def run(self):
# Use newer local version of RNAfold
call('RNALfold -T '+str(foldTemp)+' -d2 --noLP -L '+str(hairpinLength)+' < data/tmp/'+self.inPath+' > data/tmp/'+self.inPath+'.folds', shell=True)
# Use older version of RNAfold
# call('progs/ViennaRNA-1.8.5/Progs/RNALfold -T '+str(foldTemp)+' -d2 -noLP -L '+str(hairpinLength)+' < data/tmp/'+self.inPath+' > data/tmp/'+self.inPath+'.folds', shell=True)
FoldOps.filter_hairpins('data/tmp/'+self.inPath+'.folds', 'data/tmp/'+self.inPath+'.hairpins', minMFE, basePairs)
FileConversion.RNAL_to_fasta('data/tmp/'+self.inPath+'.hairpins', 'data/tmp/folds_from_'+self.inPath)
sl = SequenceList()
sl.load_fasta('data/tmp/folds_from_'+self.inPath)
# sl.remove_all_redundant()
sl.export_fasta('data/tmp/'+self.inPath+'nrhairpins')
def run(self):
print "Finding all folds in " + self.inPath + " with RNALfold."
call(
'progs/ViennaRNA-1.8.5/Progs/RNALfold -d2 -noLP -L 120 < data/tmp/'
+ self.inPath + ' > data/tmp/' + self.inPath + '.folds',
shell=True)
print "Filtering folds in " + self.inPath + " down to hairpins."
FoldOps.filter_hairpins('data/tmp/' + self.inPath + '.folds',
'data/tmp/' + self.inPath + '.hairpins')
FileConversion.RNAL_to_fasta('data/tmp/' + self.inPath + '.hairpins',
'data/tmp/folds_from_' + self.inPath)
print "Removing redundant hairpins from " + self.inPath + "."
sl = SequenceList()
sl.load_fasta('data/tmp/folds_from_' + self.inPath)
sl.remove_all_redundant()
sl.export_fasta('data/tmp/' + self.inPath + 'nrhairpins')
import classes.FastaOperations as fo
from classes.SequenceList import *
# fo.split_fasta('data/folds_from_AHGY01.fa', 10)
for i in range(10):
sl = SequenceList()
sl.load_fasta('data/folds_from_AHGY01.fa.'+str(i))
sl.remove_redundant()
sl.export_fasta('data/AHGY01.fa.nr.hairpins'+'.'+str(i))
print str((i+1)*10)+'% complete removing redundant hairpins'
fo.merge_fasta('data/AHGY01.fa.nr.hairpins', 10)
