update env, test files, readme

zavolanlab · Oct 27, 2023 · 47da31d · 47da31d
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diff --git a/environment.yml b/environment.yml
@@ -19,5 +19,7 @@ dependencies:
   - mypy
   - pylint
   - pytest
+  - bedtools
+  - riblast
   - pip:
     - '-e .'
diff --git a/scRNAsim_toolz/priming_site_predictor/README.md b/scRNAsim_toolz/priming_site_predictor/README.md
@@ -21,6 +21,12 @@ options:
 ```
 
 Example:
+
+RIblast usage:
+```
+RIblast db -i tests/priming_site_predictor/files/riblast_test_files/dbRNA_test.fa -o tests/priming_site_predictor/files/riblast_test_files/test_db
+RIblast ris -i tests/priming_site_predictor/files/riblast_test_files/queryRNA_test.fa -o tests/priming_site_predictor/files/RIBlast_output_example.txt -d tests/priming_site_predictor/files/riblast_test_files/test_db
+```
 ```
 priming-site-predictor --riblast-output tests/priming_site_predictor/files/RIBlast_output_example.txt --output-filename priming_sites.gtf
 ```

diff --git a/scRNAsim_toolz/sequence_extractor/README.md b/scRNAsim_toolz/sequence_extractor/README.md
@@ -23,8 +23,15 @@ options:
 ```
 
 Example:
+```
+sequence-extractor --mode pre_bedtools --input-gtf-file tests/sequence_extractor/files/test.gtf --output-bed-file tests/sequence_extractor/files/output.bed
+gunzip -k tests/sequence_extractor/files/human.chr1.fa.gz 
+bedtools getfasta -fi tests/sequence_extractor/files/human.chr1.fa -bed tests/sequence_extractor/files/output.bed -name -s -fo tests/sequence_extractor/files/output.fasta
+sequence-extractor --mode post_bedtools --input-fasta-file tests/sequence_extractor/files/output.fasta --polyA-length 250 --output-file-name polyA_output.fa
+
+sequence-extractor --mode post_bedtools --input-fasta-file tests/sequence_extractor/files/post_bedtools_test.fa --polyA-length 250 --output-file-name polyA_output.fa
+```
 
-`sequence-extractor --mode post_bedtools --input-fasta-file tests/sequence_extractor/files/post_bedtools_test.fa --polyA-length 250 --output-file-name polyA_output.fa`
 ## Overview 
 
 Given a gtf specification of transcript exon/intron structures and the genome sequence, construct the nucleotide sequence of the transcripts and add poly(A) tails.

diff --git a/...ctor/files/yeast_test_files/dbRNA_test.fa → ...or/files/riblast_test_files/dbRNA_test.fa b/...ctor/files/yeast_test_files/dbRNA_test.fa → ...or/files/riblast_test_files/dbRNA_test.fa
diff --git a/...r/files/yeast_test_files/queryRNA_test.fa → ...files/riblast_test_files/queryRNA_test.fa b/...r/files/yeast_test_files/queryRNA_test.fa → ...files/riblast_test_files/queryRNA_test.fa
diff --git a/tests/sequence_extractor/files/human.chr1.fa.gz b/tests/sequence_extractor/files/human.chr1.fa.gz
diff --git a/tests/sequence_extractor/files/test.gtf b/tests/sequence_extractor/files/test.gtf
@@ -1,4 +1,3 @@
-seqname	source	feature	start	end	score	strand	frame	free_text
 1	havana	exon	1980	2000	.	-	.	gene_id "GENE2"; transcript_id "TRANSCRIPT2_0"; exon_number "1"; exon_id "ENSE00001890219"; transcript_support_level "1";
 1	havana	exon	1900	1950	.	-	.	gene_id "GENE2"; transcript_id "TRANSCRIPT2_0"; exon_number "2"; exon_id "ENSE00003507205"; transcript_support_level "1";
 1	havana	exon	1800	1850	.	-	.	gene_id "GENE2"; transcript_id "TRANSCRIPT2_0"; exon_number "3"; exon_id "ENSE00003477500"; transcript_support_level "1";
-Original file line number
+Diff line change
@@ Expand Up / @@ -19,5 +19,7 @@ dependencies: @@
       - mypy
       - pylint
       - pytest
+      - bedtools
+      - riblast
       - pip:
         - '-e .'