttccagccggtttc -tccaattttgaaggaatgaggagctacatagacaatatagacccaaaaggagcaatagag -agaaatctagcaaggatgtctcccttagtatcagtcacacctaaaaagttgacatgggag -gacctaagaccaatagggcctcacatttacgatcatgagctaccagaagttccatataat -gcctttcttctaatgtctgatgaactaggattggccaatatgactgagggaaagtctaaa -aaaccgaagacattagccaaagaatgtttagaaagatactcaacactacgggatcaaact -gacccaatattaataatgaaaagcgagaaagctaacgaaaatttcttatggaagctttgg -agagactgtgtaaatacaataagtaatgaggaagcaagtaacgaattacagaaaaccaat -tatgccaaatgggccacaggggatggattaacataccagaaaataatgaaagaagtagca -atagatgacgagacaatgtgccaagaagagcctaaaatccctaacaaatgtagagtggct -gcttgggttcaaacagagatgaatctattgagcactctgacaagtaaaagagctctggac -ctaccagaaatagggccagacatagcgcctgtagagcatgtaggaagtgaaagaaggaaa -tactttgttaacgaaatcaactactgtaaggcctctacagttatgatgaagtatgtgctt -tttcatacttcattgttgaatgaaagcaatgccagcatgggaaaatacaaagtaatacca -ataaccaacagagtagtaaatgaaaaaggagaaagtttcgacatgctttacggtttggcg -gttaaaggacaatctcatctgaggggagatactgatgttgtaacagttgtaacttttgaa -tttagtagtacagatcccagggtggacacaggaaagtggccaaaatatactgtgtttagg -attggctccctatttgtgagtgggagggaaaaatctgtgtacttgtattgcagagtgaat -ggcacaaataagatccaaatgaaatggggaatggaagctagaagatgtttgcttcaatca -atgcaacaaatggaggcaattgttgaacaggaatcatcaatacaaggatatgacatgacc -aaagcctgtttcaagggagacagagtaaatagccccaaaactttcagtattggaactcaa -gaaggaaaactagtaaaaggatcctttggaaaagcactaagagtaatatttactaaatgc -ttgatgcactatgtatttgggaatgctcaattggaggggtttagtgctgagtctaggaga -cttctattgttgattcaagcattaaaggacagaaagggtccttgggtgttcgacttagag -ggaatgtattctggaatagaagaatgtattagcaacaacccttgggtgatacagagtgta -tactggttcaatgaatggttggccgttgaaaaggaggggagcaaagtgttggaatcagtg -gatgaagtaatggatgaataa ->A/Texas/566913/2016_HA -atgaaggcaataattgtactactcatggtagtaacatccaatgcagatcgaatctgcact -gggataacatcgtcaaactcaccacatgtcgtcaaaactgctactcaaggggaggtcaat -gtgactggtgtaataccactgacaacaacacccaccaaatctcattttgcaaatctcaaa -ggaacagaaaccagggggaaactatgcccaaaatgcctaaactgcacagatctggatgta -gccttgggcagaccaaaatgcacagggaaaataccctctgcaagggtttcaatactccat -gaagtcagacctgttacgtctgggtgctttcctataatgcatgatagaacaaaaattaga -cagctgcctaaccttctccgaggatacgaacatgtcaggttatcaactcacaacgttatc -aatacagaagatgcaccaggaggaccctatgaaattggaacctcagggtcttgcctcaac -attaccaatggaaaaggattcttcgcaacaatggcttgggccgtcccaaaaaacaaaaca -gcaacaaatccattaacaatagaagtaccatacatttgtacagaagaagaagaccaaatt -accgtttgggggttccactctgacgaagagacccaaatggcaagactctatggggattca -aagccccagaagttcacctcatctgccaacggagtgaccacacactacgtctcacagatt -ggtggcttcccaaatcaaacagaagacggaggactaccacaaagtggcagaattgttgtt -gattacatggtgcaaaaatctggaaaaacaggaacaattacctatcaaagaggtatttta -ttgcctcaaaaggtgtggtgcgcaagtggcaagagcaaggtaataaaaggatccttgccc -ttaattggagaagcagattgcctccatgaaaaatacggtggattaaacaaaagcaagcct -tactacacaggggaacatgcaaaggccataggaaattgcccaatatgggtgaaaacaccc -ttgaagctggccaatggaaccaaatatagacctcctgcaaaactgttaaaggaaagaggt -ttcttcggagccattgctggtttcttagaaggaggatgggaaggaatgattgcaggttgg -cacggatacacatcccatggggcacatggagtagcagtggcagctgaccttaagagcact -caagaggccataaacaagataacaaaaaatctcaactctttgagtgagctggaagtaaag -aatcttcaaagactaagcggtgccatggatgaactccacaacgaaatactagaactagat -gagaaagtggatgatctcagagctgatacaataagctcacagatagaactcgcagtcctg -ctttccaatgaaggaataataaacagtgaagatgaacatctcttggcgcttgaaagaaag -ctgaagaaaatgctgggcccctctgctgtagagataggaaatggatgctttgaaaccaaa -cacaagtgcaaccaaacctgtctcgacagaatagctgctggtacctttgatgcaggagaa -ttttctctccccacctttgattcactgaatattactgctgcatctttaaatgacgatgga -ttggacaatcatactatactgctttactactcaactgctgcctccagtttggctgtaaca -ctgatgatagctatctttgttgtttatatggtctccagagacaatgtttcttgctccatt -tgtctataa ->A/Texas/566913/2016_NP -atgtccaacatggatatcgacggtatgaacactgggacaattgacaaaacaccggaagaa -ataacttctggaaccagtgggacaaccagaccaatcattagaccagcaacccttgcccca -ccaagcaacaaacgaacccgtaacccatctccggaaagagcaaccacaagcagtgaagat -gatgtcggaaggaaagcccaaaagaagcagaccccgacagagataaagaagagcgtctac -aacatggtggtgaaactgggcgaattctacaaccagatgatggttaaagctggactcaat -gatgacatggagagaaatctaatccaaaatgcacatgccgtggagagaattttattggct -gccactgatgacaagaaaaccgagttccagaagaaaaagaatgccagagatgtcaaagaa -gggaaggaagaaatagatcacaacaaaacaggaggcaccttttacaagatggtaagagat -gataaaaccatctatttcagccctataagaattacctttttaaaagaagaggtgaaaaca -atgtacaaaaccaccatggggagtgatggcttcagtggattaaatcacataatgattggg -cattcgcagatgaatgatgtctgtttccaaagatcaaaggcactaaaaagagttggactt -gatccttcattaatcagtacctttgcgggaagcacagtccccagaagatcaggtgcgact -ggtgttgcaatcaagggaggtggaaccttagtggctgaagccattcgatttataggaaga -gcaatggcagacagagggctattgagagacattaaaaccaagactgcctatgaaaagatt -cttctgaatctaaagaacaaatgctctgcgccccaacaaaaggctctagttgatcaagtg -atcggaagcagaaatccggggattgcagacattgaagatctaaccctgcttgctcgtagt -atggtcgttgttaggccctctgtggcaagcaaagtggtgcttcccataagcatttacgcc -aaaatacctcaactagggttcaatgttgaagagtactctatggttgggtacgaagccatg -gctctttacaatatggcaacacctgtttccatattaagaatgggagatgatgcaaaggat -aaatcgcaattattcttcatgtcttgcttcggagctgcctatgaagacctgagagttttg -tctgcattaacaggcacagaattcaagcctagatcagcattaaaatgtaagggtttccat -gttccagcaaaggaacaggtagaaggaatgggagcagctctgatgtccatcaagctccag -ttttgggctccgatgaccagatctggggggaacgaagcaggtggagacggagggtctggc -caaataagctgcagcccagtgtttgcagtggagagacctattgctttaagcaagcaagct -gtaagaagaatgctgtcaatgaatattgaggggcgtgatgcagatgtcaaaggaaatcta -ctcaagatgatgaatgactcaatggctaagaaaaccagtggaaatgctttcattgggaag -aaaatgttccaaatatcagacaaaaacaaaaccaatcccattgaaattccaattaagcag -accatccccaatttcttctttgggagggacacagcagaggattatgatgacctcgattat -taa ->A/Texas/566913/2016_NA -atgaacaatgttaccctcaactatacaaacgttaaccctatttctcacatcagggggagt -attattatcactatatgtgtcagcttcattatcatacttactatattcggatatattgct -aaaattctcacaaacagaaataactgcaccaacaatgccattggattgtgcaaacgcatc -aaatgttcaggctgtgaaccgttctgcaacaaaaggggcgacacttcttctcccagaacc -ggagtggacatacccgcgtttatcttgcccgggctcaacctttcagaaagcactcctaat -tagccctcatagattcggagaaaccaaaggaaactcagctcccttgataataagggaacc -ttttgttgcttgtggaccaaatgaatgcaaacactttgctttaactcattatgcagccca -accagggggatactacaatggaacaagaggagacagaaacaagctgaggcatctaatttc -agtcaaattgggcaaaatcccaacagtagagaactccattttccatatggcagcatggag -cgggtccgcgtgccatgatggtaaggaatggacatatatcggagttgatggccctgacaa -taatgcattgctcaaagtaaaatatggagaagcatatactgacacataccattcctatgc -aaacaacatcctaagaacacaagaaagtgcctgcaattgcatcgggggaaattgttatct -aatgataactgatggctcagcttcaggtgttagtgaatgcagatttcttaagattcgaga -gggccgaataataaaagaaatatttccaacaggaagagtaaaacacactgaggaatgcac -atgcggatttgccagtaataaaaccatagaatgtgcctgtagagacaacaggtacacagc -caaaagaccttttgtcaaattaaacgtggagactgatacagcagaaataagattgatgtg -tacagatacttatttggacacccccagaccaaatgatggaagcataacaggcccttgtga -atctgatggggaagaggggagtggaggcatcaaaggaggattcgttcatcaaagaatgaa -atccaagattggaaggtggtactctcgaacgatgtctaaaactgaaaggatggggatgga -actgtatgtcaagtatggtggagacccatgggctgacagtgatgccctagtttttagtgg -agtaatgatttcaatgaaagaacctggttggtattcctttggcttcgaaatcaaagataa -gaaatgcgatgtcccctgtattgggatagagatggtacatgatggtggaaaagagacttg -gcactcagcagcaacagccatttactgtttaatgggctcaggacagctgctgtgggacac -tgtcacaggtgttgatatggctctgtaa ->A/Texas/566913/2016_MP -atgtcgctgtttggagacacaattgcctacttgctttcattgatagaagatggagaaggc -aaagcagaactagcagaaaagttacactgttggtttggtgggaaagaatttgacctagac -tcagccttggaatggataaaaaacaaaagatgcttaactgatatacaaaaagcactaatt -ggtgcctctatatgctttttaaaacccaaagaccaggaaagaaaaagaagattcatcaca -gagcccttatcaggaatgggaacaacagcaacaaaaaagaaaggcctgattctggctgag -agaaaaatgagaaaatgtgtgagctttcatgaagcatttgaaatagcagaaggccatgaa -agctcagcgctactatactgtctcatggtcatgtacctgaatcctggaaattattcgatg -caagtaaaactaggaacgctctgtgctttatgcgagaaacaagcatcacattcacacaga -gctcatagcagagcagctagatcttcagtgcctggagtaagacgagaaatgcaaatggtc -tcagctatgaacacagcaaaaacgatgaatggaatgggaaaaggagaagacgtccaaaag -ctggcagaagagttgcaaagcaacattggagtgctgagatctcttggggcaagtcaaaag -aatggggaagggattgcaaaggatgtaatggaagtgctaaagcagagctccatgggaaat -tcagctcttgtgaagaaatatctataatgctcgaaccatttcagattcttacaatttgtt -cttttatcttatcagctctccatttcatggcttggacaatagggcatttgaatcaaataa -aaagaggaataaacatgaaaatacgaataaaaggtccaaacaaagagacaataaacagag -aggtatcaattttgaggcacagttaccaaaaagaaatccaggccaaagaaacaatgaagg -aagtgctctctgacaacatggaggtattgaatgaccacataataattgaggggctttctg -ccgaagagataataaaaatgggtgaaacagttttggagatagaagaattgcattaa ->A/Texas/566913/2016_NS -atggcgaacaacaacatgaccacaacacaaattgaggtgggtccgggagcaaccaatgcc -accataaactttgaagcaggaattctggagtgctatgaaaggctttcatggcaaagagcc -cttgactaccccggtcaagaccgcctaaacagactaaaaagaaaattagagtcaagaata -aagactcacaacaaaagtgagcctgaaagtaaaaggatgtcccttgaagagagaaaagca -attggagtaaaaatgatgaaagtactcctatttatgaatccgtctgctggaattgaaggg -tttgagccacactgtatgaacagttcctcaaatagcaactgtacgaaatacaattggacc -gattacccttcaacaccagagaggtgctttgatgacatagaggaagaaccagaggatgtt -gatggcccaactgaaatagtattaagggacatgaacaacaaagatgcaaggcaaaagata -aaggaggaagtaaacactcagaaagaagggaagttccgtttgacaataaaaagggatatg -cgtaatgtattgtccttgagagtgttggtaaatggaactttcctcaaacaccccaatgga -tacaagtccttatcaactctgcatagattaaatgcatatgaccagagtggaaggcttgtt -gctaaacttgttgccactgatgatcttacagtggaggatgaagaagatggccatcggatc -ctcaactcactcttcgagcgtctcaatgaaggacattcaaagccaattcgagcagctgaa -actgcggtgggagtcttatcccaatttggtcaagagcaccgattatcaccagaagaggga -tacaattagattggtcacggaagaactttatcttttaagtaaaagaattgatgataacat -actattccacaaaacagtgatagctaacagccccataatagctgacatggttgtatcatt -atcattattagaaacattgtatgaaatgaaggatgtggttgaagtgtacagcaggcagtg -cttgtga diff --git a/TEST_FLU/submission_files/GENBANK/source.src b/TEST_FLU/submission_files/GENBANK/source.src deleted file mode 100644 index e3de14e..0000000 --- a/TEST_FLU/submission_files/GENBANK/source.src +++ /dev/null @@ -1,17 +0,0 @@ -Sequence_ID organism Collection_date strain BioProject strain country host serotype isolation_source note -CDC-XX-566912.1 Influenza A virus 2016-12-28 XX-566912 PRJNA217342 A/California/566912/2016 USA: California Homo sapiens; gender F; age 92 H3N2 Nasal Wash passage: PMK1 -CDC-XX-566912.2 Influenza A virus 2016-12-28 XX-566912 PRJNA217342 A/California/566912/2016 USA: California Homo sapiens; gender F; age 92 H3N2 Nasal Wash passage: PMK1 -CDC-XX-566912.3 Influenza A virus 2016-12-28 XX-566912 PRJNA217342 A/California/566912/2016 USA: California Homo sapiens; gender F; age 92 H3N2 Nasal Wash passage: PMK1 -CDC-XX-566912.4 Influenza A virus 2016-12-28 XX-566912 PRJNA217342 A/California/566912/2016 USA: California Homo sapiens; gender F; age 92 H3N2 Nasal Wash passage: PMK1 -CDC-XX-566912.5 Influenza A virus 2016-12-28 XX-566912 PRJNA217342 A/California/566912/2016 USA: California Homo sapiens; gender F; age 92 H3N2 Nasal Wash passage: PMK1 -CDC-XX-566912.6 Influenza A virus 2016-12-28 XX-566912 PRJNA217342 A/California/566912/2016 USA: California Homo sapiens; gender F; age 92 H3N2 Nasal Wash passage: PMK1 -CDC-XX-566912.7 Influenza A virus 2016-12-28 XX-566912 PRJNA217342 A/California/566912/2016 USA: California Homo sapiens; gender F; age 92 H3N2 Nasal Wash passage: PMK1 -CDC-XX-566912.8 Influenza A virus 2016-12-28 XX-566912 PRJNA217342 A/California/566912/2016 USA: California Homo sapiens; gender F; age 92 H3N2 Nasal Wash passage: PMK1 -CDC-XX-566913.1 Influenza A virus 2016-11-10 XX-566913 PRJNA217342 A/Texas/566913/2016 USA: Texas Homo sapiens; gender M; age 21 H3N2 Nasal Wash passage: PMK1 -CDC-XX-566913.2 Influenza A virus 2016-11-10 XX-566913 PRJNA217342 A/Texas/566913/2016 USA: Texas Homo sapiens; gender M; age 21 H3N2 Nasal Wash passage: PMK1 -CDC-XX-566913.3 Influenza A virus 2016-11-10 XX-566913 PRJNA217342 A/Texas/566913/2016 USA: Texas Homo sapiens; gender M; age 21 H3N2 Nasal Wash passage: PMK1 -CDC-XX-566913.4 Influenza A virus 2016-11-10 XX-566913 PRJNA217342 A/Texas/566913/2016 USA: Texas Homo sapiens; gender M; age 21 H3N2 Nasal Wash passage: PMK1 -CDC-XX-566913.5 Influenza A virus 2016-11-10 XX-566913 PRJNA217342 A/Texas/566913/2016 USA: Texas Homo sapiens; gender M; age 21 H3N2 Nasal Wash passage: PMK1 -CDC-XX-566913.6 Influenza A virus 2016-11-10 XX-566913 PRJNA217342 A/Texas/566913/2016 USA: Texas Homo sapiens; gender M; age 21 H3N2 Nasal Wash passage: PMK1 -CDC-XX-566913.7 Influenza A virus 2016-11-10 XX-566913 PRJNA217342 A/Texas/566913/2016 USA: Texas Homo sapiens; gender M; age 21 H3N2 Nasal Wash passage: PMK1 -CDC-XX-566913.8 Influenza A virus 2016-11-10 XX-566913 PRJNA217342 A/Texas/566913/2016 USA: Texas Homo sapiens; gender M; age 21 H3N2 Nasal Wash passage: PMK1 diff --git a/TEST_FLU/submission_files/GENBANK/submission.xml b/TEST_FLU/submission_files/GENBANK/submission.xml deleted file mode 100644 index 0f19f1b..0000000 --- a/TEST_FLU/submission_files/GENBANK/submission.xml +++ /dev/null @@ -1,22 +0,0 @@ - - - - flu_test_submission - This is a test submission - - CDC - - - - - - genbank-submission-package - - BankIt_influenza_api - yes - - TEST_FLU - - - - diff --git a/TEST_FLU/submission_files/SRA/raw_reads_location.txt b/TEST_FLU/submission_files/SRA/raw_reads_location.txt deleted file mode 100644 index 98558f6..0000000 --- a/TEST_FLU/submission_files/SRA/raw_reads_location.txt +++ /dev/null @@ -1,4 +0,0 @@ -/scicomp/home-pure/psv4/seqsender_master/seqsender/TEST_FLU/raw_reads/fastq_2_R1.fastq.gz -/scicomp/home-pure/psv4/seqsender_master/seqsender/TEST_FLU/raw_reads/fastq_2_R2.fastq.gz -/scicomp/home-pure/psv4/seqsender_master/seqsender/TEST_FLU/raw_reads/fastq_1_R2.fastq.gz -/scicomp/home-pure/psv4/seqsender_master/seqsender/TEST_FLU/raw_reads/fastq_1_R1.fastq.gz diff --git a/TEST_FLU/submission_files/SRA/submission.xml b/TEST_FLU/submission_files/SRA/submission.xml deleted file mode 100644 index 0a95ef3..0000000 --- a/TEST_FLU/submission_files/SRA/submission.xml +++ /dev/null @@ -1,78 +0,0 @@ - - - - flu_test_submission - This is a test submission - - CDC - - - Jane - Doe - - - - - - - - generic-data - - - generic-data - - Helix COVID-19 and Flu Test - Illumina NovaSeq 6000 - AMPLICON - VIRAL RNA - RT-PCR - PAIRED - Helix Hybrid-Capture Test - latf-load - - - PRJNA217342 - - - - - XX-566912 - - - - XX-566912 - - - - - - - generic-data - - - generic-data - - Helix COVID-19 and Flu Test - Illumina NovaSeq 6000 - AMPLICON - VIRAL RNA - RT-PCR - PAIRED - Helix Hybrid-Capture Test - latf-load - - - PRJNA217342 - - - - - XX-566913 - - - - XX-566913 - - - - diff --git a/TEST_FLU/submission_report_status.csv b/TEST_FLU/submission_report_status.csv deleted file mode 100644 index bdb9d49..0000000 --- a/TEST_FLU/submission_report_status.csv +++ /dev/null @@ -1,17 +0,0 @@ -ncbi-sample_name,ncbi-sequence_name,biosample_status,biosample_accession,biosample_message,sra_status,sra_accession,sra_message,genbank_status,genbank_accession,genbank_message -XX-566912,CDC-XX-566912.1,,,,,,,,, -XX-566912,CDC-XX-566912.2,,,,,,,,, -XX-566912,CDC-XX-566912.3,,,,,,,,, -XX-566912,CDC-XX-566912.4,,,,,,,,, -XX-566912,CDC-XX-566912.5,,,,,,,,, -XX-566912,CDC-XX-566912.6,,,,,,,,, -XX-566912,CDC-XX-566912.7,,,,,,,,, -XX-566912,CDC-XX-566912.8,,,,,,,,, -XX-566913,CDC-XX-566913.1,,,,,,,,, -XX-566913,CDC-XX-566913.2,,,,,,,,, -XX-566913,CDC-XX-566913.3,,,,,,,,, -XX-566913,CDC-XX-566913.4,,,,,,,,, -XX-566913,CDC-XX-566913.5,,,,,,,,, -XX-566913,CDC-XX-566913.6,,,,,,,,, -XX-566913,CDC-XX-566913.7,,,,,,,,, -XX-566913,CDC-XX-566913.8,,,,,,,,,