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foldClusters.py
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foldClusters.py
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import sys, subprocess, argparse, os
import numpy as np
import externalpaths
from plotClusters import RPCluster
sys.path.append(externalpaths.structureanalysistools())
from ArcPlot import ArcPlot
from pairmap_analysis import PairMap
import RNAStructureObjects as RNAtools
import foldPK
def writeFiles(clusters, outprefix, nog=False, nou=False):
seqfilename = '{0}.fa'.format(outprefix)
with open(seqfilename, 'w') as seqfile:
seqfile.write('>sequence\n')
for n in clusters.profiles[0].sequence:
seqfile.write(n)
dmsfilenames = []
for i in range(len(clusters.profiles)):
n = '{0}-{1}.dms'.format(outprefix, i)
dmsfilenames.append(n)
prof = clusters.profiles[i].normprofile
nts = clusters.profiles[i].nts
seq = clusters.profiles[i].sequence
with open(n, 'w') as dmsfile:
for j in range(len(prof)):
if np.isnan(prof[j]) or (nog and seq[j]=='G') or (nou and seq[j]=='U'):
dmsfile.write('{} -999\n'.format(nts[j]))
else:
dmsfile.write('{} {:.4f}\n'.format(nts[j], prof[j]))
return seqfilename, dmsfilenames
def parseArgs():
prs = argparse.ArgumentParser(description='Perform RNAstructure modeling and plot results for all models from a BM')
prs.add_argument('inputReactivity',type=str, help="Path of clustering reactivity file (-reactivities.txt)")
prs.add_argument('output', type=str, help='Prefix for writing output files')
prs.add_argument('--bp', type=str, help="Prefix for bp files. I.e. if your pairmap files are test-[]-pairmap.bp, you should pass '--bp test'")
prs.add_argument('--prob', action='store_true', help='compute pairing probability (partition)')
prs.add_argument('--pk', action='store_true', help='fold using ShapeKnots (default is to use Fold)')
prs.add_argument('--nog', action='store_true', help='mask Gs (set to no-data)')
prs.add_argument('--nou', action='store_true', help='mask Us (set to no-data)')
return prs.parse_args()
if __name__=='__main__':
args = parseArgs()
foldpath = externalpaths.rnastructure()+'/Fold'
skpath = externalpaths.rnastructure()+'/ShapeKnots'
pfunpath = externalpaths.rnastructure()+'/partition'
pplotpath = externalpaths.rnastructure()+'/ProbabilityPlot'
if not args.pk and not os.path.isfile(foldpath):
exit('Path to RNAstructure:fold is invalid! Check directory path in externalpaths!')
elif args.pk and not os.path.isfile(skpath):
exit('Path to RNAstructure:ShapeKnots is invalid! Check directory path in externalpaths!')
elif args.prob:
if not os.path.isfile(pfunpath):
exit('Path to RNAstructure:partition is invalid! Check directory path in externalpaths!')
elif not os.path.isfile(pplotpath):
exit('Path to RNAstructure:ProbabilityPlot is invalid! Check directory path in externalpaths!')
clusters = RPCluster(args.inputReactivity)
seqfile, dmsfiles = writeFiles(clusters, args.output, nog=args.nog, nou=args.nou)
for i,dfile in enumerate(dmsfiles):
if args.prob:
command = [pfunpath, seqfile, dfile[:-4]+'.pfs', '--dmsnt', dfile]
if args.bp:
command.extend(('-x', args.bp+'-{}-pairmap.bp'.format(i)))
print(command)
subprocess.call(command)
command = [pplotpath, '-t', dfile[:-4]+'.pfs', dfile[:-4]+'.dp']
print(command)
subprocess.call(command)
elif not args.pk:
command = [foldpath, seqfile, dfile[:-4]+'.ct', '--dmsnt', dfile]
if args.bp:
command.extend(('-x', args.bp+'-{}-pairmap.bp'.format(i)))
print(command)
subprocess.call(command)
else:
if args.bp:
foldPK.iterativeShapeKnots(skpath, seqfile, dfile[:-4], dmsfile=dfile,
bpfile=args.bp+'-{}-pairmap.bp'.format(i))
else:
foldPK.iterativeShapeKnots(skpath, seqfile, dfile[:-4], dmsfile=dfile)
aplot = ArcPlot(title = '{} P={:.3f}'.format(args.output, clusters.population[i]), fasta=seqfile)
if args.prob:
aplot.addPairProb( RNAtools.DotPlot(dfile[:-4]+'.dp') )
elif args.pk:
aplot.addCT( RNAtools.CT(dfile[:-4]+'.f.ct') )
else:
aplot.addCT( RNAtools.CT(dfile[:-4]+'.ct') )
aplot.readProfile(dfile, dms=True)
if args.bp:
aplot.addPairMap( PairMap(args.bp+'-{}-pairmap.txt'.format(i)), panel=-1)
aplot.writePlot( dfile[:-4]+'.pdf')