Mercurial > repos > bgruening > trna_prediction

comparison tRNAscan.py @ 2:358f58401cd6 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
author bgruening
date Wed, 26 Jul 2017 10:14:05 -0400
parents d34f31cbc9dd
children
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1:d788d1abe238 2:358f58401cd6
6 import sys 6 import sys
7 from Bio import SeqIO 7 from Bio import SeqIO
8 from Bio.SeqRecord import SeqRecord 8 from Bio.SeqRecord import SeqRecord
9 import subprocess 9 import subprocess
10 10
11
12 def main(args): 11 def main(args):
13 """ 12 """
14 Call from galaxy: 13 Call from galaxy:
15 tRNAscan.py $organism $mode $showPrimSecondOpt $disablePseudo $showCodons $tabular_output $inputfile $fasta_output 14 tRNAscan.py $organism $mode $showPrimSecondOpt $disablePseudo $showCodons $tabular_output $inputfile $fasta_output
16 15
17 tRNAscan-SE $organism $mode $showPrimSecondOpt $disablePseudo $showCodons -d -Q -y -q -b -o $tabular_output $inputfile; 16 tRNAscan-SE $organism $mode $showPrimSecondOpt $disablePseudo $showCodons -Q -y -q -b -o $tabular_output $inputfile;
18 """ 17 """
19 cmd = """tRNAscan-SE -Q -y -q -b %s""" % ' '.join( args[:-1] ) 18 cmd = """tRNAscan-SE -Q -y -q -b %s""" % ' '.join( args[:-1] )
20 child = subprocess.Popen(cmd.split(), 19 child = subprocess.Popen(cmd.split(),
21 stdout=subprocess.PIPE, stderr=subprocess.PIPE) 20 stdout=subprocess.PIPE, stderr=subprocess.PIPE)
22 stdout, stderr = child.communicate() 21 stdout, stderr = child.communicate()