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Diffchecker Desktop Diffchecker चलाने का सबसे सुरक्षित तरीका। Diffchecker Desktop ऐप पाएं: आपके diffs कभी आपके कंप्यूटर से बाहर नहीं जाते!Desktop पाएं

leafcutter_cluster.py VS leafcutter_cluster_regtools.py

बनाया गया 6 वर्ष पहलेDiff कभी समाप्त नहीं होता

36 हटाए गए

लाइनें
कुल
हटाया गया

अक्षर
कुल
हटाया गया

इस सुविधा का उपयोग जारी रखने के लिए, अपग्रेड करें Diffchecker Pro मूल्य देखें

489 लाइनें

94 जोड़े गए

लाइनें
कुल
जोड़ा गया

अक्षर
कुल
जोड़ा गया

इस सुविधा का उपयोग जारी रखने के लिए, अपग्रेड करें Diffchecker Pro मूल्य देखें

534 लाइनें

#!/usr/bin/env python

# https://github.com/griffithlab/regtools

# /home/yangili1/tools/regtools/build/regtools junctions extract -a 8 -i 50 -I 500000 bamfile.bam -o outfile.junc

# Using regtools speeds up the junction extraction step by an order of magnitude or more

import sys

import tempfile

import os

import gzip

import shutil

def main(options,libl):

pool_junc_reads(libl, options)

if options.cluster == None:

refine_clusters(options)

pool_junc_reads(libl, options)

refine_clusters(options)

sort_junctions(libl, options)

merge_junctions(options)

get_numers(options)

def pool_junc_reads(flist, options):

outPrefix = options.outprefix

rundir = options.rundir

maxIntronLen = int(options.maxintronlen)

checkchrom = options.checkchrom

useStrand = options.strand

outFile = "%s/%s_pooled"%(rundir,outPrefix)

chromLst = ["chr%d"%x for x in range(1,23)]+['chrX','chrY']+["%d"%x for x in range(1,23)]+['X','Y']

by_chrom = {}

for libl in flist:

lib = libl.strip()

if not os.path.isfile(lib):

continue

if options.verbose:

sys.stderr.write("scanning %s...\n"%lib)

if lib[-3:] == ".gz": F = gzip.open(lib)

for ln in open(lib):

else: F = open(lib)

for ln in F:

lnsplit=ln.split()

if len(lnsplit)<6:

sys.stderr.write("Error in %s \n" % lib)

continue

chrom, A, B, dot, counts, strand = lnsplit

chrom, A, B, dot, counts, strand, rA,rb, rgb, blockCount, blockSize, blockStarts = lnsplit

if int(blockCount) > 2:

print ln

continue

if not useStrand:

strand = "NA"

if checkchrom and (chrom not in chromLst): continue

A, B = int(A), int(B)+1

Aoff, Boff = blockSize.split(",")

A, B = int(A)+int(Aoff), int(B)-int(Boff)+1

if B-A > int(maxIntronLen): continue

try: by_chrom[(chrom,strand)][(A,B)] = int(counts) + by_chrom[(chrom, strand)][(A,B)]

try: by_chrom[(chrom,strand)][(A,B)] = int(counts) + by_chrom[(chrom,strand)][(A,B)]

except:

try: by_chrom[(chrom,strand)][(A,B)] = int(counts)

except: by_chrom[(chrom, strand)] = {(A,B):int(counts)}

except: by_chrom[(chrom,strand)] = {(A,B):int(counts)}

fout = file(outFile, 'w')

Ncluster = 0

sys.stderr.write("Parsing...\n")

for chrom in by_chrom:

read_ks = [k for k,v in by_chrom[chrom].items() if v >= 3] # a junction must have at least 3 reads

read_ks.sort()

sys.stderr.write("%s:%s.."%chrom)

clu = cluster_intervals(read_ks)[0]

for cl in clu:

if len(cl) > 1: # if cluster has more than one intron

if len(cl) > 0: # 1 if cluster has more than one intron

buf = '%s:%s '%chrom

for interval, count in [(x, by_chrom[chrom][x]) for x in cl]:

buf += "%d:%d" % interval + ":%d"%count+ " "

fout.write(buf+'\n')

Ncluster += 1

sys.stderr.write("\nWrote %d clusters..\n"%Ncluster)

fout.close()

def sort_junctions(libl, options):

chromLst = ["chr%d"%x for x in range(1,23)]+['chrX','chrY']+["%d"%x for x in range(1,23)]+['X','Y']

outPrefix = options.outprefix

rundir = options.rundir

refined_cluster = "%s/%s_refined"%(rundir,outPrefix)

checkchrom = options.checkchrom

useStrand = options.strand

if options.cluster == None:

refined_cluster = "%s/%s_refined"%(rundir,outPrefix)

else:

refined_cluster = options.cluster

runName = "%s/%s"%(rundir, outPrefix)

exons, cluExons = {}, {}

cluN = 0

for ln in open(refined_cluster):

chrom = ln.split()[0]

chrom = tuple(chrom.split(":"))

cluN += 1

for exon in ln.split()[1:]:

A, B, count = exon.split(":")

if chrom not in exons:

exons[chrom] = {}

exons[chrom][(int(A),int(B))] = cluN

if cluN not in cluExons:

cluExons[cluN] = []

cluExons[cluN].append((chrom, A, B))

merges = {}

for ll in libl:

lib=ll.rstrip()

if not os.path.isfile(lib):

continue

libN = lib

if libN not in merges:

merges[libN] = []

merges[libN].append(lib)

fout_runlibs = file(runName+"_sortedlibs",'w')

for libN in merges:

libName = "%s/%s"%(rundir,libN.split('/')[-1])

by_chrom = {}

foutName = libName+'.%s.sorted.gz'%(runName.split("/")[-1])

fout_runlibs.write(foutName+'\n')

if options.verbose:

sys.stderr.write("Sorting %s..\n"%libN)

if len(merges[libN]) > 1:

if options.verbose:

sys.stderr.write("merging %s...\n"%(" ".join(merges[libN])))

else:

pass

fout = gzip.open(foutName,'w')

fout.write("chrom %s\n"%libN.split("/")[-1].split(".junc")[0])

for lib in merges[libN]:

if lib[-3:] == ".gz": F = gzip.open(lib)

else: F = open(lib)

for ln in open(lib):

for ln in F:

lnsplit=ln.split()

if len(lnsplit)<6:

sys.stderr.write("Error in %s \n" % lib)

continue

chrom, start, end, dot, count, strand = ln.split()

chrom, A, B, dot, count, strand, rA,rb, rgb, blockCount, blockSize, blockStarts = lnsplit

if int(blockCount) > 2:

print ln

continue

if not useStrand:

strand = "NA"

if checkchrom and (chrom not in chromLst): continue

chrom = (chrom, strand)

Aoff, Boff = blockSize.split(",")

A, B = int(A)+int(Aoff), int(B)-int(Boff)+1

chrom = (chrom,strand)

if chrom not in by_chrom:

by_chrom[chrom] = {}

intron = (int(start), int(end)+1)

intron = (A, B)

if intron in by_chrom[chrom]:

by_chrom[chrom][intron] += int(count)

else:

by_chrom[chrom][intron] = int(count)

for clu in cluExons:

buf = []

ks = cluExons[clu]

ks.sort()

tot = 0

for exon in ks:

chrom, start, end = exon

chrom = tuple(chrom.split(":"))

start, end = int(start), int(end)

if chrom not in by_chrom:

pass

elif (start,end) in by_chrom[chrom]:

tot += by_chrom[chrom][(start,end)]

for exon in ks:

chrom, start, end = exon

start, end = int(start), int(end)

chrom = tuple(chrom.split(":"))

chromID, strand = chrom

if chrom not in by_chrom:

buf.append("%s:%d:%d:clu_%d_%s 0/%d\n"%(chromID,start, end,clu, strand, tot))

elif (start,end) in by_chrom[chrom]:

buf.append("%s:%d:%d:clu_%d_%s %d/%d\n"%(chromID,start, end, clu,strand, by_chrom[chrom][(start,end)], tot))

else:

buf.append("%s:%d:%d:clu_%d_%s 0/%d\n"%(chromID,start, end,clu,strand, tot))

fout.write("".join(buf))

fout.close()

fout_runlibs.close()

def refine_clusters(options):

outPrefix = options.outprefix

rundir = options.rundir

minratio = float(options.mincluratio)

minclureads = int(options.minclureads)

minreads = int(options.minreads)

inFile = "%s/%s_pooled"%(rundir,outPrefix)

outFile = "%s/%s_refined"%(rundir,outPrefix)

fout = file(outFile,'w')

Ncl = 0

for ln in open(inFile):

clu = []

totN = 0

chrom = ln.split()[0]

for ex in ln.split()[1:]:

A, B, N = ex.split(":")

clu.append(((int(A),int(B)), int(N)))

totN += int(N)

if totN < minclureads: continue

if options.const:

if len(clu) == 1:

buf = '%s ' % chrom

for interval, count in clu:

buf += "%d:%d" % interval + ":%d"%(count)+ " "

Ncl += 1

fout.write(buf+'\n')

for cl in refine_linked(clu):

rc = refine_cluster(cl,minratio, minreads)

if len(rc) > 0:

for clu in rc:

buf = '%s ' % chrom

for interval, count in clu:

buf += "%d:%d" % interval + ":%d"%(count)+ " "

Ncl += 1

fout.write(buf+'\n')

sys.stderr.write("Split into %s clusters...\n"%Ncl)

fout.close()

def merge_junctions(options):

''' function to merge junctions '''

outPrefix = options.outprefix

rundir = options.rundir

fnameout = "%s/%s"%(rundir,outPrefix)

flist = "%s/%s_sortedlibs"%(rundir, outPrefix)

lsts = []

for ln in open(flist):

lsts.append(ln.strip())

if options.verbose:

sys.stderr.write("merging %d junction files...\n"%(len(lsts)))

# Change 300 if max open file is < 300

N = min([300, max([100, int(len(lsts)**(0.5))])])

tmpfiles = []

while len(lsts) > 1:

clst = []

for i in range(0,(len(lsts)/N)+1):

lst = lsts[N*i:N*(i+1)]

if len(lst) > 0:

clst.append(lst)

lsts = []

for lst in clst:

if len(lst) == 0: continue

tmpfile = tempfile.mktemp()

os.mkdir(tmpfile)

foutname = tmpfile+"/tmpmerge.gz"

fout = gzip.open(foutname,'w')

merge_files(lst, fout, options)

lsts.append(foutname)

tmpfiles.append(foutname)

fout.close()

shutil.move(lsts[0], fnameout+"_perind.counts.gz")

if not options.const:

shutil.move(lsts[0], fnameout+"_perind.counts.gz")

else:

shutil.move(lsts[0], fnameout+"_perind.constcounts.gz")

def merge_files(fnames, fout, options):

fopen = []

for fname in fnames:

if fname[-3:] == ".gz":

fopen.append(gzip.open(fname))

else:

fopen.append(open(fname))

finished = False

N = 0

while not finished:

N += 1

if N % 50000 == 0:

sys.stderr.write(".")

buf = []

for f in fopen:

ln = f.readline().split()

if len(ln) == 0:

finished = True

break

chrom = ln[0]

data = ln[1:]

if len(buf) == 0:

buf.append(chrom)

buf += data

if len(buf) > 0:

if buf[0] == "chrom":

if options.verbose:

sys.stderr.write("merging %d files"%(len(buf)-1))

fout.write(" ".join(buf)+'\n')

else:

break

sys.stderr.write(" done.\n")

for fin in fopen:

fin.close()

def cluster_intervals(E):

''' Clusters intervals together. '''

E.sort()

if len(E) == 0:

return [], []

current = E[0]

Eclusters, cluster = [], []

i = 0

while i < len(E):

if overlaps(E[i], current):

cluster.append(E[i])

else:

Eclusters.append(cluster)

cluster = [E[i]]

current = (E[i][0], max([current[1], E[i][1]]))

i += 1

if len(cluster) > 0:

Eclusters.append(cluster)

return Eclusters, E

def overlaps(A,B):

'''

Checks if A and B overlaps

'''

if A[1] < B[0] or B[1] < A[0]:

return False

else: return True

def refine_linked(clusters):

unassigned = [x for x in clusters[1:]]

current = [clusters[0]]

splicesites = set([current[0][0][0],current[0][0][1]])

newClusters = []

while len(unassigned) > 0:

finished = False

while not finished:

finished = True

torm = []

for intron in unassigned:

inter, count = intron

start, end = inter

if start in splicesites or end in splicesites:

current.append(intron)

splicesites.add(start)

splicesites.add(end)

finished = False

torm.append(intron)

for intron in torm:

unassigned.remove(intron)

newClusters.append(current)

current = []

if len(unassigned) > 0:

current = [unassigned[0]]

splicesites = set([current[0][0][0],current[0][0][1]])

unassigned = unassigned[1:]

return newClusters

def refine_cluster(clu, cutoff, readcutoff):

''' for each exon in the cluster compute the ratio of reads, if smaller than cutoff,

remove and recluster '''

remove = []

dic = {}

intervals = []

reCLU = False

totN = 0

for inter, count in clu:

totN += count

for inter, count in clu:

if (count/float(totN) >= cutoff and count >= readcutoff):

intervals.append(inter)

dic[inter] = count

else:

reCLU = True

if len(intervals) == 0: return []

# This makes sure that after trimming, the clusters are still good

Atmp, B = cluster_intervals(intervals)

A = []

for cl in Atmp:

for c in refine_linked([(x,0) for x in cl]):

if len(c) > 0:

A.append([x[0] for x in c])

if len(A) == 1:

rc = [(x, dic[x]) for x in A[0]]

if len(rc) > 1:

if reCLU:

return refine_cluster([(x, dic[x]) for x in A[0]], cutoff, readcutoff)

else:

return [[(x, dic[x]) for x in A[0]]]

else:

return []

NCs = []

for c in A:

if len(c) > 1:

NC = refine_cluster([(x, dic[x]) for x in c], cutoff, readcutoff)

NCs += NC

return NCs

def get_numers(options):

outPrefix = options.outprefix

rundir = options.rundir

fname = "%s/%s_perind.counts.gz"%(rundir,outPrefix)

fnameout = "%s/%s_perind_numers.counts.gz"%(rundir,outPrefix)

if not options.const:

fname = "%s/%s_perind.counts.gz"%(rundir,outPrefix)

fnameout = "%s/%s_perind_numers.counts.gz"%(rundir,outPrefix)

else:

fname = "%s/%s_perind.constcounts.gz"%(rundir,outPrefix)

fnameout = "%s/%s_perind_numers.constcounts.gz"%(rundir,outPrefix)

input_file=gzip.open(fname, 'rb')

fout = gzip.open(fnameout,'w')

first_line=True

for l in input_file:

if first_line:

fout.write(" ".join(l.strip().split(" ")[1:])+'\n') # print the sample names

first_line=False

else:

l=l.strip()

words=l.split(" ")

fout.write(words[0]+ " "+ " ".join( [ g.split("/")[0] for g in words[1:] ] ) +'\n')

input_file.close()

fout.close()

if __name__ == "__main__":

from optparse import OptionParser

parser = OptionParser()

parser.add_option("-j", "--juncfiles", dest="juncfiles",

help="text file with all junction files to be processed")

parser.add_option("-o", "--outprefix", dest="outprefix", default = 'leafcutter',

help="output prefix (default leafcutter)")

parser.add_option("-q", "--quiet",

action="store_false", dest="verbose", default=True,

help="don't print status messages to stdout")

parser.add_option("-r", "--rundir", dest="rundir", default='./',

help="write to directory (default ./)")

parser.add_option("-l", "--maxintronlen", dest="maxintronlen", default = 100000,

help="maximum intron length in bp (default 100,000bp)")

parser.add_option("-m", "--minclureads", dest="minclureads", default = 30,

help="minimum reads in a cluster (default 30 reads)")

parser.add_option("-M", "--minreads", dest="minreads", default = 5,

help="minimum reads for an intron (default 5 reads)")

help="minimum reads in a cluster (default 5 reads)")

parser.add_option("-p", "--mincluratio", dest="mincluratio", default = 0.001,

help="minimum fraction of reads in a cluster that support a junction (default 0.001)")

parser.add_option("-k", "--checkchrom", dest="checkchrom", default = False,

help="check that the chromosomes are well formated e.g. chr1, chr2, ..., or 1, 2, ... (default=False)")

parser.add_option("-s", "--strand", dest="strand", default = False,

parser.add_option("-c", "--cluster", dest="cluster", default = None,

help="use strand info (default=False)")

help="refined cluster file when clusters are already made")

parser.add_option("-k", "--checkchrom", dest="checkchrom", action="store_true",default = False,

help="check that the chromosomes are well formated e.g. chr1, chr2, ..., or 1, 2, ...")

parser.add_option("-C", "--includeconst", dest="const", action="store_true",default = False,

help="also include constitutive introns")

parser.add_option("-s", "--strand", dest="strand", default = True,

help="use strand info (default=True)")

(options, args) = parser.parse_args()

if options.juncfiles == None:

sys.stderr.write("Error: no junction file provided...\n")

exit(0)

# Get the junction file list

libl = []

for junc in open(options.juncfiles):

junc = junc.strip()

try:

open(junc)

except:

sys.stderr.write("%s does not exist... check your junction files.\n"%junc)

exit(0)

libl.append(junc)

main(options, libl)

सेव किए गए Diffs

ऑरिजनल टेक्स्ट

फ़ाइल खोलें

#!/usr/bin/env python

import sys
import tempfile
import os
import gzip
import shutil

def main(options,libl):
    
    pool_junc_reads(libl, options)
    refine_clusters(options)
    sort_junctions(libl, options)
    merge_junctions(options)
    get_numers(options)

def pool_junc_reads(flist, options):

outPrefix = options.outprefix
    rundir = options.rundir
    maxIntronLen = int(options.maxintronlen)
    checkchrom = options.checkchrom
    useStrand = options.strand

outFile = "%s/%s_pooled"%(rundir,outPrefix)
    
    chromLst = ["chr%d"%x for x in range(1,23)]+['chrX','chrY']+["%d"%x for x in range(1,23)]+['X','Y']
    by_chrom = {}
    for libl in flist:
        
        lib = libl.strip()
        if not os.path.isfile(lib):
            continue

if options.verbose:
            sys.stderr.write("scanning %s...\n"%lib)

if lib[-3:] == ".gz": F = gzip.open(lib)
        else: F = open(lib)
        for ln in F:
            
            lnsplit=ln.split()
            if len(lnsplit)<6: 
                sys.stderr.write("Error in %s \n" % lib)
                continue
            chrom, A, B, dot, counts, strand = lnsplit
            
            if not useStrand:
                strand = "NA"
            if checkchrom and (chrom not in chromLst): continue
            A, B = int(A), int(B)+1
            if B-A > int(maxIntronLen): continue
            try: by_chrom[(chrom,strand)][(A,B)] = int(counts) + by_chrom[(chrom, strand)][(A,B)]
            except: 
                try: by_chrom[(chrom,strand)][(A,B)] = int(counts)
                except: by_chrom[(chrom, strand)] = {(A,B):int(counts)}

fout = file(outFile, 'w')
    Ncluster = 0
    sys.stderr.write("Parsing...\n")
    for chrom in by_chrom:
        read_ks = [k for k,v in by_chrom[chrom].items() if v >= 3] # a junction must have at least 3 reads
        read_ks.sort()
        sys.stderr.write("%s:%s.."%chrom)
        clu = cluster_intervals(read_ks)[0]
        for cl in clu:
            if len(cl) > 1: # if cluster has more than one intron  
                buf = '%s:%s '%chrom
                for interval, count in [(x, by_chrom[chrom][x]) for x in cl]:
                    buf += "%d:%d" % interval + ":%d"%count+ " "
                fout.write(buf+'\n')
            Ncluster += 1
    sys.stderr.write("\nWrote %d clusters..\n"%Ncluster)
    fout.close()

def sort_junctions(libl, options):

chromLst = ["chr%d"%x for x in range(1,23)]+['chrX','chrY']+["%d"%x for x in range(1,23)]+['X','Y'] 
    outPrefix = options.outprefix
    rundir = options.rundir
    refined_cluster = "%s/%s_refined"%(rundir,outPrefix)
    checkchrom = options.checkchrom
    useStrand = options.strand
    runName = "%s/%s"%(rundir, outPrefix)

exons, cluExons = {}, {}
    cluN = 0

for ln in open(refined_cluster):
        chrom = ln.split()[0]
        chrom = tuple(chrom.split(":"))
        cluN += 1
        for exon in ln.split()[1:]:
            A, B, count = exon.split(":")
            if chrom not in exons:
                exons[chrom] = {}

exons[chrom][(int(A),int(B))] = cluN
            if cluN not in cluExons:
                cluExons[cluN] = []
            cluExons[cluN].append((chrom, A, B))

merges = {}
    for ll in libl:
        lib=ll.rstrip()
        if not os.path.isfile(lib):
            continue
        libN = lib
        if libN not in merges:
            merges[libN] = []
        merges[libN].append(lib)

fout_runlibs = file(runName+"_sortedlibs",'w')

for libN in merges:
        libName = "%s/%s"%(rundir,libN.split('/')[-1])
        by_chrom = {}
        foutName = libName+'.%s.sorted.gz'%(runName.split("/")[-1])

fout_runlibs.write(foutName+'\n')

if options.verbose:   
            sys.stderr.write("Sorting %s..\n"%libN)
        if len(merges[libN]) > 1:
            if options.verbose:   
                sys.stderr.write("merging %s...\n"%(" ".join(merges[libN])))
        else:
            pass
        fout = gzip.open(foutName,'w')

fout.write("chrom %s\n"%libN.split("/")[-1].split(".junc")[0])

for lib in merges[libN]:
            if lib[-3:] == ".gz": F = gzip.open(lib)
            else: F = open(lib)
            for ln in F:

lnsplit=ln.split()
                if len(lnsplit)<6: 
                    sys.stderr.write("Error in %s \n" % lib)
                    continue
                chrom, start, end, dot, count, strand = ln.split()
                if not useStrand:
                    strand = "NA"
                if checkchrom and (chrom not in chromLst): continue
                chrom = (chrom, strand)
                if chrom not in by_chrom:
                    by_chrom[chrom] = {}
                intron = (int(start), int(end)+1)
                if intron in by_chrom[chrom]:
                    by_chrom[chrom][intron] += int(count)
                else:
                    by_chrom[chrom][intron] = int(count)

for clu in cluExons:
            buf = []
            ks = cluExons[clu]
            ks.sort()
            tot = 0
            for exon in ks:
                chrom, start, end = exon
                start, end = int(start), int(end)
                if chrom not in by_chrom:
                    pass
                elif (start,end) in by_chrom[chrom]:
                    tot += by_chrom[chrom][(start,end)]
            for exon in ks:
            
                chrom, start, end = exon
                start, end = int(start), int(end)
                chromID, strand = chrom
                if chrom not in by_chrom:
                    buf.append("%s:%d:%d:clu_%d_%s 0/%d\n"%(chromID,start, end,clu, strand, tot))
                elif (start,end) in by_chrom[chrom]:                
                    buf.append("%s:%d:%d:clu_%d_%s %d/%d\n"%(chromID,start, end, clu,strand, by_chrom[chrom][(start,end)], tot))
                else:
                    buf.append("%s:%d:%d:clu_%d_%s 0/%d\n"%(chromID,start, end,clu,strand, tot))
        
            fout.write("".join(buf))
        fout.close()
    fout_runlibs.close()

def refine_clusters(options):
    
    outPrefix = options.outprefix
    rundir = options.rundir
    minratio = float(options.mincluratio)
    minclureads = int(options.minclureads)
    minreads = int(options.minreads)

inFile = "%s/%s_pooled"%(rundir,outPrefix)
    outFile = "%s/%s_refined"%(rundir,outPrefix)

fout = file(outFile,'w')
    Ncl = 0
    for ln in open(inFile):
        clu = []
        totN = 0
        chrom = ln.split()[0]
        for ex in ln.split()[1:]:
            A, B, N = ex.split(":")
            clu.append(((int(A),int(B)), int(N)))
            totN += int(N)
        if totN < minclureads: continue
       
        for cl in refine_linked(clu):
            rc = refine_cluster(cl,minratio, minreads)
            if len(rc) > 0:
                for clu in rc:
                    buf = '%s ' % chrom
                    for interval, count in clu:
                        buf += "%d:%d" % interval + ":%d"%(count)+ " "
                    Ncl += 1
                    fout.write(buf+'\n')
    sys.stderr.write("Split into %s clusters...\n"%Ncl)
    fout.close()

def merge_junctions(options):    
    ''' function to merge junctions '''

outPrefix = options.outprefix
    rundir = options.rundir
    fnameout = "%s/%s"%(rundir,outPrefix)
    flist = "%s/%s_sortedlibs"%(rundir, outPrefix)
    
    lsts = []
    for ln in open(flist):
        lsts.append(ln.strip())
    if options.verbose:
        sys.stderr.write("merging %d junction files...\n"%(len(lsts)))
    
    # Change 300 if max open file is < 300
    N = min([300, max([100, int(len(lsts)**(0.5))])])

tmpfiles = []
    while len(lsts) > 1:    
        clst = []
        
        for i in range(0,(len(lsts)/N)+1): 
            lst = lsts[N*i:N*(i+1)]
            if len(lst) > 0:
                clst.append(lst)
        lsts = []
    
        for lst in clst:
            if len(lst) == 0: continue
            tmpfile = tempfile.mktemp()
            os.mkdir(tmpfile)
            foutname = tmpfile+"/tmpmerge.gz"
            fout = gzip.open(foutname,'w')
            
            merge_files(lst, fout, options)
            lsts.append(foutname)
            tmpfiles.append(foutname)
            fout.close()
    
    shutil.move(lsts[0], fnameout+"_perind.counts.gz")

def merge_files(fnames, fout, options):

fopen = []
    for fname in fnames:
        if fname[-3:] == ".gz":
            fopen.append(gzip.open(fname))
        else:
            fopen.append(open(fname))

finished = False
    N = 0
    while not finished:
        N += 1
        if N % 50000 == 0: 
            sys.stderr.write(".")
        buf = []
        for f in fopen:
            ln = f.readline().split()
            if len(ln) == 0: 
                finished = True
                break
            chrom = ln[0]
            data = ln[1:]
            if len(buf) == 0:
                buf.append(chrom)
            buf += data
        if len(buf) > 0:
            if buf[0] == "chrom":
                if options.verbose:
                    sys.stderr.write("merging %d files"%(len(buf)-1))
            fout.write(" ".join(buf)+'\n')
        else:
            break

sys.stderr.write(" done.\n")
    for fin in fopen:
        fin.close()

def cluster_intervals(E):
    ''' Clusters intervals together. '''
    E.sort()
    if len(E) == 0:
        return [], []
    current = E[0]
    Eclusters, cluster = [], []

i = 0
    while i < len(E):

if overlaps(E[i], current):
            cluster.append(E[i])
        else:
            Eclusters.append(cluster)
            cluster = [E[i]]
        current = (E[i][0], max([current[1], E[i][1]]))
        i += 1

if len(cluster) > 0:
        
        Eclusters.append(cluster)

return Eclusters, E

def overlaps(A,B):
    '''
    Checks if A and B overlaps
    '''

if A[1] < B[0] or B[1] < A[0]:
        return False
    else: return True

def refine_linked(clusters):

unassigned = [x for x in clusters[1:]]
    current = [clusters[0]]
    splicesites = set([current[0][0][0],current[0][0][1]])
    newClusters = []
    while len(unassigned) > 0:
        finished = False
    
        while not finished:
            finished = True
            torm = []
            for intron in unassigned:
                inter, count = intron
                start, end = inter
                if start in splicesites or end in splicesites:
                    current.append(intron)
                    splicesites.add(start)
                    splicesites.add(end)
                    finished = False
                    torm.append(intron)
            for intron in torm:
                unassigned.remove(intron)
        newClusters.append(current)
        current = []
        if len(unassigned) > 0:
            current = [unassigned[0]]
            splicesites = set([current[0][0][0],current[0][0][1]])
            unassigned = unassigned[1:]
    return newClusters

def refine_cluster(clu, cutoff, readcutoff):
    ''' for each exon in the cluster compute the ratio of reads, if smaller than cutoff,
    remove and recluster '''
    
    remove = []
    dic = {}
    intervals = []

reCLU = False
    totN = 0

for inter, count in clu:
        totN += count
    for inter, count in clu:
        if (count/float(totN) >= cutoff and count >= readcutoff):
            intervals.append(inter)
            dic[inter] = count
        else:
            reCLU = True
    if len(intervals) == 0: return []
    
    # This makes sure that after trimming, the clusters are still good
    Atmp, B = cluster_intervals(intervals)
    A = []
    for cl in Atmp:
        for c in refine_linked([(x,0) for x in cl]):
            if len(c) > 0:
                A.append([x[0] for x in c])
    
    if len(A) == 1:
        rc = [(x, dic[x]) for x in A[0]]
        if len(rc) > 1:
            if reCLU:
                return refine_cluster([(x, dic[x]) for x in A[0]], cutoff, readcutoff)
            else:
                return [[(x, dic[x]) for x in A[0]]]
        else:
            return []
    NCs = []
    for c in A:
        if len(c) > 1:
            NC = refine_cluster([(x, dic[x]) for x in c], cutoff, readcutoff)
            NCs += NC
    return NCs

def get_numers(options):
    outPrefix = options.outprefix
    rundir = options.rundir
    fname = "%s/%s_perind.counts.gz"%(rundir,outPrefix)
    fnameout = "%s/%s_perind_numers.counts.gz"%(rundir,outPrefix)
    input_file=gzip.open(fname, 'rb')
    fout = gzip.open(fnameout,'w')
    first_line=True
    
    for l in input_file:
        if first_line:
            fout.write(" ".join(l.strip().split(" ")[1:])+'\n') # print the sample names
            first_line=False
        else:
            l=l.strip()
            words=l.split(" ")
            
            fout.write(words[0]+ " "+ " ".join( [ g.split("/")[0] for g in words[1:] ] ) +'\n')

input_file.close()
    fout.close()

if __name__ == "__main__":

from optparse import OptionParser

parser = OptionParser()

parser.add_option("-j", "--juncfiles", dest="juncfiles",
                  help="text file with all junction files to be processed")

parser.add_option("-o", "--outprefix", dest="outprefix", default = 'leafcutter',
                  help="output prefix (default leafcutter)")

parser.add_option("-q", "--quiet",
                  action="store_false", dest="verbose", default=True,
                  help="don't print status messages to stdout")

parser.add_option("-r", "--rundir", dest="rundir", default='./',
                  help="write to directory (default ./)")
    
    parser.add_option("-l", "--maxintronlen", dest="maxintronlen", default = 100000,
                  help="maximum intron length in bp (default 100,000bp)")

parser.add_option("-m", "--minclureads", dest="minclureads", default = 30,
                  help="minimum reads in a cluster (default 30 reads)")

parser.add_option("-M", "--minreads", dest="minreads", default = 5,
                  help="minimum reads for an intron (default 5 reads)")

parser.add_option("-p", "--mincluratio", dest="mincluratio", default = 0.001,
                  help="minimum fraction of reads in a cluster that support a junction (default 0.001)")
    parser.add_option("-k", "--checkchrom", dest="checkchrom", default = False,
                  help="check that the chromosomes are well formated e.g. chr1, chr2, ..., or 1, 2, ... (default=False)")

parser.add_option("-s", "--strand", dest="strand", default = False,
                  help="use strand info (default=False)")

(options, args) = parser.parse_args()

if options.juncfiles == None:
        sys.stderr.write("Error: no junction file provided...\n")
        exit(0)
    
    # Get the junction file list
    libl = []
    for junc in open(options.juncfiles):
        junc = junc.strip()
        try:
            open(junc)
        except: 
            sys.stderr.write("%s does not exist... check your junction files.\n"%junc)
            exit(0)
        libl.append(junc)

main(options, libl)

परिवर्तित टेक्स्ट

फ़ाइल खोलें

# https://github.com/griffithlab/regtools
# /home/yangili1/tools/regtools/build/regtools junctions extract -a 8 -i 50 -I 500000 bamfile.bam -o outfile.junc
# Using regtools speeds up the junction extraction step by an order of magnitude or more

import sys
import tempfile
import os
import gzip
import shutil

def main(options,libl):
    
    if options.cluster == None:
        pool_junc_reads(libl, options)
        refine_clusters(options)
        
    sort_junctions(libl, options)
    merge_junctions(options)
    get_numers(options)

def pool_junc_reads(flist, options):

outPrefix = options.outprefix
    rundir = options.rundir
    maxIntronLen = int(options.maxintronlen)
    checkchrom = options.checkchrom
    useStrand = options.strand

if options.verbose:
            sys.stderr.write("scanning %s...\n"%lib)

for ln in open(lib):
            
            lnsplit=ln.split()
            if len(lnsplit)<6: 
                sys.stderr.write("Error in %s \n" % lib)
                continue
            chrom, A, B, dot, counts, strand, rA,rb, rgb, blockCount, blockSize, blockStarts = lnsplit
            if int(blockCount) > 2:
                print ln
                continue
            if not useStrand:
                strand = "NA"            
            if checkchrom and (chrom not in chromLst): continue
            Aoff, Boff = blockSize.split(",")
            A, B = int(A)+int(Aoff), int(B)-int(Boff)+1
    
            if B-A > int(maxIntronLen): continue
            try: by_chrom[(chrom,strand)][(A,B)] = int(counts) + by_chrom[(chrom,strand)][(A,B)]
            except: 
                try: by_chrom[(chrom,strand)][(A,B)] = int(counts)
                except: by_chrom[(chrom,strand)] = {(A,B):int(counts)}

fout = file(outFile, 'w')
    Ncluster = 0
    sys.stderr.write("Parsing...\n")
    for chrom in by_chrom:
        read_ks = [k for k,v in by_chrom[chrom].items() if v >= 3] # a junction must have at least 3 reads
        read_ks.sort()
        
        sys.stderr.write("%s:%s.."%chrom)
        clu = cluster_intervals(read_ks)[0]
        for cl in clu:
    
            if len(cl) > 0: # 1 if cluster has more than one intron  
                buf = '%s:%s '%chrom
                for interval, count in [(x, by_chrom[chrom][x]) for x in cl]:
                    buf += "%d:%d" % interval + ":%d"%count+ " "
                fout.write(buf+'\n')
                Ncluster += 1
    sys.stderr.write("\nWrote %d clusters..\n"%Ncluster)
    fout.close()

def sort_junctions(libl, options):

chromLst = ["chr%d"%x for x in range(1,23)]+['chrX','chrY']+["%d"%x for x in range(1,23)]+['X','Y'] 
    outPrefix = options.outprefix
    rundir = options.rundir
    checkchrom = options.checkchrom
    useStrand = options.strand

if options.cluster == None:
        refined_cluster = "%s/%s_refined"%(rundir,outPrefix)
    else:
        refined_cluster = options.cluster
    runName = "%s/%s"%(rundir, outPrefix)

exons, cluExons = {}, {}
    cluN = 0

for ln in open(refined_cluster):
        chrom = ln.split()[0]
        cluN += 1
        for exon in ln.split()[1:]:
            A, B, count = exon.split(":")
            if chrom not in exons:
                exons[chrom] = {}
            exons[chrom][(int(A),int(B))] = cluN
            if cluN not in cluExons:
                cluExons[cluN] = []
            cluExons[cluN].append((chrom, A, B))

fout_runlibs = file(runName+"_sortedlibs",'w')

for libN in merges:
        libName = "%s/%s"%(rundir,libN.split('/')[-1])
        by_chrom = {}
        foutName = libName+'.%s.sorted.gz'%(runName.split("/")[-1])

fout_runlibs.write(foutName+'\n')

fout.write("chrom %s\n"%libN.split("/")[-1].split(".junc")[0])

for lib in merges[libN]:
        
            for ln in open(lib):

lnsplit=ln.split()
                if len(lnsplit)<6: 
                    sys.stderr.write("Error in %s \n" % lib)
                    continue
                chrom, A, B, dot, count, strand, rA,rb, rgb, blockCount, blockSize, blockStarts = lnsplit
                if int(blockCount) > 2:
                    print ln
                    continue
                if not useStrand:
                    strand = "NA"            
                if checkchrom and (chrom not in chromLst): continue
                Aoff, Boff = blockSize.split(",")
                A, B = int(A)+int(Aoff), int(B)-int(Boff)+1
                chrom = (chrom,strand)
                if chrom not in by_chrom:
                    by_chrom[chrom] = {}
                intron = (A, B)
                
                if intron in by_chrom[chrom]:
                    by_chrom[chrom][intron] += int(count)
                else:
                    by_chrom[chrom][intron] = int(count)
                
        for clu in cluExons:
            buf = []
            ks = cluExons[clu]
            ks.sort()
            tot = 0
            for exon in ks:
                chrom, start, end = exon
                chrom = tuple(chrom.split(":"))
                start, end = int(start), int(end)
                if chrom not in by_chrom:
                    pass
                elif (start,end) in by_chrom[chrom]:
                    tot += by_chrom[chrom][(start,end)]
            for exon in ks:
            
                chrom, start, end = exon
                start, end = int(start), int(end)
                chrom = tuple(chrom.split(":"))
                chromID, strand = chrom
                if chrom not in by_chrom:
                    buf.append("%s:%d:%d:clu_%d_%s 0/%d\n"%(chromID,start, end,clu, strand, tot))
                elif (start,end) in by_chrom[chrom]:
                    buf.append("%s:%d:%d:clu_%d_%s %d/%d\n"%(chromID,start, end, clu,strand, by_chrom[chrom][(start,end)], tot))
                else:
                    buf.append("%s:%d:%d:clu_%d_%s 0/%d\n"%(chromID,start, end,clu,strand, tot))
        
            fout.write("".join(buf))
        fout.close()
    fout_runlibs.close()

inFile = "%s/%s_pooled"%(rundir,outPrefix)
    outFile = "%s/%s_refined"%(rundir,outPrefix)
    fout = file(outFile,'w')

Ncl = 0
    for ln in open(inFile):
        clu = []
        totN = 0
        chrom = ln.split()[0]
        for ex in ln.split()[1:]:
            A, B, N = ex.split(":")
            clu.append(((int(A),int(B)), int(N)))
            totN += int(N)
        
        if totN < minclureads: continue

if options.const:
            if len(clu) == 1:
                buf = '%s ' % chrom
                for interval, count in clu:
                    buf += "%d:%d" % interval + ":%d"%(count)+ " "
                Ncl += 1
                fout.write(buf+'\n')
        
        for cl in refine_linked(clu):
            rc = refine_cluster(cl,minratio, minreads)
            
            if len(rc) > 0:
                for clu in rc:
                    buf = '%s ' % chrom
                    for interval, count in clu:
                        buf += "%d:%d" % interval + ":%d"%(count)+ " "
                    Ncl += 1
                    fout.write(buf+'\n')

sys.stderr.write("Split into %s clusters...\n"%Ncl)
    fout.close()

def merge_junctions(options):    
    ''' function to merge junctions '''

outPrefix = options.outprefix
    rundir = options.rundir
    
    fnameout = "%s/%s"%(rundir,outPrefix)

flist = "%s/%s_sortedlibs"%(rundir, outPrefix)
    
    lsts = []
    for ln in open(flist):
        lsts.append(ln.strip())
    if options.verbose:
        sys.stderr.write("merging %d junction files...\n"%(len(lsts)))
    
    # Change 300 if max open file is < 300
    N = min([300, max([100, int(len(lsts)**(0.5))])])

tmpfiles = []
    while len(lsts) > 1:    
        clst = []
        
        for i in range(0,(len(lsts)/N)+1): 
            lst = lsts[N*i:N*(i+1)]
            if len(lst) > 0:
                clst.append(lst)
        lsts = []
    
        for lst in clst:
            if len(lst) == 0: continue
            tmpfile = tempfile.mktemp()
            os.mkdir(tmpfile)
            foutname = tmpfile+"/tmpmerge.gz"
            fout = gzip.open(foutname,'w')
            
            merge_files(lst, fout, options)
            lsts.append(foutname)
            tmpfiles.append(foutname)
            fout.close()
            
    if not options.const:
        shutil.move(lsts[0], fnameout+"_perind.counts.gz")
    else:
        shutil.move(lsts[0], fnameout+"_perind.constcounts.gz")

def merge_files(fnames, fout, options):

fopen = []
    for fname in fnames:
        if fname[-3:] == ".gz":
            fopen.append(gzip.open(fname))
        else:
            fopen.append(open(fname))

sys.stderr.write(" done.\n")
    for fin in fopen:
        fin.close()

def cluster_intervals(E):
    ''' Clusters intervals together. '''
    E.sort()
    current = E[0]
    Eclusters, cluster = [], []

i = 0
    while i < len(E):

if len(cluster) > 0:
        
        Eclusters.append(cluster)

return Eclusters, E

def overlaps(A,B):
    '''
    Checks if A and B overlaps
    '''

if A[1] < B[0] or B[1] < A[0]:
        return False
    else: return True

def refine_linked(clusters):

reCLU = False
    totN = 0

def get_numers(options):
    outPrefix = options.outprefix
    rundir = options.rundir

if not options.const:                                                                                                                                                                                                                                                                                                                           
        fname = "%s/%s_perind.counts.gz"%(rundir,outPrefix)                                                                                                                                                                                                                                                                                        
        fnameout = "%s/%s_perind_numers.counts.gz"%(rundir,outPrefix)
    else:
        fname = "%s/%s_perind.constcounts.gz"%(rundir,outPrefix)
        fnameout = "%s/%s_perind_numers.constcounts.gz"%(rundir,outPrefix)
    
    input_file=gzip.open(fname, 'rb')
    fout = gzip.open(fnameout,'w')
    first_line=True
    
    for l in input_file:
        if first_line:
            fout.write(" ".join(l.strip().split(" ")[1:])+'\n') # print the sample names
            first_line=False
        else:
            l=l.strip()
            words=l.split(" ")
            
            fout.write(words[0]+ " "+ " ".join( [ g.split("/")[0] for g in words[1:] ] ) +'\n')

input_file.close()
    fout.close()

if __name__ == "__main__":

from optparse import OptionParser

parser = OptionParser()

parser.add_option("-j", "--juncfiles", dest="juncfiles",
                  help="text file with all junction files to be processed")

parser.add_option("-o", "--outprefix", dest="outprefix", default = 'leafcutter',
                  help="output prefix (default leafcutter)")

parser.add_option("-q", "--quiet",
                  action="store_false", dest="verbose", default=True,
                  help="don't print status messages to stdout")

parser.add_option("-m", "--minclureads", dest="minclureads", default = 30,
                  help="minimum reads in a cluster (default 30 reads)")

parser.add_option("-M", "--minreads", dest="minreads", default = 5,
                  help="minimum reads in a cluster (default 5 reads)")

parser.add_option("-p", "--mincluratio", dest="mincluratio", default = 0.001,
                  help="minimum fraction of reads in a cluster that support a junction (default 0.001)")

parser.add_option("-c", "--cluster", dest="cluster", default = None,
                  help="refined cluster file when clusters are already made")

parser.add_option("-k", "--checkchrom", dest="checkchrom", action="store_true",default = False,
                  help="check that the chromosomes are well formated e.g. chr1, chr2, ..., or 1, 2, ...")
    
    parser.add_option("-C", "--includeconst", dest="const", action="store_true",default = False,
                  help="also include constitutive introns")

parser.add_option("-s", "--strand", dest="strand", default = True,
                      help="use strand info (default=True)")
    
    (options, args) = parser.parse_args()

main(options, libl)