#!/usr/bin/env python
"""
doBlast.py
Author: Tony Papenfuss
Date: Fri Oct 20 12:26:08 EST 2006
"""
import os, sys, glob
from useful import extractRootName
cmd = 'blast -p tblastn -d %s -i %s -o %s'
blastdb = '/database/opossum/assembly/blastdb/assembly'
filenames = glob.glob('seq/*')
for filename in filenames:
name = extractRootName(filename)
print name
oFilename = 'blast/%s.txt' % name
os.system(cmd % (blastdb, filename, oFilename))
#!/usr/bin/env python
"""
doBlast.py
Author: Tony Papenfuss
Date: Fri Oct 20 12:26:08 EST 2006
"""
import os, sys, glob
from useful import extractRootName
cmd = "blast -p tblastn -d %s -i %s -o %s"
blastdb = "/database/opossum/assembly/blastdb/assembly"
filenames = glob.glob("seq/*")
for filename in filenames:
name = extractRootName(filename)
print name
oFilename = "blast/%s.txt" % name
os.system(cmd % (blastdb, filename, oFilename))
ioDir = sys.argv[1]
os.chdir(ioDir)
oFile = open('checkResults.txt', 'w')
sys.stdout = oFile
hmmerModel = {
'round1': '../../HMMs/Defensin_beta.hmm',
'round2': '../../HMMs/Defensin_beta_new.hmm'}[ioDir]
writer = fasta.MfaWriter('peptides.fa')
annotFile = open('annot.txt', 'w')
annotFilenames = glob.glob('gsAnnotations/*.txt')
for annotFilename in annotFilenames:
name = extractRootName(annotFilename)
print '>>>', name + '\n'
annotFilename = 'gsAnnotations/%s.txt' % name
annotation = open(annotFilename).readlines()
predictions = parseGenscan(annotation)
pepFilename = 'gsPeptides/%s.fa' % name
peptides = fasta.load_mfa(pepFilename)
peptides = [(h.split()[0],s) for h,s in peptides]
peptides = dict(peptides)
print 'Lengths'
for h in peptides:
print h, len(peptides[h])
print
ioDir = sys.argv[1]
os.chdir(ioDir)
oFile = open('checkResults.txt', 'w')
sys.stdout = oFile
hmmerModel = {
'round1': '../../HMMs/Defensin_beta.hmm',
'round2': '../../HMMs/Defensin_beta_new.hmm'
}[ioDir]
writer = fasta.MfaWriter('peptides.fa')
annotFile = open('annot.txt', 'w')
annotFilenames = glob.glob('gsAnnotations/*.txt')
for annotFilename in annotFilenames:
name = extractRootName(annotFilename)
print '>>>', name + '\n'
annotFilename = 'gsAnnotations/%s.txt' % name
annotation = open(annotFilename).readlines()
predictions = parseGenscan(annotation)
pepFilename = 'gsPeptides/%s.fa' % name
peptides = fasta.load_mfa(pepFilename)
peptides = [(h.split()[0], s) for h, s in peptides]
peptides = dict(peptides)
print 'Lengths'
for h in peptides:
print h, len(peptides[h])
print