def main():
parser = argparse.ArgumentParser( description='Report coverage gaps/dips from a samtools mpileup file')
## output file to be written
parser.add_argument('-i', '--input_file', type=str, required=True, help='Path to an input mpileup file to be read' )
parser.add_argument('-o', '--output_file', type=str, required=False, help='Path to an output file to be created' )
parser.add_argument('-f', '--fasta_file', type=str, required=True, help='Reference fasta file, against which reads were aligned. Needed for low 3-prime end coverage' )
parser.add_argument('-mcd', '--min_coverage_depth', type=int, required=True, help='Min coverage depth, below which is reported' )
parser.add_argument('-mcs', '--min_coverage_span', type=int, required=False, help='Coverage window size, the avg of which is calculated for depth cutoff' )
parser.add_argument('-eb', '--end_buffer', type=int, required=False, default=0, help='If specified, gaps this far from either end of the molecule will not be reported.' )
args = parser.parse_args()
# Check, this isn't ready yet:
if args.min_coverage_span is not None:
raise Exception("ERROR: Sorry, --min_coverage_span not yet implemented.")
if args.output_file is None:
out_fh = sys.stdout
else:
out_fh = open(args.output_file, 'wt')
lengths = utils.fasta_sizes_from_file(args.fasta_file)
stats = {'total_molecules': 0, 'total_bases': 0, 'depth_sum': 0}
# In mpileup gaps are reported either with positions of coverage 0 OR omitted rows.
depths = list()
current_seq_id = None
for line in open(args.input_file):
contig, this_coord, base, depth = line.split("\t")[0:4]
this_coord = int(this_coord)
# new molecule
if contig != current_seq_id:
stats['total_molecules'] += 1
# purge the last one
if current_seq_id != None:
print_spans(current_seq_id, depths, args.min_coverage_depth, out_fh, stats, lengths, args.end_buffer)
depths = [0] * lengths[contig]
current_seq_id = contig
depths[this_coord - 1] = depth
print_spans(current_seq_id, depths, args.min_coverage_depth, out_fh, stats, lengths, args.end_buffer)
print("INFO: Total molecules: {0}".format(stats['total_molecules']), file=sys.stderr)
print("INFO: Total bases : {0}".format(stats['total_bases']), file=sys.stderr)
print("INFO: Avg cov depth : {0}x".format(int(stats['depth_sum'] / stats['total_bases'])), file=sys.stderr)
def main():
parser = argparse.ArgumentParser( description='Parse BLAST output and report coverage of queries')
## output file to be written
parser.add_argument('-f', '--fasta_file', type=str, required=True, help='FASTA file of query.fasta (for lengths)' )
parser.add_argument('-b', '--blast_file', type=str, required=True, help='BLAST output using -m 8 or -m 9 options' )
#parser.add_argument('-e', '--evalue_cutoff', type=str, required=False, help='E-value cutoff' )
parser.add_argument('-slpc', '--subject_length_percentage_cutoff', type=int, required=False, help='Ignore hits from transcripts of length > N% relative to the query transcript' )
parser.add_argument('-sf', '--subject_fasta', type=str, required=False, help='Only required if -slpc is passed. FASTA file of the sub' )
parser.add_argument('-o', '--output_base', type=str, required=True, help='base name/path for output. Two files starting with this will be created' )
args = parser.parse_args()
qsizes = utils.fasta_sizes_from_file(args.fasta_file)
if args.subject_fasta is not None:
ssizes = utils.fasta_sizes_from_file(args.subject_fasta)
all_fh = open("{0}.cov.all.perc.txt".format(args.output_base), 'wt')
longest_fh = open("{0}.cov.longest.perc.txt".format(args.output_base), 'wt')
current_query_id = None
covs_all = None
match_segments = dict()
longest_match_length = None
for line in open(args.blast_file):
if line.startswith('#'): continue
line = line.rstrip()
cols = line.split("\t")
query_id = cols[0]
subj_id = cols[1]
qstart = int(cols[6])
qend = int(cols[7])
if args.subject_length_percentage_cutoff is not None:
perc_length_diff = (ssizes[subj_id] / qsizes[query_id]) * 100
if perc_length_diff > args.subject_length_percentage_cutoff:
continue
if query_id != current_query_id:
if current_query_id is not None:
# report last coverage
# first the 'all' coverage
all_cov_perc = (qsizes[current_query_id] - covs_all.count(0)) / qsizes[current_query_id]
all_fh.write("{0}\t{1:.1f}\n".format(current_query_id, all_cov_perc * 100))
# now the 'longest' coverage
longest_cov_transcript_id = None
longest_cov_perc = None
for tid in match_segments:
# calculate coverage of this tid
this_cov = [0] * qsizes[current_query_id]
for seg in match_segments[tid]:
for i in range(seg[0] - 1, seg[1]):
this_cov[i] += 1
this_cov_perc = (len(this_cov) - this_cov.count(0)) / len(this_cov)
if longest_cov_perc is None or this_cov_perc > longest_cov_perc:
longest_cov_perc = this_cov_perc
longest_cov_transcript_id = tid
print("LOG: transcript {0} covers {1} (len:{3}) best at {2:.1f}%".format(longest_cov_transcript_id, current_query_id, longest_cov_perc * 100, len(this_cov)))
longest_fh.write("{0}\t{1:.1f}\t{2}\n".format(current_query_id, longest_cov_perc * 100, longest_cov_transcript_id))
# now reset and init this transcript
current_query_id = query_id
covs_all = [0] * qsizes[query_id]
longest_match_length = None
match_segments = dict()
# now handle this row
if subj_id not in match_segments:
match_segments[subj_id] = list()
match_segments[subj_id].append([qstart, qend])
for i in range(qstart - 1, qend):
covs_all[i] += 1
# handle last ones
# first the 'all' coverage
all_cov_perc = (qsizes[current_query_id] - covs_all.count(0)) / qsizes[current_query_id]
all_fh.write("{0}\t{1:.1f}\n".format(current_query_id, all_cov_perc * 100))
# now the 'longest' coverage
longest_cov_transcript_id = None
longest_cov_perc = None
for tid in match_segments:
# calculate coverage of this tid
this_cov = [0] * qsizes[current_query_id]
for seg in match_segments[tid]:
for i in range(seg[0] - 1, seg[1]):
this_cov[i] += 1
this_cov_perc = (len(this_cov) - this_cov.count(0)) / len(this_cov)
if longest_cov_perc is None or this_cov_perc > longest_cov_perc:
longest_cov_perc = this_cov_perc
longest_cov_transcript_id = tid
print("LOG: transcript {0} covers {1} (len:{3}) best at {2:.1f}%".format(longest_cov_transcript_id, current_query_id, longest_cov_perc * 100, len(this_cov)))
longest_fh.write("{0}\t{1:.1f}\n".format(current_query_id, longest_cov_perc * 100))
all_fh.close()
longest_fh.close()
def main():
parser = argparse.ArgumentParser(
description='Parse BLAST output and report coverage of queries')
## output file to be written
parser.add_argument('-f',
'--fasta_file',
type=str,
required=True,
help='FASTA file of query.fasta (for lengths)')
parser.add_argument('-b',
'--blast_file',
type=str,
required=True,
help='BLAST output using -m 8 or -m 9 options')
#parser.add_argument('-e', '--evalue_cutoff', type=str, required=False, help='E-value cutoff' )
parser.add_argument(
'-slpc',
'--subject_length_percentage_cutoff',
type=int,
required=False,
help=
'Ignore hits from transcripts of length > N% relative to the query transcript'
)
parser.add_argument(
'-sf',
'--subject_fasta',
type=str,
required=False,
help='Only required if -slpc is passed. FASTA file of the sub')
parser.add_argument(
'-o',
'--output_base',
type=str,
required=True,
help=
'base name/path for output. Two files starting with this will be created'
)
args = parser.parse_args()
qsizes = utils.fasta_sizes_from_file(args.fasta_file)
if args.subject_fasta is not None:
ssizes = utils.fasta_sizes_from_file(args.subject_fasta)
all_fh = open("{0}.cov.all.perc.txt".format(args.output_base), 'wt')
longest_fh = open("{0}.cov.longest.perc.txt".format(args.output_base),
'wt')
current_query_id = None
covs_all = None
match_segments = dict()
longest_match_length = None
for line in open(args.blast_file):
if line.startswith('#'): continue
line = line.rstrip()
cols = line.split("\t")
query_id = cols[0]
subj_id = cols[1]
qstart = int(cols[6])
qend = int(cols[7])
if args.subject_length_percentage_cutoff is not None:
perc_length_diff = (ssizes[subj_id] / qsizes[query_id]) * 100
if perc_length_diff > args.subject_length_percentage_cutoff:
continue
if query_id != current_query_id:
if current_query_id is not None:
# report last coverage
# first the 'all' coverage
all_cov_perc = (qsizes[current_query_id] -
covs_all.count(0)) / qsizes[current_query_id]
all_fh.write("{0}\t{1:.1f}\n".format(current_query_id,
all_cov_perc * 100))
# now the 'longest' coverage
longest_cov_transcript_id = None
longest_cov_perc = None
for tid in match_segments:
# calculate coverage of this tid
this_cov = [0] * qsizes[current_query_id]
for seg in match_segments[tid]:
for i in range(seg[0] - 1, seg[1]):
this_cov[i] += 1
this_cov_perc = (len(this_cov) -
this_cov.count(0)) / len(this_cov)
if longest_cov_perc is None or this_cov_perc > longest_cov_perc:
longest_cov_perc = this_cov_perc
longest_cov_transcript_id = tid
print(
"LOG: transcript {0} covers {1} (len:{3}) best at {2:.1f}%"
.format(longest_cov_transcript_id, current_query_id,
longest_cov_perc * 100, len(this_cov)))
longest_fh.write("{0}\t{1:.1f}\t{2}\n".format(
current_query_id, longest_cov_perc * 100,
longest_cov_transcript_id))
# now reset and init this transcript
current_query_id = query_id
covs_all = [0] * qsizes[query_id]
longest_match_length = None
match_segments = dict()
# now handle this row
if subj_id not in match_segments:
match_segments[subj_id] = list()
match_segments[subj_id].append([qstart, qend])
for i in range(qstart - 1, qend):
covs_all[i] += 1
# handle last ones
# first the 'all' coverage
all_cov_perc = (qsizes[current_query_id] -
covs_all.count(0)) / qsizes[current_query_id]
all_fh.write("{0}\t{1:.1f}\n".format(current_query_id, all_cov_perc * 100))
# now the 'longest' coverage
longest_cov_transcript_id = None
longest_cov_perc = None
for tid in match_segments:
# calculate coverage of this tid
this_cov = [0] * qsizes[current_query_id]
for seg in match_segments[tid]:
for i in range(seg[0] - 1, seg[1]):
this_cov[i] += 1
this_cov_perc = (len(this_cov) - this_cov.count(0)) / len(this_cov)
if longest_cov_perc is None or this_cov_perc > longest_cov_perc:
longest_cov_perc = this_cov_perc
longest_cov_transcript_id = tid
print("LOG: transcript {0} covers {1} (len:{3}) best at {2:.1f}%".format(
longest_cov_transcript_id, current_query_id, longest_cov_perc * 100,
len(this_cov)))
longest_fh.write("{0}\t{1:.1f}\n".format(current_query_id,
longest_cov_perc * 100))
all_fh.close()
longest_fh.close()
def main():
parser = argparse.ArgumentParser(
description='Report coverage gaps/dips from a samtools mpileup file')
## output file to be written
parser.add_argument('-i',
'--input_file',
type=str,
required=True,
help='Path to an input mpileup file to be read')
parser.add_argument('-o',
'--output_file',
type=str,
required=False,
help='Path to an output file to be created')
parser.add_argument(
'-f',
'--fasta_file',
type=str,
required=True,
help=
'Reference fasta file, against which reads were aligned. Needed for low 3-prime end coverage'
)
parser.add_argument('-mcd',
'--min_coverage_depth',
type=int,
required=True,
help='Min coverage depth, below which is reported')
parser.add_argument(
'-mcs',
'--min_coverage_span',
type=int,
required=False,
help=
'Coverage window size, the avg of which is calculated for depth cutoff'
)
parser.add_argument(
'-eb',
'--end_buffer',
type=int,
required=False,
default=0,
help=
'If specified, gaps this far from either end of the molecule will not be reported.'
)
args = parser.parse_args()
# Check, this isn't ready yet:
if args.min_coverage_span is not None:
raise Exception(
"ERROR: Sorry, --min_coverage_span not yet implemented.")
if args.output_file is None:
out_fh = sys.stdout
else:
out_fh = open(args.output_file, 'wt')
lengths = utils.fasta_sizes_from_file(args.fasta_file)
stats = {'total_molecules': 0, 'total_bases': 0, 'depth_sum': 0}
# In mpileup gaps are reported either with positions of coverage 0 OR omitted rows.
depths = list()
current_seq_id = None
for line in open(args.input_file):
contig, this_coord, base, depth = line.split("\t")[0:4]
this_coord = int(this_coord)
# new molecule
if contig != current_seq_id:
stats['total_molecules'] += 1
# purge the last one
if current_seq_id != None:
print_spans(current_seq_id, depths, args.min_coverage_depth,
out_fh, stats, lengths, args.end_buffer)
depths = [0] * lengths[contig]
current_seq_id = contig
depths[this_coord - 1] = depth
print_spans(current_seq_id, depths, args.min_coverage_depth, out_fh, stats,
lengths, args.end_buffer)
print("INFO: Total molecules: {0}".format(stats['total_molecules']),
file=sys.stderr)
print("INFO: Total bases : {0}".format(stats['total_bases']),
file=sys.stderr)
print("INFO: Avg cov depth : {0}x".format(
int(stats['depth_sum'] / stats['total_bases'])),
file=sys.stderr)
