def parse_gpdfile(tdir,gpdfile,smoothing_factor):
# Go through the long reads and make a genepred
if gpdfile != '-':
fr = FileBasics.GenericFileReader(gpdfile)
else:
fr = sys.stdin
seennames = {}
longreadnumber = 0
of_gpd = open(tdir+'/longreads.gpd','w')
while True:
line = fr.readline()
if not line: break
if re.match('^#',line): #skip comments
continue
longreadnumber += 1
entry = GenePredBasics.smooth_gaps( \
GenePredBasics.line_to_entry(line.rstrip()) \
,smoothing_factor)
readname = entry['name']
if readname in seennames:
sys.stderr.write("Warning: repeat name '"+readname+"'\n")
#set our first name to our bin
entry['name'] = str(longreadnumber)
gline = GenePredBasics.entry_to_line(entry)
of_gpd.write(gline+"\n")
fr.close()
of_gpd.close()
def get_exons_from_seqs(seqs, d, spcf):
sind = 0
oline = ''
for seq in seqs:
sind += 1
psec = 'P' #primary or secondary
if sind > 1: psec = 'S'
d1 = d.copy()
d1['rname'] = seq[1]
if seq[2] == '+': d1['flag'] = 0
else: d1['flag'] = 16
d1['pos'] = seq[3]
d1['cigar'] = seq[4]
d1['cigar_array'] = SamBasics.parse_cigar(seq[4])
skips = set(['H', 'D', 'N'])
total_length = 0
possible_matches = 0
indels = 0
qstart = 0
if d1['cigar_array'][0]['op'] == 'S':
qstart = d1['cigar_array'][0]['val']
if d1['cigar_array'][0]['op'] == 'H':
qstart = d1['cigar_array'][0]['val']
for ce in d1['cigar_array']:
if ce['op'] not in skips:
total_length += ce['val']
if ce['op'] == 'M': possible_matches += ce['val']
elif ce['op'] == 'I':
indels += ce['val']
elif ce['op'] == 'D' and ce['val'] < 68:
indels += ce['val']
fakeseq = 'N' * total_length
d1['seq'] = fakeseq
nline = SamBasics.entry_to_line(d1)
pline = spcf.convert_line(nline)
pentry = PSLBasics.line_to_entry(pline)
#mismatch_count = -1
#if sind == 1 and args.reference_genome: #for primary alignments we can calculate the number of matches
# for i in range(0,len(pentry['blockSizes'])):
# tseq = spcf.genome[pentry['tName']][pentry['tStarts'][i]:pentry['tStarts'][i]+pentry['blockSizes'][i]]
# qseq = sequence[pentry['qStarts'][i]:pentry['qStarts'][i]+pentry['blockSizes'][i]]
# print pentry['blockSizes'][i]
# print tseq
# print qseq
# for j in range(0,len(tseq)):
# if tseq[j].upper() != qseq[j].upper(): mismatch_count += 1
gline = PSLBasics.convert_entry_to_genepred_line(pentry)
gentry = GenePredBasics.line_to_entry(gline)
gsmooth = GenePredBasics.smooth_gaps(gentry, 68)
for i in range(0, len(gsmooth['exonStarts'])):
oline += gsmooth['chrom'] + "\t" + str(
gsmooth['exonStarts'][i]) + "\t" + str(
gsmooth['exonEnds']
[i]) + "\t" + gsmooth['strand'] + "\t" + gsmooth[
'name'] + "\t" + str(possible_matches) + "\t" + str(
indels) + "\t" + psec + "\t" + str(qstart) + "\n"
return oline
def main():
parser = argparse.ArgumentParser(description='Use reference junctions when they are close',formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--min_intron_size',type=int,default=68,help="INT min intron size")
parser.add_argument('--min_local_support',type=int,default=0,help="INT min number of junctions within search_size of a junction in order to count it")
parser.add_argument('--search_size',type=int,default=10,help="INT search space for reference")
parser.add_argument('--output_fake_psl',help="FASTAFILE reference genome to make a fake PSL output")
parser.add_argument('psl',help="PSLFILENAME or '-' for STDIN")
parser.add_argument('reference_genepred',help="FASTAFILENAME for reference genepred")
args = parser.parse_args()
cpus = multiprocessing.cpu_count()
genome = {}
if args.output_fake_psl:
genome = read_fasta_into_hash(args.output_fake_psl)
#read in the reference genepred first
gpf = GenePredBasics.GenePredFile(args.reference_genepred)
#lets sort entries by chromosome
ref = {}
for e in [x.entry for x in gpf.entries]:
if len(e['exonStarts']) <= 1: continue
if e['chrom'] not in ref:
ref[e['chrom']] = {}
for i in range(1,len(e['exonStarts'])):
if e['exonEnds'][i-1] not in ref[e['chrom']]:
ref[e['chrom']][e['exonEnds'][i-1]] = {}
if e['exonStarts'][i]+1 not in ref[e['chrom']][e['exonEnds'][i-1]]:
ref[e['chrom']][e['exonEnds'][i-1]][e['exonStarts'][i]+1] = e['strand']
#Stored all junctions as 1-base
read_info = {}
pf = GenericFileReader(args.psl)
fcount_total = 0
while True:
line = pf.readline()
if not line: break
if re.match('^#',line): continue
line = line.rstrip()
pe = PSLBasics.line_to_entry(line)
if len(pe['tStarts']) != len(pe['blockSizes']) or len(pe['qStarts']) != len(pe['blockSizes']):
sys.stderr.write("WARNING invalid psl\n")
continue
genepred_line = PSLBasics.convert_entry_to_genepred_line(pe)
ge = GenePredBasics.smooth_gaps(GenePredBasics.line_to_entry(genepred_line),args.min_intron_size)
refjuns = {}
if pe['tName'] in ref: refjuns = ref[pe['tName']]
new_ge = nudge(pe,ge,refjuns,args)
if args.output_fake_psl:
new_psl_line = GenePredBasics.entry_to_fake_psl_line(new_ge,genome)
print new_psl_line
else:
print GenePredBasics.entry_to_line(new_ge)
def main():
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('genepred',help="FILENAME or use - for STDIN")
parser.add_argument('--smoothing_size',type=int,default=68,help="INT no gaps less than this size")
args = parser.parse_args()
inf = sys.stdin
if args.genepred != '-':
inf = open(args.genepred)
for line in inf:
e = GenePredBasics.line_to_entry(line)
e2 = GenePredBasics.smooth_gaps(e,args.smoothing_size)
print GenePredBasics.entry_to_line(e2)
def get_exons_from_seqs(seqs,d,spcf):
sind = 0
oline = ''
for seq in seqs:
sind+=1
psec = 'P' #primary or secondary
if sind > 1: psec = 'S'
d1 = d.copy()
d1['rname'] = seq[1]
if seq[2] == '+': d1['flag'] = 0
else: d1['flag'] = 16
d1['pos'] = seq[3]
d1['cigar'] = seq[4]
d1['cigar_array'] = SamBasics.parse_cigar(seq[4])
skips = set(['H','D','N'])
total_length = 0
possible_matches = 0
indels = 0
qstart = 0
if d1['cigar_array'][0]['op'] == 'S':
qstart = d1['cigar_array'][0]['val']
if d1['cigar_array'][0]['op'] == 'H':
qstart = d1['cigar_array'][0]['val']
for ce in d1['cigar_array']:
if ce['op'] not in skips:
total_length += ce['val']
if ce['op'] == 'M': possible_matches += ce['val']
elif ce['op'] == 'I':
indels += ce['val']
elif ce['op'] == 'D' and ce['val'] < 68:
indels += ce['val']
fakeseq = 'N'*total_length
d1['seq'] = fakeseq
nline = SamBasics.entry_to_line(d1)
pline = spcf.convert_line(nline)
pentry = PSLBasics.line_to_entry(pline)
#mismatch_count = -1
#if sind == 1 and args.reference_genome: #for primary alignments we can calculate the number of matches
# for i in range(0,len(pentry['blockSizes'])):
# tseq = spcf.genome[pentry['tName']][pentry['tStarts'][i]:pentry['tStarts'][i]+pentry['blockSizes'][i]]
# qseq = sequence[pentry['qStarts'][i]:pentry['qStarts'][i]+pentry['blockSizes'][i]]
# print pentry['blockSizes'][i]
# print tseq
# print qseq
# for j in range(0,len(tseq)):
# if tseq[j].upper() != qseq[j].upper(): mismatch_count += 1
gline = PSLBasics.convert_entry_to_genepred_line(pentry)
gentry = GenePredBasics.line_to_entry(gline)
gsmooth = GenePredBasics.smooth_gaps(gentry,68)
for i in range(0,len(gsmooth['exonStarts'])):
oline += gsmooth['chrom'] + "\t" + str(gsmooth['exonStarts'][i])+"\t"+str(gsmooth['exonEnds'][i])+"\t"+gsmooth['strand']+"\t"+gsmooth['name']+"\t"+str(possible_matches)+"\t"+str(indels)+"\t"+psec+"\t"+str(qstart)+"\n"
return oline
def main():
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('genepred', help="FILENAME or use - for STDIN")
parser.add_argument('--smoothing_size',
type=int,
default=68,
help="INT no gaps less than this size")
args = parser.parse_args()
inf = sys.stdin
if args.genepred != '-':
inf = open(args.genepred)
for line in inf:
e = GenePredBasics.line_to_entry(line)
e2 = GenePredBasics.smooth_gaps(e, args.smoothing_size)
print GenePredBasics.entry_to_line(e2)
def main():
parser = argparse.ArgumentParser(description="Convert a psl file into a target formated genepred file.")
parser.add_argument('--fill_gaps',type=int,default=0,help="Close gaps this size or smaller.")
parser.add_argument('input_name',help="Input PSL file, use - to indicate STDIN.")
args = parser.parse_args()
pslfilehandle = sys.stdin
if args.input_name != '-':
pslfilehandle = open(args.input_name)
with pslfilehandle as infile:
for line in infile:
psl_entry = PSLBasics.line_to_entry(line)
genepred_line = PSLBasics.convert_entry_to_genepred_line(psl_entry)
if args.fill_gaps > 0:
genepred_entry = GenePredBasics.line_to_entry(genepred_line)
genepred_entry2 = GenePredBasics.smooth_gaps(genepred_entry,args.fill_gaps)
genepred_line = GenePredBasics.entry_to_line(genepred_entry2)
print genepred_line
def main():
parser = argparse.ArgumentParser(
description='Use reference junctions when they are close',
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--min_intron_size',
type=int,
default=68,
help="INT min intron size")
parser.add_argument(
'--min_local_support',
type=int,
default=0,
help=
"INT min number of junctions within search_size of a junction in order to count it"
)
parser.add_argument('--search_size',
type=int,
default=10,
help="INT search space for reference")
parser.add_argument(
'--output_fake_psl',
help="FASTAFILE reference genome to make a fake PSL output")
parser.add_argument('psl', help="PSLFILENAME or '-' for STDIN")
parser.add_argument('reference_genepred',
help="FASTAFILENAME for reference genepred")
args = parser.parse_args()
cpus = multiprocessing.cpu_count()
genome = {}
if args.output_fake_psl:
genome = read_fasta_into_hash(args.output_fake_psl)
#read in the reference genepred first
gpf = GenePredBasics.GenePredFile(args.reference_genepred)
#lets sort entries by chromosome
ref = {}
for e in [x.entry for x in gpf.entries]:
if len(e['exonStarts']) <= 1: continue
if e['chrom'] not in ref:
ref[e['chrom']] = {}
for i in range(1, len(e['exonStarts'])):
if e['exonEnds'][i - 1] not in ref[e['chrom']]:
ref[e['chrom']][e['exonEnds'][i - 1]] = {}
if e['exonStarts'][i] + 1 not in ref[e['chrom']][e['exonEnds'][i -
1]]:
ref[e['chrom']][e['exonEnds'][i - 1]][e['exonStarts'][i] +
1] = e['strand']
#Stored all junctions as 1-base
read_info = {}
pf = GenericFileReader(args.psl)
fcount_total = 0
while True:
line = pf.readline()
if not line: break
if re.match('^#', line): continue
line = line.rstrip()
pe = PSLBasics.line_to_entry(line)
if len(pe['tStarts']) != len(pe['blockSizes']) or len(
pe['qStarts']) != len(pe['blockSizes']):
sys.stderr.write("WARNING invalid psl\n")
continue
genepred_line = PSLBasics.convert_entry_to_genepred_line(pe)
ge = GenePredBasics.smooth_gaps(
GenePredBasics.line_to_entry(genepred_line), args.min_intron_size)
refjuns = {}
if pe['tName'] in ref: refjuns = ref[pe['tName']]
new_ge = nudge(pe, ge, refjuns, args)
if args.output_fake_psl:
new_psl_line = GenePredBasics.entry_to_fake_psl_line(
new_ge, genome)
print new_psl_line
else:
print GenePredBasics.entry_to_line(new_ge)
