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)