Added a database configuration parameter to the blast wrapper. Renamed the files.

bin/module_blast_swissprot.py → bin/run_blastp.py

@@ -6,19 +6,15 @@ from os import system
 blastp_tool = config.load_config()['tools'].get('blastp', 'blastp')
 
 parser = argparse.ArgumentParser(description='Identify homologues in the swissprot database')
-parser.add_argument('--info', '-i', action='store_true')
 parser.add_argument('--fasta', '-f', required=True, help='A fasta file with aminoacid sequences')
+parser.add_argument('--database', '-d', required=True, help='Database to search in')
 parser.add_argument('--output', '-o', required=True, help='The result file')
 parser.add_argument('--evalue', '-e', default='0.0001', help='Evalue cutoff')
 parser.add_argument('--alignment', '-a', action='store_true', help='Include alignments in btop format')
-
 args = parser.parse_args()
-if args.info:
-    print("blast against swissprot\n")
-    exit(0)
 
 format = '7 qseqid sseqid pident qstart qend sstart send evalue bitscore'
 if args.alignment:
     format += ' btop'
 
-system(blastp_tool + " -db /vol/biodb/uniprot/uniprot_sprot.fasta -num_threads 7 -outfmt '" + format + "' -out " + args.output + " -query " + args.fasta)
+system(blastp_tool + " -db " + args.database + " -num_threads 7 -outfmt '" + format + "' -out " + args.output + " -query " + args.fasta)

modules/blast_vs_swissprot.yaml

@@ -8,8 +8,12 @@ name: 'blastp_swissprot'
 info: 'blastp analysis against swissprot'
 
 # The name of the script for the analysis step. Must take a --fasta parameter
-analysis_script: 'module_blast_swissprot.py'
+analysis_script: 'run_blastp.py'
 
 # The name of the result to json converter script. Must take one parameter, the
 # result file from the analysis_script
-converter_script: 'convert_blast_swissprot.py'
+converter_script: 'convert_blastp.py'
+
+parameters:
+    database: '/vol/biodb/uniprot/uniprot_sprot.fasta'
+    evalue: 1e-10