Commit 5bf47604 authored by Lukas Jelonek's avatar Lukas Jelonek
Browse files

Added --output option to analysis scripts

parent 43fe9e23
......@@ -8,6 +8,7 @@ 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('--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')
......@@ -20,4 +21,4 @@ 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 - -query " + args.fasta)
system(blastp_tool + " -db /vol/biodb/uniprot/uniprot_sprot.fasta -num_threads 7 -outfmt '" + format + "' -out " + args.output + " -query " + args.fasta)
......@@ -8,6 +8,7 @@ signalp_tool = config.load_config()['tools'].get('signalp', 'signalp')
parser = argparse.ArgumentParser(description='Find signal peptides in amino acid sequences')
parser.add_argument('--fasta', '-f', required=True, help='A fasta file with aminoacid sequences')
parser.add_argument('--organism', '-o', choices=['euk', 'gram+', 'gram-'], default='euk', help='The organism type')
parser.add_argument('--output', required=True, help='The output file')
args = parser.parse_args()
system(signalp_tool + " -t " + args.organism + " " + args.fasta)
system(signalp_tool + " -t " + args.organism + " " + args.fasta + " > " + args.output)
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