def readfiles(indir):
ext = 'fa'
files = iseqlib.getfiles(indir, ext)
sample2freqs = {}
for file in files:
sample = file.rstrip(ext).rstrip('.')
freqs = readfile( os.path.join(indir, file) )
sample2freqs[sample] = freqs
return sample2freqs
def main():
parser = iseqlib.initOptions()
addOptions(parser)
options, args = parser.parse_args()
if options.minExpFreq > 0 and not options.sample2total:
parser.error("--sample2total is required as --minExpandedFreq > 0\n")
if options.sample2total:
options.sample2total = readSample2total(options.sample2total)
ext = 'xml'
infiles = iseqlib.getfiles(options.indir, ext)
outbasename = os.path.join(options.outdir, options.basename)
fh1 = open("%s-1.txt" %outbasename, 'w')
fh2 = open("%s-2.txt" %outbasename, 'w')
fh3 = open("%s-3.txt" %outbasename, 'w')
fh4 = open("%s-4.txt" %outbasename, 'w')
type2count = {}
type2clones = {}
for file in infiles:
infile = os.path.join(options.indir, file)
vjname = file.rstrip(ext).rstrip('.')
clone2hits = readNcbiXml(infile, options)
separateClusters(clone2hits, options.sample2total, options.minExpFreq, options.minExpSize, options.minExpClones, options.minMotifClones, vjname, fh1, fh2, fh3, fh4, type2count, type2clones)
fh1.close()
fh2.close()
fh3.close()
fh4.close()
#summary stats:
summaryFile = "%s-summary.txt" %outbasename
fh = open(summaryFile, 'w')
fh.write("#min similarity: %f\n#min length: %d\n#min size to be called expanded clones: %d\n#min number of expanded clones required for type 1: %d\n#min number of clones supported a single motif for type 2: %d\n" %(options.minPos, options.minLen, options.minExpSize, options.minExpClones, options.minMotifClones))
for type, count in type2count.iteritems():
fh.write("%s\t%d\n" %(type, count))
fh.close()
#Print type2clones:
v2seq = {}
if options.vfile:
v2seq = readVfile(options.vfile)
type2index = {}
for type, header2vj2seq in type2clones.iteritems():
outfile = getFaFilename(type, outbasename)
f = open(outfile, 'w')
f.write("#%s\n" %type)
for header, vj2seq in header2vj2seq.iteritems():
for vj, seq in vj2seq.iteritems():
#f.write(">%s;%s\n" %(header, vj))
#reformat header:
sample, id, size = getCloneInfo( ";".join(header.split(";")[:3]) )
header = "%s;%s;%d;%s" % (sample.lstrip('as'), seq, size, vj)
f.write(">%s\n" %header)
v = vj.split(".")[0]
if v in v2seq:
seq = v2seq[v] + seq
f.write("%s\n" %seq)
f.close()
def main():
parser = iseqlib.initOptions()
addOptions(parser)
options, args = parser.parse_args()
if options.minExpFreq > 0 and not options.sample2total:
parser.error("--sample2total is required as --minExpandedFreq > 0\n")
if options.sample2total:
options.sample2total = readSample2total(options.sample2total)
ext = 'txt'
infiles = iseqlib.getfiles(options.indir, ext)
outbasename = os.path.join(options.outdir, options.basename)
fh1 = open("%s-1.txt" %outbasename, 'w')
fh2 = open("%s-2.txt" %outbasename, 'w')
fh3 = open("%s-3.txt" %outbasename, 'w')
fh4 = open("%s-4.txt" %outbasename, 'w')
fh5 = open("%s-5.txt" %outbasename, 'w')
type2count = {}
type2clusters = {}
totalseq = 0
expseq = 0
for file in infiles:
infile = os.path.join(options.indir, file)
vjname = file.rstrip(ext).rstrip('.')
clusters = readBlastclustOutfiles(infile, vjname, options)
total, exp = separateClusters(clusters, options.minExpFreq, options.minExpSize, options.minExpClones, fh1, fh2, fh3, fh4, fh5, type2count, type2clusters)
totalseq += total
expseq += exp
fh1.close()
fh2.close()
fh3.close()
fh4.close()
fh5.close()
#summary stats:
summaryFile = "%s-summary.txt" %outbasename
fh = open(summaryFile, 'w')
fh.write("#min size to be called expanded clones: %d\n#min number of expanded clones required for type 1: %d\n" %(options.minExpSize, options.minExpClones))
id2info = clusterId2info()
fh.write("Total number of clones: %d\n" %totalseq)
fh.write("Total number of expanded clones: %d\n" %expseq)
for type in sorted(type2count.keys()):
fh.write("%d\t%s\t%d\n" %(type, id2info[type], type2count[type]))
fh.close()
#Print type2clones:
#Read v files:
v2seq = {}
if options.vfile:
v2seq = readFaFile(options.vfile)
#Read fasta files:
ext = 'fa'
infiles = iseqlib.getfiles(options.fadir, ext)
vj2id2seq = {}
for file in infiles:
infile = os.path.join(options.fadir, file)
vjname = file.rstrip(ext).rstrip('.')
vj2id2seq[vjname] = readFaFile(infile)
for type, clusters in type2clusters.iteritems():
outfile = "%s-%d.fa" %(outbasename, type)
f = open(outfile, 'w')
f.write("#Type: %s\n" %type)
clusters = sorted(clusters, key=lambda c: c.totalReads, reverse=True)
for cluster in clusters:
f.write("#Cluster %s\n" %cluster.getDesc())
id2seq = vj2id2seq[cluster.vj]
v = cluster.vj.split(".")[0]
vseq = ""
if v in v2seq:
vseq = v2seq[v]
for clone in cluster.clones:
seq = id2seq[ clone.desc ]
cdr3seq = seq[ len(vseq): ]
header = "%s;%s;%d;%s" %(clone.sample, cdr3seq, clone.size, cluster.vj)
f.write(">%s\n" %header)
f.write("%s\n" %seq)
f.close()