def go(self):
"""Execution function: runs TAMO.MD.Meme.Meme and catches the output in self.output for access from MDAP."""
import time
# write a temp fasta file of coregulated seqs to use as input to Meme(file=TempFasta)
ctimeStr = time.ctime().replace(' ','_')
fileName = 'tempFastaOfCoRegSeqs.MDAP.%s.fas' %(ctimeStr)
tFasta = open(fileName, 'w')
tFastaTxt = Fasta.text(self.coRegSeqs[0])
tFasta.write(tFastaTxt)
# Call TAMO to do its thing:
self.output = Meme(file=fileName, width='', extra_args=self.extra_args, bfile=self.bfile)
# delete temp file
os.remove(fileName)
def go(self):
"""Execution function: coordinates options used and background GC calculation, then runs
TAMO.MD.AlignAce.MetaAce and catches the output in self.output for access from MDAP.
Output is TAMO.AligAce result object."""
import time
# Calc GC background of genomic sequences representing the
# entire data set if requested.
if self.mdapOptions['background'] == 1:
self.dataStats = seqStats.calcStats(self.mdapArgs[0])
self.gcback = self.dataStats['percentGC']
# write a temp fasta file of coregulated seqs to use as input to Meme(file=TempFasta)
ctimeStr = time.ctime().replace(' ','_')
fileName = 'tempFastaOfCoRegSeqs.MDAP.%s.fas' %(ctimeStr)
tFasta = open(fileName, 'w')
tFastaTxt = Fasta.text(self.coRegSeqs[0])
tFasta.write(tFastaTxt)
# call TAMO to do its thing
self.output = MetaAce(fileName, self.width, self.iterations, self.gcback)
pass
from TAMO.seq import Fasta
from gusPyCode.defs.bioDefs import geneList2FastaDict
from gusPyCode.defs.mosqData import promoterSeqPaths
geneList = map(lambda l: l.strip(), \
open('/Users/biggus/Documents/James/Collaborations/Campbell/data/CCupAt4Days.gte2x.genes.txt', 'rU'))
sourceFasta = promoterSeqPaths.Aa_2000bpUp_hardMasked_shuf1
oFile = '/Users/biggus/Documents/James/Collaborations/Campbell/data/CCupAt4Days.gte2x.masked.shuffled.1.fas'
newFasta = geneList2FastaDict(geneList, sourceFasta, hardMasked=True)
newFasta = Fasta.text(newFasta)
oFile = open(oFile, 'w')
oFile.write(newFasta)
print 'Done'
