def loadPecan(iFileHandle, renamer=firstWord):
"""
Load pecan alignment data.
"""
aln = Alignment()
for h, s in FastaFile(iFileHandle):
try:
aln.add(renamer(h), s)
except Exception, e:
print e
#!/usr/bin/env python """ testTextIndex.py Author: Tony Papenfuss Date: Thu May 29 11:44:36 EST 2008 """ import os, sys from fasta import FastaFile filename = 'tumour_sample.fa' f = FastaFile(filename, indexed=True, clobber=True, method='pickle')
end = int(tokens[7])
strand = {'1': '+', '-1': '-'}[tokens[8]]
try:
for contig in contigData[chrom].find(start-500, end+500):
annotated.add(contig.value[0])
except:
pass
print 'Parse toxprot alignments'
iFilename = '../toxprot/tblastn_toxprot_v_genome.txt'
for b in BlastFile(iFilename):
chrom = b.subjectId.split(':')[0]
try:
for contig in contigData[chrom].find(b.sStart, b.sEnd):
annotated.add(contig.value[0])
except:
pass
print "Write out what's left over"
writer = FastaFile('unannotated_contigs.fa', 'w')
for chrom in contigData:
for contig in contigData[chrom].intervals:
if not contig.value[0] in annotated and len(contig.value[4])>60:
name,chrom,start,end,seq = contig.value
writer('%s %s:%i-%i' % (name,chrom,start,end), seq)
writer.close()
def saveFasta(self, oFileHandle, **kw):
writer = FastaFile(oFileHandle, 'w')
for name in self.order:
writer.write(name, self.seqDict[name])
writer.close()
Author: Tony Papenfuss
Date: Tue Mar 18 14:27:10 EST 2008
"""
import os, sys
def rule():
print '-' * 80
from fasta import FastaFile
f = FastaFile('HSP100.fa')
rule()
print 'readOne'
print f.readOne()
print f.readOne()
rule()
print 'readAll'
print f.readAll()
rule()
print 'Mapping'
f.asMapping()
print f
rule()
rule()
Author: Tony Papenfuss
Date: Tue Mar 18 14:27:10 EST 2008
"""
import os, sys
def rule():
print '-'*80
from fasta import FastaFile
f = FastaFile('HSP100.fa')
rule()
print 'readOne'
print f.readOne()
print f.readOne()
rule()
print 'readAll'
print f.readAll()
rule()
print 'Mapping'
f.asMapping()
print f
rule()
rule()
#!/usr/bin/env python """ testTextIndex.py Author: Tony Papenfuss Date: Thu May 29 11:44:36 EST 2008 """ import os, sys from fasta import FastaFile filename = 'tumour_sample.fa' f = FastaFile(filename, indexed=True, clobber=False, method='db') x = f[9000:9100]
def saveFasta(self, oFileHandle, **kw):
writer = FastaFile(oFileHandle, 'w')
for name in self.order:
writer.write(name, self.seqDict[name])
writer.close()
#!/usr/bin/env python """ testTextIndex.py Author: Tony Papenfuss Date: Thu May 29 11:44:36 EST 2008 """ import os, sys from fasta import FastaFile filename = '/Users/papenfuss/databases/devil/transcriptome/reads/combined.fa' f = FastaFile(filename, indexed=True, clobber=True, method='text')