From 8afcd646ef4b76d1ce7ea37fedac25da5d519fac Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C3=A1t=C3=A9=20Balajti?= Date: Fri, 27 Oct 2023 10:39:04 +0200 Subject: [PATCH] refactor: update folder structure --- .gitignore | 2 ++ .../inputs => cdna_generator/files}/.gitkeep | 0 .../{test_files => files}/Example_GTF_Input.GTF | 0 tests/cdna_generator/{test_files => files}/cDNA.csv | 0 tests/cdna_generator/{test_files => files}/cDNA.fasta | 0 .../{test_files => files}/copy_number_file.csv | 0 .../{test_files => files}/copy_number_input.csv | 0 .../cdna_generator/{test_files => files}/transcript.fasta | 8 ++++---- .../cdna_generator/{test_files => files}/yeast_example.fa | 0 tests/fragment_selector/{test_files => files}/test.csv | 0 tests/fragment_selector/{test_files => files}/test.fasta | 0 .../fragment_selector/{test_files => files}/test_tab.csv | 0 .../{test_files => files}/RIBlast_output_example.txt | 0 .../{test_files => files}/output_transcripts_df.gtf | 0 .../{test_files => files}/primer1.fasta | 0 .../{test_files => files}/test_fasta.fasta | 0 .../{test_files => files}/yeast_test_files/dbRNA_test.fa | 0 .../yeast_test_files/queryRNA_test.fa | 0 .../{fasta_testfile => files}/50_seqs_50_1000_bp.fasta | 0 .../{test_files => files}/post_bedtools_test.fa | 0 tests/sequence_extractor/{test_files => files}/test.bed | 0 tests/sequence_extractor/{test_files => files}/test.gtf | 0 tests/sequence_extractor/{test_files => files}/test_1.fa | 0 tests/sequence_extractor/{test_files => files}/test_2.fa | 0 .../{test_files => files}/Annotation1.gtf | 0 .../{test_files => files}/Annotations2.gtf | 0 .../{test_files => files}/Transcript1.csv | 0 .../{test_files => files}/Transcript2.tsv | 0 tests/transcript_sampler/{inputs => files}/expression.csv | 0 tests/transcript_sampler/{inputs => files}/new_test.gtf | 0 tests/transcript_sampler/{inputs => files}/test.gtf | 0 .../{inputs => files}/test_dict_repr_trans.txt | 0 .../test_gencode.vM31.annotation_intermediat_file.txt | 0 .../transcript_sampler/{inputs => files}/test_gene_exprL | 0 .../{inputs => files}/test_gene_exprL_csv.csv | 0 .../{inputs => files}/test_ref_output.tsv | 0 36 files changed, 6 insertions(+), 4 deletions(-) rename tests/{transcript_sampler/inputs => cdna_generator/files}/.gitkeep (100%) rename tests/cdna_generator/{test_files => files}/Example_GTF_Input.GTF (100%) rename tests/cdna_generator/{test_files => files}/cDNA.csv (100%) rename tests/cdna_generator/{test_files => files}/cDNA.fasta (100%) rename tests/cdna_generator/{test_files => files}/copy_number_file.csv (100%) rename tests/cdna_generator/{test_files => files}/copy_number_input.csv (100%) rename tests/cdna_generator/{test_files => files}/transcript.fasta (83%) rename tests/cdna_generator/{test_files => files}/yeast_example.fa (100%) rename tests/fragment_selector/{test_files => files}/test.csv (100%) rename tests/fragment_selector/{test_files => files}/test.fasta (100%) rename tests/fragment_selector/{test_files => files}/test_tab.csv (100%) rename tests/priming_site_predictor/{test_files => files}/RIBlast_output_example.txt (100%) rename tests/priming_site_predictor/{test_files => files}/output_transcripts_df.gtf (100%) rename tests/priming_site_predictor/{test_files => files}/primer1.fasta (100%) rename tests/priming_site_predictor/{test_files => files}/test_fasta.fasta (100%) rename tests/priming_site_predictor/{test_files => files}/yeast_test_files/dbRNA_test.fa (100%) rename tests/priming_site_predictor/{test_files => files}/yeast_test_files/queryRNA_test.fa (100%) rename tests/read_sequencer/{fasta_testfile => files}/50_seqs_50_1000_bp.fasta (100%) rename tests/sequence_extractor/{test_files => files}/post_bedtools_test.fa (100%) rename tests/sequence_extractor/{test_files => files}/test.bed (100%) rename tests/sequence_extractor/{test_files => files}/test.gtf (100%) rename tests/sequence_extractor/{test_files => files}/test_1.fa (100%) rename tests/sequence_extractor/{test_files => files}/test_2.fa (100%) rename tests/structure_generator/{test_files => files}/Annotation1.gtf (100%) rename tests/structure_generator/{test_files => files}/Annotations2.gtf (100%) rename tests/structure_generator/{test_files => files}/Transcript1.csv (100%) rename tests/structure_generator/{test_files => files}/Transcript2.tsv (100%) rename tests/transcript_sampler/{inputs => files}/expression.csv (100%) rename tests/transcript_sampler/{inputs => files}/new_test.gtf (100%) rename tests/transcript_sampler/{inputs => files}/test.gtf (100%) rename tests/transcript_sampler/{inputs => files}/test_dict_repr_trans.txt (100%) rename tests/transcript_sampler/{inputs => files}/test_gencode.vM31.annotation_intermediat_file.txt (100%) rename tests/transcript_sampler/{inputs => files}/test_gene_exprL (100%) rename tests/transcript_sampler/{inputs => files}/test_gene_exprL_csv.csv (100%) rename tests/transcript_sampler/{inputs => files}/test_ref_output.tsv (100%) diff --git a/.gitignore b/.gitignore index ad4a1f1..25a5a19 100644 --- a/.gitignore +++ b/.gitignore @@ -174,3 +174,5 @@ poetry.toml pyrightconfig.json # End of https://www.toptal.com/developers/gitignore/api/python + +.vscode diff --git a/tests/transcript_sampler/inputs/.gitkeep b/tests/cdna_generator/files/.gitkeep similarity index 100% rename from tests/transcript_sampler/inputs/.gitkeep rename to tests/cdna_generator/files/.gitkeep diff --git a/tests/cdna_generator/test_files/Example_GTF_Input.GTF b/tests/cdna_generator/files/Example_GTF_Input.GTF similarity index 100% rename from tests/cdna_generator/test_files/Example_GTF_Input.GTF rename to tests/cdna_generator/files/Example_GTF_Input.GTF diff --git a/tests/cdna_generator/test_files/cDNA.csv b/tests/cdna_generator/files/cDNA.csv similarity index 100% rename from tests/cdna_generator/test_files/cDNA.csv rename to tests/cdna_generator/files/cDNA.csv diff --git a/tests/cdna_generator/test_files/cDNA.fasta b/tests/cdna_generator/files/cDNA.fasta similarity index 100% rename from tests/cdna_generator/test_files/cDNA.fasta rename to tests/cdna_generator/files/cDNA.fasta diff --git a/tests/cdna_generator/test_files/copy_number_file.csv b/tests/cdna_generator/files/copy_number_file.csv similarity index 100% rename from tests/cdna_generator/test_files/copy_number_file.csv rename to tests/cdna_generator/files/copy_number_file.csv diff --git a/tests/cdna_generator/test_files/copy_number_input.csv b/tests/cdna_generator/files/copy_number_input.csv similarity index 100% rename from tests/cdna_generator/test_files/copy_number_input.csv rename to tests/cdna_generator/files/copy_number_input.csv diff --git a/tests/cdna_generator/test_files/transcript.fasta b/tests/cdna_generator/files/transcript.fasta similarity index 83% rename from tests/cdna_generator/test_files/transcript.fasta rename to tests/cdna_generator/files/transcript.fasta index bb37ee2..d1c83a1 100644 --- a/tests/cdna_generator/test_files/transcript.fasta +++ b/tests/cdna_generator/files/transcript.fasta @@ -1,8 +1,8 @@ ->1 +>Transcript_1 GAUAGCUAGAGGAUUCUCAGAGGAGAAGCUAGAGGAGCUAGAGGAGCUAGAGGAGCUAGAGGAGCUAGAGG ->2 +>Transcript_2 AGCUAGAGGAUAGCUAGAGGAUAGCUAGAGGAUAGCUAGAGGAGCUAGAGGAGCUAGAGGAGCUAGAGG ->3 +>Transcript_3 AGCUAGAGGAUAGCUAGAGGAUAGCUAGAGGAUAGCUAGAGGAUAGCUAGAGGAGCUAGAGG ->4 +>Transcript_4 AGCUAGAGGAUAGCUAGAGGAUAGCUAGAGGAUAGCUAGAGGAUAGCUAGAGGAGCUAGAGGAGCUAGAGG diff --git a/tests/cdna_generator/test_files/yeast_example.fa b/tests/cdna_generator/files/yeast_example.fa similarity index 100% rename from tests/cdna_generator/test_files/yeast_example.fa rename to tests/cdna_generator/files/yeast_example.fa diff --git a/tests/fragment_selector/test_files/test.csv b/tests/fragment_selector/files/test.csv similarity index 100% rename from tests/fragment_selector/test_files/test.csv rename to tests/fragment_selector/files/test.csv diff --git a/tests/fragment_selector/test_files/test.fasta b/tests/fragment_selector/files/test.fasta similarity index 100% rename from tests/fragment_selector/test_files/test.fasta rename to tests/fragment_selector/files/test.fasta diff --git a/tests/fragment_selector/test_files/test_tab.csv b/tests/fragment_selector/files/test_tab.csv similarity index 100% rename from tests/fragment_selector/test_files/test_tab.csv rename to tests/fragment_selector/files/test_tab.csv diff --git a/tests/priming_site_predictor/test_files/RIBlast_output_example.txt b/tests/priming_site_predictor/files/RIBlast_output_example.txt similarity index 100% rename from tests/priming_site_predictor/test_files/RIBlast_output_example.txt rename to tests/priming_site_predictor/files/RIBlast_output_example.txt diff --git a/tests/priming_site_predictor/test_files/output_transcripts_df.gtf b/tests/priming_site_predictor/files/output_transcripts_df.gtf similarity index 100% rename from tests/priming_site_predictor/test_files/output_transcripts_df.gtf rename to tests/priming_site_predictor/files/output_transcripts_df.gtf diff --git a/tests/priming_site_predictor/test_files/primer1.fasta b/tests/priming_site_predictor/files/primer1.fasta similarity index 100% rename from tests/priming_site_predictor/test_files/primer1.fasta rename to tests/priming_site_predictor/files/primer1.fasta diff --git a/tests/priming_site_predictor/test_files/test_fasta.fasta b/tests/priming_site_predictor/files/test_fasta.fasta similarity index 100% rename from tests/priming_site_predictor/test_files/test_fasta.fasta rename to tests/priming_site_predictor/files/test_fasta.fasta diff --git a/tests/priming_site_predictor/test_files/yeast_test_files/dbRNA_test.fa b/tests/priming_site_predictor/files/yeast_test_files/dbRNA_test.fa similarity index 100% rename from tests/priming_site_predictor/test_files/yeast_test_files/dbRNA_test.fa rename to tests/priming_site_predictor/files/yeast_test_files/dbRNA_test.fa diff --git a/tests/priming_site_predictor/test_files/yeast_test_files/queryRNA_test.fa b/tests/priming_site_predictor/files/yeast_test_files/queryRNA_test.fa similarity index 100% rename from tests/priming_site_predictor/test_files/yeast_test_files/queryRNA_test.fa rename to tests/priming_site_predictor/files/yeast_test_files/queryRNA_test.fa diff --git a/tests/read_sequencer/fasta_testfile/50_seqs_50_1000_bp.fasta b/tests/read_sequencer/files/50_seqs_50_1000_bp.fasta similarity index 100% rename from tests/read_sequencer/fasta_testfile/50_seqs_50_1000_bp.fasta rename to tests/read_sequencer/files/50_seqs_50_1000_bp.fasta diff --git a/tests/sequence_extractor/test_files/post_bedtools_test.fa b/tests/sequence_extractor/files/post_bedtools_test.fa similarity index 100% rename from tests/sequence_extractor/test_files/post_bedtools_test.fa rename to tests/sequence_extractor/files/post_bedtools_test.fa diff --git a/tests/sequence_extractor/test_files/test.bed b/tests/sequence_extractor/files/test.bed similarity index 100% rename from tests/sequence_extractor/test_files/test.bed rename to tests/sequence_extractor/files/test.bed diff --git a/tests/sequence_extractor/test_files/test.gtf b/tests/sequence_extractor/files/test.gtf similarity index 100% rename from tests/sequence_extractor/test_files/test.gtf rename to tests/sequence_extractor/files/test.gtf diff --git a/tests/sequence_extractor/test_files/test_1.fa b/tests/sequence_extractor/files/test_1.fa similarity index 100% rename from tests/sequence_extractor/test_files/test_1.fa rename to tests/sequence_extractor/files/test_1.fa diff --git a/tests/sequence_extractor/test_files/test_2.fa b/tests/sequence_extractor/files/test_2.fa similarity index 100% rename from tests/sequence_extractor/test_files/test_2.fa rename to tests/sequence_extractor/files/test_2.fa diff --git a/tests/structure_generator/test_files/Annotation1.gtf b/tests/structure_generator/files/Annotation1.gtf similarity index 100% rename from tests/structure_generator/test_files/Annotation1.gtf rename to tests/structure_generator/files/Annotation1.gtf diff --git a/tests/structure_generator/test_files/Annotations2.gtf b/tests/structure_generator/files/Annotations2.gtf similarity index 100% rename from tests/structure_generator/test_files/Annotations2.gtf rename to tests/structure_generator/files/Annotations2.gtf diff --git a/tests/structure_generator/test_files/Transcript1.csv b/tests/structure_generator/files/Transcript1.csv similarity index 100% rename from tests/structure_generator/test_files/Transcript1.csv rename to tests/structure_generator/files/Transcript1.csv diff --git a/tests/structure_generator/test_files/Transcript2.tsv b/tests/structure_generator/files/Transcript2.tsv similarity index 100% rename from tests/structure_generator/test_files/Transcript2.tsv rename to tests/structure_generator/files/Transcript2.tsv diff --git a/tests/transcript_sampler/inputs/expression.csv b/tests/transcript_sampler/files/expression.csv similarity index 100% rename from tests/transcript_sampler/inputs/expression.csv rename to tests/transcript_sampler/files/expression.csv diff --git a/tests/transcript_sampler/inputs/new_test.gtf b/tests/transcript_sampler/files/new_test.gtf similarity index 100% rename from tests/transcript_sampler/inputs/new_test.gtf rename to tests/transcript_sampler/files/new_test.gtf diff --git a/tests/transcript_sampler/inputs/test.gtf b/tests/transcript_sampler/files/test.gtf similarity index 100% rename from tests/transcript_sampler/inputs/test.gtf rename to tests/transcript_sampler/files/test.gtf diff --git a/tests/transcript_sampler/inputs/test_dict_repr_trans.txt b/tests/transcript_sampler/files/test_dict_repr_trans.txt similarity index 100% rename from tests/transcript_sampler/inputs/test_dict_repr_trans.txt rename to tests/transcript_sampler/files/test_dict_repr_trans.txt diff --git a/tests/transcript_sampler/inputs/test_gencode.vM31.annotation_intermediat_file.txt b/tests/transcript_sampler/files/test_gencode.vM31.annotation_intermediat_file.txt similarity index 100% rename from tests/transcript_sampler/inputs/test_gencode.vM31.annotation_intermediat_file.txt rename to tests/transcript_sampler/files/test_gencode.vM31.annotation_intermediat_file.txt diff --git a/tests/transcript_sampler/inputs/test_gene_exprL b/tests/transcript_sampler/files/test_gene_exprL similarity index 100% rename from tests/transcript_sampler/inputs/test_gene_exprL rename to tests/transcript_sampler/files/test_gene_exprL diff --git a/tests/transcript_sampler/inputs/test_gene_exprL_csv.csv b/tests/transcript_sampler/files/test_gene_exprL_csv.csv similarity index 100% rename from tests/transcript_sampler/inputs/test_gene_exprL_csv.csv rename to tests/transcript_sampler/files/test_gene_exprL_csv.csv diff --git a/tests/transcript_sampler/inputs/test_ref_output.tsv b/tests/transcript_sampler/files/test_ref_output.tsv similarity index 100% rename from tests/transcript_sampler/inputs/test_ref_output.tsv rename to tests/transcript_sampler/files/test_ref_output.tsv