def main(inputfile, outputfile, gfffile, gffmin, gffmax, takeStop, upstream,
downstream, verbose):
takeStart = True
if takeStop:
takeStart = False
sites = ParclipSiteContainer()
sites.loadFromFile(inputfile)
anno = gff.GFF(gfffile)
anno.filterSize(gffmin, gffmax)
anno.getChromosomePositions()
if anno.size() < 10:
print('Warning: Low number of annotation enries! ' + str(anno.size()))
fsites = ParclipSiteContainer()
percent_old = 0
percent_new = 0
for i in range(sites.size()):
if anno.isAround(sites.chrs[i], sites.pos[i], sites.strand[i],
takeStart, upstream, downstream)[1]:
fsites.addSite(sites.chrs[i], sites.pos[i], sites.m[i], sites.r[i],
sites.result[i], sites.strand[i], sites.occ[i])
percent_new = round(i / sites.size() * 100)
if percent_new > percent_old:
if verbose:
functions.showProgress(i, anno.size(), 'selecting sites')
percent_old = percent_new
fsites.save2File(outputfile)
def main(parclipA, parclipB, outfile, width, verbose):
quantiles = [0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0]
total = (len(quantiles)-1)*(len(quantiles)-1)
total_count = 0
if verbose:
functions.showProgress(total_count, total, 'Calculating Jaccard-Index')
fc = open(outfile, 'w')
for q1 in range(len(quantiles)-1):
a = ParclipSiteContainer()
a.loadFromFile(parclipA)
aq = getEntries(a,quantiles[q1], quantiles[q1+1])
#removeEntries(a,quantiles[q1], quantiles[q1+1])
for q2 in range(len(quantiles)-1):
b = ParclipSiteContainer()
b.loadFromFile(parclipB)
#removeEntries(b,quantiles[q2], quantiles[q2+1])
bq = getEntries(b,quantiles[q2], quantiles[q2+1])
intersect = 0
for j in range(bq.size()):
if aq.exactSearch(bq.chrs[j], bq.pos[j], bq.strand[j], width=width)[1]:
intersect += 1
jaccard = intersect/(aq.size()+bq.size()-intersect)
#print('q1: '+str(quantiles[q1])+' q2: '+str(quantiles[q2])+' '+str(round(jaccard,4)))
fc.write(str(round(jaccard,4))+'\t')
total_count += 1
if verbose:
functions.showProgress(total_count, total, 'Calculating Jaccard-Index')
fc.write('\n')
print('')
fc.close()
def main(inputfile, outputfile):
if os.path.isfile(inputfile) == False:
print('Inputfile: '+inputfile+' does not exist')
sys.exit(-1)
sites = ParclipSiteContainer()
sites.loadFromFile(inputfile)
for i in range(sites.size()):
sites.occ[i] = sites.m[i]/sites.r[i]
sites.save2File(outputfile)
def main(parclipA, parclipB, start, stop, width, anno=None, annowidth=100,
logRatio=False, verbose=False):
tmpA = ParclipSiteContainer()
dataB = ParclipSiteContainer()
tmpA.loadFromFile(parclipA)
tmpA.sort(key='occ')
dataB.loadFromFile(parclipB)
if start < 0 or stop < start or stop >= tmpA.size():
print('Bullshit start and stop indices. Come on! Concentrate!')
sys.exit()
dataA = parclipsites.ParclipSites('')
total = stop - start
count = 0
i = start
while count < total and i < (tmpA.size()-1):
if verbose:
functions.showProgress(count,total-1,'Selecting PAR-CLIP sites')
if anno == None:
dataA.addSite(tmpA.chrs[i], tmpA.pos[i], tmpA.m[i], tmpA.r[i],
tmpA.result[i], tmpA.strand[i], tmpA.occ[i])
count +=1
else:
if anno.isInside(tmpA.chrs[i], tmpA.pos[i], tmpA.strand[i],
annowidth, annowidth)[1]:
dataA.addSite(tmpA.chrs[i], tmpA.pos[i], tmpA.m[i], tmpA.r[i],
tmpA.result[i], tmpA.strand[i], tmpA.occ[i])
count +=1
i += 1
coloc = 1
count_coloc = 1
if verbose:
print('\n')
for i in range(dataA.size()):
values = dataB.getValues(dataA.chrs[i], dataA.pos[i], dataA.strand[i], True, width, width)
if values != None:
count_coloc += 1
coloc += max(values)
if verbose:
functions.showProgress(i, (dataA.size()-1), 'Collecting colocolization data')
coloc = coloc / count_coloc
if verbose:
print('')
if logRatio:
return math.log( coloc/functions.getQuantile(dataB.occ,0.5) ,2)
else:
return coloc
def main(parclipfile, outputfile, gfffile, downstream, upstream, gene, sense, minSize,
maxSize, verbose, vstring=''):
anno = gff.GFF(gfffile)
anno.filterSize(minSize, maxSize)
pc = ParclipSiteContainer()
pc.loadFromFile(parclipfile)
with open(outputfile, 'w') as fc_out:
for g in range(anno.size()):
if verbose:
functions.showProgress(g, (anno.size() - 1), vstring)
if anno.strand[g] == '+':
values_upstream = pc.getValues(anno.chr[g], anno.start[g], anno.strand[g],
sense, upstream, gene)
values_dostream = pc.getValues(anno.chr[g], anno.stop[g], anno.strand[g],
sense, gene, downstream)
else:
values_upstream = pc.getValues(anno.chr[g], anno.stop[g], anno.strand[g],
sense, upstream, gene)
values_dostream = pc.getValues(anno.chr[g], anno.start[g], anno.strand[g],
sense, gene, downstream)
if values_upstream is not None and values_dostream is not None:
print(*chain(values_upstream, values_dostream), sep='\t', file=fc_out)
if verbose:
print()
from mockinbird.utils import ParclipSiteContainer
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='Takes PAR-CLIP sites and a genome and saves genomic sequences as fasta file around PAR-CLIP sites according to the given parameters.', epilog="contact: [email protected]")
parser.add_argument('sites', help='PAR-CLIP file *.table')
parser.add_argument('genome', help='path to genome')
parser.add_argument('fafile', help='output filename')
parser.add_argument('filterGFF', help='set path to GFF if sites should be removed that overlap with the GFF [default = '']', default='')
parser.add_argument('start', help='start index of PAR-CLIP sites [default=0]', type=int, default = 0)
parser.add_argument('stop', help='stop index of PAR-CLIP sites [default=1500]', type=int, default = 1500)
parser.add_argument('width', help='number of nt +/- the crosslink site [default=15]', type=int, default = 15)
parser.add_argument('additionalFilterWidth', help='number of nt that are added to the start/stop indices of the GFF annotations', type=int, default = 20)
parser.add_argument('key', help='set key that is used for PAR-CLIP site ordering [default = \'occ\'], options: [\'occ\', \'m\', \'r\', \'mr\', \'pvalue\']', default='occ')
parser.add_argument('-v','--verbose', dest='verbose', action="store_true", default=False, help='verbose output')
args = parser.parse_args()
yeast = genome.Genome(args.genome, False)
sites = ParclipSiteContainer()
sites.loadFromFile(args.sites)
if args.verbose:
print('#sites : '+str(sites.size()))
if args.filterGFF != '':
anno = gff.GFF(args.filterGFF)
sites = sites.removeSitesLocatedInGFF(anno, args.additionalFilterWidth)
print('#sites after removal: '+str(sites.size()))
sites.sort(args.key)
sites.save2Fasta(yeast, args.fafile, args.start, args.stop, args.width)