refactor: update folder structure

zavolanlab · Oct 27, 2023 · 8afcd64 · 8afcd64
1 parent efc1f23
commit 8afcd64
Show file tree

Hide file tree

Showing 36 changed files with 6 additions and 4 deletions.
diff --git 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 → tests/cdna_generator/files/.gitkeep b/tests/transcript_sampler/inputs/.gitkeep → tests/cdna_generator/files/.gitkeep
diff --git a/...enerator/test_files/Example_GTF_Input.GTF → ...dna_generator/files/Example_GTF_Input.GTF b/...enerator/test_files/Example_GTF_Input.GTF → ...dna_generator/files/Example_GTF_Input.GTF
diff --git a/tests/cdna_generator/test_files/cDNA.csv → tests/cdna_generator/files/cDNA.csv b/tests/cdna_generator/test_files/cDNA.csv → tests/cdna_generator/files/cDNA.csv
diff --git a/tests/cdna_generator/test_files/cDNA.fasta → tests/cdna_generator/files/cDNA.fasta b/tests/cdna_generator/test_files/cDNA.fasta → tests/cdna_generator/files/cDNA.fasta
diff --git a/...generator/test_files/copy_number_file.csv → ...cdna_generator/files/copy_number_file.csv b/...generator/test_files/copy_number_file.csv → ...cdna_generator/files/copy_number_file.csv
diff --git a/...enerator/test_files/copy_number_input.csv → ...dna_generator/files/copy_number_input.csv b/...enerator/test_files/copy_number_input.csv → ...dna_generator/files/copy_number_input.csv
diff --git a/...dna_generator/test_files/transcript.fasta → tests/cdna_generator/files/transcript.fasta b/...dna_generator/test_files/transcript.fasta → 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/...dna_generator/test_files/yeast_example.fa → tests/cdna_generator/files/yeast_example.fa b/...dna_generator/test_files/yeast_example.fa → tests/cdna_generator/files/yeast_example.fa
diff --git a/tests/fragment_selector/test_files/test.csv → tests/fragment_selector/files/test.csv b/tests/fragment_selector/test_files/test.csv → tests/fragment_selector/files/test.csv
diff --git a/...s/fragment_selector/test_files/test.fasta → tests/fragment_selector/files/test.fasta b/...s/fragment_selector/test_files/test.fasta → tests/fragment_selector/files/test.fasta
diff --git a/...fragment_selector/test_files/test_tab.csv → tests/fragment_selector/files/test_tab.csv b/...fragment_selector/test_files/test_tab.csv → tests/fragment_selector/files/test_tab.csv
diff --git a/...tor/test_files/RIBlast_output_example.txt → ...redictor/files/RIBlast_output_example.txt b/...tor/test_files/RIBlast_output_example.txt → ...redictor/files/RIBlast_output_example.txt
diff --git a/...ctor/test_files/output_transcripts_df.gtf → ...predictor/files/output_transcripts_df.gtf b/...ctor/test_files/output_transcripts_df.gtf → ...predictor/files/output_transcripts_df.gtf
diff --git a/...g_site_predictor/test_files/primer1.fasta → ...riming_site_predictor/files/primer1.fasta b/...g_site_predictor/test_files/primer1.fasta → ...riming_site_predictor/files/primer1.fasta
diff --git a/...ite_predictor/test_files/test_fasta.fasta → ...ing_site_predictor/files/test_fasta.fasta b/...ite_predictor/test_files/test_fasta.fasta → ...ing_site_predictor/files/test_fasta.fasta
diff --git a/...test_files/yeast_test_files/dbRNA_test.fa → ...ctor/files/yeast_test_files/dbRNA_test.fa b/...test_files/yeast_test_files/dbRNA_test.fa → ...ctor/files/yeast_test_files/dbRNA_test.fa
diff --git a/...t_files/yeast_test_files/queryRNA_test.fa → ...r/files/yeast_test_files/queryRNA_test.fa b/...t_files/yeast_test_files/queryRNA_test.fa → ...r/files/yeast_test_files/queryRNA_test.fa
diff --git a/...r/fasta_testfile/50_seqs_50_1000_bp.fasta → ..._sequencer/files/50_seqs_50_1000_bp.fasta b/...r/fasta_testfile/50_seqs_50_1000_bp.fasta → ..._sequencer/files/50_seqs_50_1000_bp.fasta
diff --git a/...xtractor/test_files/post_bedtools_test.fa → ...nce_extractor/files/post_bedtools_test.fa b/...xtractor/test_files/post_bedtools_test.fa → ...nce_extractor/files/post_bedtools_test.fa
diff --git a/tests/sequence_extractor/test_files/test.bed → tests/sequence_extractor/files/test.bed b/tests/sequence_extractor/test_files/test.bed → tests/sequence_extractor/files/test.bed
diff --git a/tests/sequence_extractor/test_files/test.gtf → tests/sequence_extractor/files/test.gtf b/tests/sequence_extractor/test_files/test.gtf → tests/sequence_extractor/files/test.gtf
diff --git a/...s/sequence_extractor/test_files/test_1.fa → tests/sequence_extractor/files/test_1.fa b/...s/sequence_extractor/test_files/test_1.fa → tests/sequence_extractor/files/test_1.fa
diff --git a/...s/sequence_extractor/test_files/test_2.fa → tests/sequence_extractor/files/test_2.fa b/...s/sequence_extractor/test_files/test_2.fa → tests/sequence_extractor/files/test_2.fa
diff --git a/...ture_generator/test_files/Annotation1.gtf → ...structure_generator/files/Annotation1.gtf b/...ture_generator/test_files/Annotation1.gtf → ...structure_generator/files/Annotation1.gtf
diff --git a/...ure_generator/test_files/Annotations2.gtf → ...tructure_generator/files/Annotations2.gtf b/...ure_generator/test_files/Annotations2.gtf → ...tructure_generator/files/Annotations2.gtf
diff --git a/...ture_generator/test_files/Transcript1.csv → ...structure_generator/files/Transcript1.csv b/...ture_generator/test_files/Transcript1.csv → ...structure_generator/files/Transcript1.csv
diff --git a/...ture_generator/test_files/Transcript2.tsv → ...structure_generator/files/Transcript2.tsv b/...ture_generator/test_files/Transcript2.tsv → ...structure_generator/files/Transcript2.tsv
diff --git a/.../transcript_sampler/inputs/expression.csv → ...s/transcript_sampler/files/expression.csv b/.../transcript_sampler/inputs/expression.csv → ...s/transcript_sampler/files/expression.csv
diff --git a/tests/transcript_sampler/inputs/new_test.gtf → tests/transcript_sampler/files/new_test.gtf b/tests/transcript_sampler/inputs/new_test.gtf → tests/transcript_sampler/files/new_test.gtf
diff --git a/tests/transcript_sampler/inputs/test.gtf → tests/transcript_sampler/files/test.gtf b/tests/transcript_sampler/inputs/test.gtf → tests/transcript_sampler/files/test.gtf
diff --git a/...t_sampler/inputs/test_dict_repr_trans.txt → ...pt_sampler/files/test_dict_repr_trans.txt b/...t_sampler/inputs/test_dict_repr_trans.txt → ...pt_sampler/files/test_dict_repr_trans.txt
diff --git a/...code.vM31.annotation_intermediat_file.txt → ...code.vM31.annotation_intermediat_file.txt b/...code.vM31.annotation_intermediat_file.txt → ...code.vM31.annotation_intermediat_file.txt
diff --git a/...transcript_sampler/inputs/test_gene_exprL → .../transcript_sampler/files/test_gene_exprL b/...transcript_sampler/inputs/test_gene_exprL → .../transcript_sampler/files/test_gene_exprL
diff --git a/...pt_sampler/inputs/test_gene_exprL_csv.csv → ...ipt_sampler/files/test_gene_exprL_csv.csv b/...pt_sampler/inputs/test_gene_exprL_csv.csv → ...ipt_sampler/files/test_gene_exprL_csv.csv
diff --git a/...script_sampler/inputs/test_ref_output.tsv → ...nscript_sampler/files/test_ref_output.tsv b/...script_sampler/inputs/test_ref_output.tsv → ...nscript_sampler/files/test_ref_output.tsv
Original file line number	Diff line number	Diff line change
Expand Up		@@ -174,3 +174,5 @@ poetry.toml
		pyrightconfig.json

		# End of https://www.toptal.com/developers/gitignore/api/python

		.vscode