def combine_quiver_results(split_dirs, output_dir, hq_filename, lq_filename, tofu_prefix=''):
"""
For each size bin result, ex: clusterOut/0to2k/all.quiveredXXX.fastq
combine it together, remember to add a prefix (ex: i0|c12, i1|c13/....)
"""
prefix_dict_hq = {}
prefix_dict_lq = {}
fout_hq = FastqWriter(os.path.join(output_dir, 'all_sizes.quivered_hq.fastq'))
fout_lq = FastqWriter(os.path.join(output_dir, 'all_sizes.quivered_lq.fastq'))
for i,d in enumerate(split_dirs):
file_hq = os.path.join(d, hq_filename) #'all_quivered_hq.100_30_0.99.fastq')
file_lq = os.path.join(d, lq_filename) #'all_quivered_lq.fastq')
print >> sys.stderr, "Adding prefix i{0}| to {1},{2}...".format(i, file_hq, file_lq)
prefix_dict_hq["i{i}HQ_{p}".format(i=i,p=tofu_prefix)] = os.path.abspath(d)
prefix_dict_lq["i{i}LQ_{p}".format(i=i,p=tofu_prefix)] = os.path.abspath(d)
for r in FastqReader(file_hq):
_name_ = "i{i}HQ_{p}|{n}".format(p=tofu_prefix, i=i, n=r.name)
fout_hq.writeRecord(_name_, r.sequence, r.quality)
for r in FastqReader(file_lq):
_name_ = "i{i}LQ_{p}|{n}".format(p=tofu_prefix, i=i, n=r.name)
fout_lq.writeRecord(_name_, r.sequence, r.quality)
fout_hq.close()
fout_lq.close()
print >> sys.stderr, "HQ quivered output combined to:", fout_hq.file.name
print >> sys.stderr, "LQ quivered output combined to:", fout_lq.file.name
return fout_hq.file.name,fout_lq.file.name,prefix_dict_hq,prefix_dict_lq
def combine_quiver_results(split_dirs, output_dir, hq_filename, lq_filename, tofu_prefix=''):
"""
For each size bin result, ex: clusterOut/0to2k/all.quiveredXXX.fastq
combine it together, remember to add a prefix (ex: i0|c12, i1|c13/....)
"""
prefix_dict_hq = {}
prefix_dict_lq = {}
fout_hq = FastqWriter(os.path.join(output_dir, 'all_sizes.quivered_hq.fastq'))
fout_lq = FastqWriter(os.path.join(output_dir, 'all_sizes.quivered_lq.fastq'))
for i,d in enumerate(split_dirs):
file_hq = os.path.join(d, hq_filename) #'all_quivered_hq.100_30_0.99.fastq')
file_lq = os.path.join(d, lq_filename) #'all_quivered_lq.fastq')
print >> sys.stderr, "Adding prefix i{0}| to {1},{2}...".format(i, file_hq, file_lq)
prefix_dict_hq["i{i}HQ_{p}".format(i=i,p=tofu_prefix)] = os.path.abspath(d)
prefix_dict_lq["i{i}LQ_{p}".format(i=i,p=tofu_prefix)] = os.path.abspath(d)
for r in FastqReader(file_hq):
_name_ = "i{i}HQ_{p}|{n}".format(p=tofu_prefix, i=i, n=r.name)
fout_hq.writeRecord(_name_, r.sequence, r.quality)
for r in FastqReader(file_lq):
_name_ = "i{i}LQ_{p}|{n}".format(p=tofu_prefix, i=i, n=r.name)
fout_lq.writeRecord(_name_, r.sequence, r.quality)
fout_hq.close()
fout_lq.close()
print >> sys.stderr, "HQ quivered output combined to:", fout_hq.file.name
print >> sys.stderr, "LQ quivered output combined to:", fout_lq.file.name
return fout_hq.file.name,fout_lq.file.name,prefix_dict_hq,prefix_dict_lq
def pick_rep(fa_fq_filename,
gff_filename,
group_filename,
output_filename,
is_fq=False,
pick_least_err_instead=True):
"""
For each group, select the representative record
If is FASTA file (is_fa False) -- then always pick the longest one
If is FASTQ file (is_fq True) -- then
If pick_least_err_instead is True, pick the one w/ least number of expected base errors
Else, pick the longest one
"""
if is_fq:
fd = LazyFastqReader(fa_fq_filename)
fout = FastqWriter(output_filename)
else:
fd = LazyFastaReader(fa_fq_filename)
fout = FastaWriter(output_filename)
coords = {}
for line in open(gff_filename):
# ex: chr1 PacBio transcript 27567 29336 . - . gene_id "PB.1"; transcript_id "PB.1.1";
raw = line.strip().split('\t')
if raw[2] == 'transcript':
tid = raw[-1].split('; ')[1].split()[1][1:-2]
coords[tid] = "{0}:{1}-{2}({3})".format(raw[0], raw[3], raw[4],
raw[6])
for line in open(group_filename):
pb_id, members = line.strip().split('\t')
print >> sys.stderr, "Picking representative sequence for", pb_id
best_id = None
best_seq = None
best_qual = None
best_err = 9999999
err = 9999999
max_len = 0
for x in members.split(','):
if is_fq and pick_least_err_instead:
err = sum(i**-(i / 10.) for i in fd[x].quality)
if (is_fq and pick_least_err_instead and err < best_err) or (
(not is_fq or not pick_least_err_instead)
and len(fd[x].sequence) >= max_len):
best_id = x
best_seq = fd[x].sequence
if is_fq:
best_qual = fd[x].quality
best_err = err
max_len = len(fd[x].sequence)
_id_ = "{0}|{1}|{2}".format(pb_id, coords[pb_id], best_id)
_seq_ = best_seq
if is_fq:
fout.writeRecord(_id_, _seq_, best_qual)
else:
fout.writeRecord(_id_, _seq_)
fout.close()
def pick_rep(fa_fq_filename, gff_filename, group_filename, output_filename, is_fq=False, pick_least_err_instead=False, bad_gff_filename=None):
"""
For each group, select the representative record
If is FASTA file (is_fa False) -- then always pick the longest one
If is FASTQ file (is_fq True) -- then
If pick_least_err_instead is True, pick the one w/ least number of expected base errors
Else, pick the longest one
"""
if is_fq:
fd = LazyFastqReader(fa_fq_filename)
fout = FastqWriter(output_filename)
else:
fd = LazyFastaReader(fa_fq_filename)
fout = FastaWriter(output_filename)
coords = {}
for line in open(gff_filename):
# ex: chr1 PacBio transcript 27567 29336 . - . gene_id "PB.1"; transcript_id "PB.1.1";
raw = line.strip().split('\t')
if raw[2] == 'transcript':
tid = raw[-1].split('; ')[1].split()[1][1:-2]
coords[tid] = "{0}:{1}-{2}({3})".format(raw[0], raw[3], raw[4], raw[6])
if bad_gff_filename is not None:
for line in open(bad_gff_filename):
raw = line.strip().split('\t')
if raw[2] == 'transcript':
tid = raw[-1].split('; ')[1].split()[1][1:-2]
coords[tid] = "{0}:{1}-{2}({3})".format(raw[0], raw[3], raw[4], raw[6])
for line in open(group_filename):
pb_id, members = line.strip().split('\t')
print >> sys.stderr, "Picking representative sequence for", pb_id
best_id = None
best_seq = None
best_qual = None
best_err = 9999999
err = 9999999
max_len = 0
for x in members.split(','):
if is_fq and pick_least_err_instead:
err = sum(i**-(i/10.) for i in fd[x].quality)
if (is_fq and pick_least_err_instead and err < best_err) or ((not is_fq or not pick_least_err_instead) and len(fd[x].sequence) >= max_len):
best_id = x
best_seq = fd[x].sequence
if is_fq:
best_qual = fd[x].quality
best_err = err
max_len = len(fd[x].sequence)
_id_ = "{0}|{1}|{2}".format(pb_id, coords[pb_id], best_id)
_seq_ = best_seq
if is_fq:
fout.writeRecord(_id_, _seq_, best_qual)
else:
fout.writeRecord(_id_, _seq_)
fout.close()
class QualityFilter(object):
"""
A tool for filtering out low-quality fastq files
"""
def __init__(self, input_fastq, output_fastq, min_accuracy=MIN_ACCURACY):
self.input_reader = FastqReader(input_fastq)
self.output_writer = FastqWriter(output_fastq)
self.min_accuracy = min_accuracy
def __call__(self):
for fastq in self.input_reader:
if predicted_accuracy(fastq) >= self.min_accuracy:
self.output_writer.writeRecord(fastq)
class QualityFilter( object ):
"""
A tool for filtering out low-quality fastq files
"""
def __init__(self, input_fastq, output_fastq, min_accuracy=MIN_ACCURACY):
self.input_reader = FastqReader(input_fastq)
self.output_writer = FastqWriter(output_fastq)
self.min_accuracy = min_accuracy
def __call__(self):
for fastq in self.input_reader:
if predicted_accuracy(fastq) >= self.min_accuracy:
self.output_writer.writeRecord( fastq )
class BarcodeTrimmer( object ):
def __init__( self, input_file, barcode_file, prefix=None, filetype=None ):
self.input_file = input_file
self.barcode_file = barcode_file
self.prefix = prefix or get_prefix( input_file )
self.filetype = filetype or get_filetype( input_file )
self.positions = {}
def run( self ):
self.parse_barcode_data()
self.open_reader()
self.open_writer()
self.trim_sequences()
def parse_barcode_data( self ):
with open( self.barcode_file ) as handle:
for entry in map(barcode._make, csv.reader(handle, delimiter='\t')):
if entry.id == 'ID':
continue
start = None if entry.end5 == 'NA' else int(entry.end5)
end = None if entry.end3 == 'NA' else int(entry.end3)
self.positions[entry.id] = (start, end)
def open_reader( self ):
if self.filetype == 'fasta':
self.reader = FastaReader( self.input_file )
elif self.filetype == 'fastq':
self.reader = FastqReader( self.input_file )
def open_writer( self ):
if self.filetype == 'fasta':
output_file = '%s.trim.fasta' % self.prefix
self.writer = FastaWriter( output_file )
elif self.filetype == 'fastq':
output_file = '%s.trim.fastq' % self.prefix
self.writer = FastqWriter( output_file )
def trim_sequences( self ):
for record in self.reader:
try:
start, end = self.positions[record.name]
except:
msg = 'Unknown sequence record "%s"!' % record.name
log.error( msg )
raise ValueError( msg )
trimmed_record = trim_record( record, start, end )
self.writer.writeRecord( trimmed_record )
class BarcodeTrimmer(object):
def __init__(self, input_file, barcode_file, prefix=None, filetype=None):
self.input_file = input_file
self.barcode_file = barcode_file
self.prefix = prefix or get_prefix(input_file)
self.filetype = filetype or get_filetype(input_file)
self.positions = {}
def run(self):
self.parse_barcode_data()
self.open_reader()
self.open_writer()
self.trim_sequences()
def parse_barcode_data(self):
with open(self.barcode_file) as handle:
for entry in map(barcode._make, csv.reader(handle,
delimiter='\t')):
if entry.id == 'ID':
continue
start = None if entry.end5 == 'NA' else int(entry.end5)
end = None if entry.end3 == 'NA' else int(entry.end3)
self.positions[entry.id] = (start, end)
def open_reader(self):
if self.filetype == 'fasta':
self.reader = FastaReader(self.input_file)
elif self.filetype == 'fastq':
self.reader = FastqReader(self.input_file)
def open_writer(self):
if self.filetype == 'fasta':
output_file = '%s.trim.fasta' % self.prefix
self.writer = FastaWriter(output_file)
elif self.filetype == 'fastq':
output_file = '%s.trim.fastq' % self.prefix
self.writer = FastqWriter(output_file)
def trim_sequences(self):
for record in self.reader:
try:
start, end = self.positions[record.name]
except:
msg = 'Unknown sequence record "%s"!' % record.name
log.error(msg)
raise ValueError(msg)
trimmed_record = trim_record(record, start, end)
self.writer.writeRecord(trimmed_record)
def pick_rep(fa_fq_filename,
sam_filename,
gff_filename,
group_filename,
output_filename,
is_fq=False,
pick_least_err_instead=False):
"""
For each group, select the representative record
If is FASTA file (is_fa False) -- then always pick the longest one
If is FASTQ file (is_fq True) -- then
If pick_least_err_instead is True, pick the one w/ least number of expected base errors
Else, pick the longest one
"""
if is_fq:
fd = LazyFastqReader(fa_fq_filename)
fout = FastqWriter(output_filename)
else:
fd = LazyFastaReader(fa_fq_filename)
fout = FastaWriter(output_filename)
# for line in open(gff_filename):
# # ex: chr1 PacBio transcript 27567 29336 . - . gene_id "PBfusion.1"; transcript_id "PBfusion.1.1";
# raw = line.strip().split('\t')
# if raw[2] == 'transcript':
# # check if this is first or 2+ part of fusion
# tid = raw[-1].split('; ')[1].split()[1][1:-2] # ex: tid = PBfusion.1.1
# gid = tid[:tid.rfind('.')] # ex: gid = PBfusion.1
# if tid.endswith('.1'):
# coords[gid] = "{0}:{1}-{2}({3})".format(raw[0], raw[3], raw[4], raw[6])
# else:
# assert gid in coords
# coords[gid] += "+{0}:{1}-{2}({3})".format(raw[0], raw[3], raw[4], raw[6])
rep_info = {}
id_to_rep = {}
for line in open(group_filename):
pb_id, members = line.strip().split('\t')
print >> sys.stderr, "Picking representative sequence for", pb_id
best_id = None
best_seq = None
best_qual = None
best_err = 9999999
err = 9999999
max_len = 0
for x in members.split(','):
if is_fq and pick_least_err_instead:
err = sum(i**-(i / 10.) for i in fd[x].quality)
if (is_fq and pick_least_err_instead and err < best_err) or (
(not is_fq or not pick_least_err_instead)
and len(fd[x].sequence) >= max_len):
best_id = x
best_seq = fd[x].sequence
if is_fq:
best_qual = fd[x].quality
best_err = err
max_len = len(fd[x].sequence)
rep_info[pb_id] = (best_id, best_seq, best_qual)
id_to_rep[best_id] = pb_id
f_gff = open(gff_filename, 'w')
coords = {}
record_storage = {
} # temporary storage for the .1 record to write in conjunction with second record
for r in BioReaders.GMAPSAMReader(sam_filename, True):
if r.qID in id_to_rep:
pb_id = id_to_rep[r.qID]
best_id, best_seq, best_qual = rep_info[pb_id]
# make coordinates & write the SAM file
if r.qID not in coords:
# this is the .1 portion
coords[r.qID] = "{0}:{1}-{2}({3})".format(
r.sID, r.sStart, r.sEnd, r.flag.strand)
isoform_index = 1
record_storage[pb_id] = r
else:
# this is the .2 portion
coords[r.qID] += "+{0}:{1}-{2}({3})".format(
r.sID, r.sStart, r.sEnd, r.flag.strand)
isoform_index = 1
old_r = record_storage[pb_id]
f_gff.write("{chr}\tPacBio\ttranscript\t{s}\t{e}\t.\t{strand}\t.\tgene_id \"{pi}\"; transcript_id \"{pi}.{j}\";\n".format(\
chr=old_r.sID, s=old_r.segments[0].start+1, e=old_r.segments[-1].end, pi=pb_id, j=isoform_index, strand=old_r.flag.strand))
for s in old_r.segments:
f_gff.write("{chr}\tPacBio\texon\t{s}\t{e}\t.\t{strand}\t.\tgene_id \"{pi}\"; transcript_id \"{pi}.{j}\";\n".format(\
chr=old_r.sID, s=s.start+1, e=s.end, pi=pb_id, j=isoform_index, strand=old_r.flag.strand))
isoform_index = 2
f_gff.write("{chr}\tPacBio\ttranscript\t{s}\t{e}\t.\t{strand}\t.\tgene_id \"{pi}\"; transcript_id \"{pi}.{j}\";\n".format(\
chr=r.sID, s=r.segments[0].start+1, e=r.segments[-1].end, pi=pb_id, j=isoform_index, strand=r.flag.strand))
for s in r.segments:
f_gff.write("{chr}\tPacBio\texon\t{s}\t{e}\t.\t{strand}\t.\tgene_id \"{pi}\"; transcript_id \"{pi}.{j}\";\n".format(\
chr=r.sID, s=s.start+1, e=s.end, pi=pb_id, j=isoform_index, strand=r.flag.strand))
f_gff.close()
for pb_id in rep_info:
best_id, best_seq, best_qual = rep_info[pb_id]
_id_ = "{0}|{1}|{2}".format(pb_id, coords[best_id], best_id)
_seq_ = best_seq
if is_fq:
fout.writeRecord(_id_, _seq_, best_qual)
else:
fout.writeRecord(_id_, _seq_)
def main():
from argparse import ArgumentParser
parser = ArgumentParser()
parser.add_argument("input_prefix", help="Input prefix")
parser.add_argument("output_prefix", help="Output prefix")
parser.add_argument("--fuzzy_junction", type=int, default=5, help="Fuzzy junction max dist (default: 5bp)")
args = parser.parse_args()
#group_filename = args.input_prefix + '.group.txt'
count_filename = args.input_prefix + '.abundance.txt'
gff_filename = args.input_prefix + '.gff'
rep_filename = args.input_prefix + '.rep.fq'
recs = defaultdict(lambda: [])
reader = GFF.collapseGFFReader(gff_filename)
for r in reader:
assert r.seqid.startswith('PB.')
recs[int(r.seqid.split('.')[1])].append(r)
good = []
f = open(args.output_prefix + '.gff', 'w')
keys = recs.keys()
keys.sort()
for k in recs:
xxx = recs[k]
filter_out_subsets(xxx, args.fuzzy_junction)
for r in xxx:
GFF.write_collapseGFF_format(f, r)
good.append(r.seqid)
f.close()
# read abundance first
f = open(count_filename)
count_header = ''
while True:
cur_pos = f.tell()
line = f.readline()
if not line.startswith('#'):
f.seek(cur_pos)
break
else:
count_header += line
d = dict((r['pbid'], r) for r in DictReader(f, delimiter='\t'))
for k,v in d.iteritems():
print k,v
f.close()
# write output rep.fq
f = FastqWriter(args.output_prefix + '.rep.fq')
for r in FastqReader(rep_filename):
if r.name.split('|')[0] in good:
f.writeRecord(r)
f.close()
# write output to .abundance.txt
f = open(args.output_prefix + '.abundance.txt', 'w')
f.write(count_header)
writer = DictWriter(f, fieldnames=['pbid','count_fl','count_nfl','count_nfl_amb','norm_fl','norm_nfl','norm_nfl_amb'], \
delimiter='\t', lineterminator='\n')
writer.writeheader()
for k in good:
r = d[k]
writer.writerow(r)
f.close()
def pick_rep(fa_fq_filename, sam_filename, gff_filename, group_filename, output_filename, is_fq=False, pick_least_err_instead=False):
"""
For each group, select the representative record
If is FASTA file (is_fa False) -- then always pick the longest one
If is FASTQ file (is_fq True) -- then
If pick_least_err_instead is True, pick the one w/ least number of expected base errors
Else, pick the longest one
"""
if is_fq:
fd = LazyFastqReader(fa_fq_filename)
fout = FastqWriter(output_filename)
else:
fd = LazyFastaReader(fa_fq_filename)
fout = FastaWriter(output_filename)
# for line in open(gff_filename):
# # ex: chr1 PacBio transcript 27567 29336 . - . gene_id "PBfusion.1"; transcript_id "PBfusion.1.1";
# raw = line.strip().split('\t')
# if raw[2] == 'transcript':
# # check if this is first or 2+ part of fusion
# tid = raw[-1].split('; ')[1].split()[1][1:-2] # ex: tid = PBfusion.1.1
# gid = tid[:tid.rfind('.')] # ex: gid = PBfusion.1
# if tid.endswith('.1'):
# coords[gid] = "{0}:{1}-{2}({3})".format(raw[0], raw[3], raw[4], raw[6])
# else:
# assert gid in coords
# coords[gid] += "+{0}:{1}-{2}({3})".format(raw[0], raw[3], raw[4], raw[6])
rep_info = {}
id_to_rep = {}
for line in open(group_filename):
pb_id, members = line.strip().split('\t')
print >> sys.stderr, "Picking representative sequence for", pb_id
best_id = None
best_seq = None
best_qual = None
best_err = 9999999
err = 9999999
max_len = 0
for x in members.split(','):
if is_fq and pick_least_err_instead:
err = sum(i**-(i/10.) for i in fd[x].quality)
if (is_fq and pick_least_err_instead and err < best_err) or ((not is_fq or not pick_least_err_instead) and len(fd[x].sequence) >= max_len):
best_id = x
best_seq = fd[x].sequence
if is_fq:
best_qual = fd[x].quality
best_err = err
max_len = len(fd[x].sequence)
rep_info[pb_id] = (best_id, best_seq, best_qual)
id_to_rep[best_id] = pb_id
f_gff = open(gff_filename, 'w')
coords = {}
record_storage = {} # temporary storage for the .1 record to write in conjunction with second record
for r in BioReaders.GMAPSAMReader(sam_filename, True):
if r.qID in id_to_rep:
pb_id = id_to_rep[r.qID]
best_id, best_seq, best_qual = rep_info[pb_id]
# make coordinates & write the SAM file
if r.qID not in coords:
# this is the .1 portion
coords[r.qID] = "{0}:{1}-{2}({3})".format(r.sID, r.sStart, r.sEnd, r.flag.strand)
isoform_index = 1
record_storage[pb_id] = r
else:
# this is the .2 portion
coords[r.qID] += "+{0}:{1}-{2}({3})".format(r.sID, r.sStart, r.sEnd, r.flag.strand)
isoform_index = 1
old_r = record_storage[pb_id]
f_gff.write("{chr}\tPacBio\ttranscript\t{s}\t{e}\t.\t{strand}\t.\tgene_id \"{pi}\"; transcript_id \"{pi}.{j}\";\n".format(\
chr=old_r.sID, s=old_r.segments[0].start+1, e=old_r.segments[-1].end, pi=pb_id, j=isoform_index, strand=old_r.flag.strand))
for s in old_r.segments:
f_gff.write("{chr}\tPacBio\texon\t{s}\t{e}\t.\t{strand}\t.\tgene_id \"{pi}\"; transcript_id \"{pi}.{j}\";\n".format(\
chr=old_r.sID, s=s.start+1, e=s.end, pi=pb_id, j=isoform_index, strand=old_r.flag.strand))
isoform_index = 2
f_gff.write("{chr}\tPacBio\ttranscript\t{s}\t{e}\t.\t{strand}\t.\tgene_id \"{pi}\"; transcript_id \"{pi}.{j}\";\n".format(\
chr=r.sID, s=r.segments[0].start+1, e=r.segments[-1].end, pi=pb_id, j=isoform_index, strand=r.flag.strand))
for s in r.segments:
f_gff.write("{chr}\tPacBio\texon\t{s}\t{e}\t.\t{strand}\t.\tgene_id \"{pi}\"; transcript_id \"{pi}.{j}\";\n".format(\
chr=r.sID, s=s.start+1, e=s.end, pi=pb_id, j=isoform_index, strand=r.flag.strand))
f_gff.close()
for pb_id in rep_info:
best_id, best_seq, best_qual = rep_info[pb_id]
_id_ = "{0}|{1}|{2}".format(pb_id, coords[best_id], best_id)
_seq_ = best_seq
if is_fq:
fout.writeRecord(_id_, _seq_, best_qual)
else:
fout.writeRecord(_id_, _seq_)
def filter_by_count(input_prefix, output_prefix, min_count):
group_filename = input_prefix + ".group.txt"
count_filename = input_prefix + ".abundance.txt"
gff_filename = input_prefix + ".gff"
rep_filename = input_prefix + ".rep.fq"
# read group
group_max_count_fl = {}
group_max_count_p = {}
f = open(group_filename)
for line in f:
# ex: PB.1.1 i0HQ_54b0ca|c58773/f30p16/700
pbid, members = line.strip().split("\t")
group_max_count_fl[pbid] = 0
group_max_count_p[pbid] = 0
members = members.split(",")
for m in members:
tmp = m.split("|")[1].split("/")[1] # ex: tmp = f30p16
fl_count, p_count = tmp.split("p")
fl_count = int(fl_count[1:])
p_count = int(p_count)
group_max_count_fl[pbid] = max(group_max_count_fl[pbid], fl_count)
group_max_count_p[pbid] = max(group_max_count_p[pbid], p_count)
f.close()
# read abundance first
f = open(count_filename)
count_header = ""
while True:
cur_pos = f.tell()
line = f.readline()
if not line.startswith("#"):
f.seek(cur_pos)
break
else:
count_header += line
d = dict((r["pbid"], r) for r in DictReader(f, delimiter="\t"))
for k, v in d.iteritems():
print k, v
f.close()
# group_max_count_p NOT used for now
good = filter(
lambda x: int(d[x]["count_fl"]) >= min_count and group_max_count_fl[x] >= min_count and group_max_count_p >= 0,
d,
)
# write output GFF
f = open(output_prefix + ".gff", "w")
for r in GFF.collapseGFFReader(gff_filename):
if r.seqid in good:
GFF.write_collapseGFF_format(f, r)
f.close()
# write output rep.fq
f = FastqWriter(output_prefix + ".rep.fq")
for r in FastqReader(rep_filename):
if r.name.split("|")[0] in good:
f.writeRecord(r)
f.close()
# write output to .abundance.txt
f = open(output_prefix + ".abundance.txt", "w")
f.write(count_header)
writer = DictWriter(
f,
fieldnames=["pbid", "count_fl", "count_nfl", "count_nfl_amb", "norm_fl", "norm_nfl", "norm_nfl_amb"],
delimiter="\t",
lineterminator="\n",
)
writer.writeheader()
for k in good:
r = d[k]
writer.writerow(r)
f.close()
def filter_by_count(input_prefix, output_prefix, min_count):
group_filename = input_prefix + '.group.txt'
count_filename = input_prefix + '.abundance.txt'
gff_filename = input_prefix + '.gff'
rep_filename = input_prefix + '.rep.fq'
# read group
group_max_count_fl = {}
group_max_count_p = {}
f = open(group_filename)
for line in f:
#ex: PB.1.1 i0HQ_54b0ca|c58773/f30p16/700
pbid, members = line.strip().split('\t')
group_max_count_fl[pbid] = 0
group_max_count_p[pbid] = 0
members = members.split(',')
for m in members:
tmp = m.split('|')[1].split('/')[1] #ex: tmp = f30p16
fl_count, p_count = tmp.split('p')
fl_count = int(fl_count[1:])
p_count = int(p_count)
group_max_count_fl[pbid] = max(group_max_count_fl[pbid], fl_count)
group_max_count_p[pbid] = max(group_max_count_p[pbid], p_count)
f.close()
# read abundance first
f = open(count_filename)
count_header = ''
while True:
cur_pos = f.tell()
line = f.readline()
if not line.startswith('#'):
f.seek(cur_pos)
break
else:
count_header += line
d = dict((r['pbid'], r) for r in DictReader(f, delimiter='\t'))
for k, v in d.iteritems():
print k, v
f.close()
# group_max_count_p NOT used for now
good = filter(
lambda x: int(d[x]['count_fl']) >= min_count and group_max_count_fl[x]
>= min_count and group_max_count_p >= 0, d)
# write output GFF
f = open(output_prefix + '.gff', 'w')
for r in GFF.collapseGFFReader(gff_filename):
if r.seqid in good: GFF.write_collapseGFF_format(f, r)
f.close()
# write output rep.fq
f = FastqWriter(output_prefix + '.rep.fq')
for r in FastqReader(rep_filename):
if r.name.split('|')[0] in good:
f.writeRecord(r)
f.close()
# write output to .abundance.txt
f = open(output_prefix + '.abundance.txt', 'w')
f.write(count_header)
writer = DictWriter(f, fieldnames=['pbid','count_fl','count_nfl','count_nfl_amb','norm_fl','norm_nfl','norm_nfl_amb'], \
delimiter='\t', lineterminator='\n')
writer.writeheader()
for k in good:
r = d[k]
writer.writerow(r)
f.close()
