Esempio n. 1
0
#!/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))
Esempio n. 2
0
#!/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))
Esempio n. 3
0
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
Esempio n. 4
0
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