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import sys
import os
import collections
import gzip
from subprocess import call
import re
from collections import defaultdict
from pybedtools import BedTool, create_interval_from_list
from pysam import AlignmentFile
import numpy as np
VERBOSE = True
def get_insert_size(bam):
"""
Compute mean insert size
:param bam: bam file
:type bam: str
:return: mean insert size
:rtype: int
"""
fbam = AlignmentFile(bam, "rb")
count = 0
isizes_raw = []
for read in fbam:
if read.is_proper_pair:
isizes_raw.append(np.abs(read.template_length))
count += 1
if count == 50000:
break
n99 = np.percentile(isizes_raw, 99)
n1 = np.percentile(isizes_raw, 1)
isizes = []
for isize in isizes_raw:
if n1 < isize < n99:
isizes.append(isize)
fbam.close()
return int(np.round(np.mean(np.round(isizes))))
def getChromLength(reference, chrom):
"""
Retrieve the length of chromosome chrom from .fai file
:param reference: the genome fasta file
:param chrom: the chromosome of interest
:type reference: file
:type chrom: str
:return: chromosome length
:rtype: int
"""
reference_fai = str(reference) + ".fai"
chroms = {}
if reference is not None and os.path.isfile(reference_fai):
with open(reference_fai) as fai_file:
for line in fai_file:
line_items = line.strip().split("\t")
name, length = line_items[0:2]
name = name.split(" ")[0]
chroms[name] = int(length)
if chrom not in chroms:
raise KeyError('the chromosome '+chrom+' is not in the *.fai file....')
return chroms[chrom]
def fetchId(bamfile):
"""
Fetch sample id in a bam file
:param bamfile: the bam file
:type bamfile: file
:return: sample name
:rtype: str
"""
bamfile_fin = AlignmentFile(bamfile, 'rb')
name = bamfile_fin.header['RG'][0]['SM']
bamfile_fin.close()
return name
_Contig = collections.namedtuple('Contig', ['name', 'length'])
def get_contigs(reference):
"""
Retrieve the contigs (chromosomes) from the genome fasta file
:param reference: the genome fasta file
:type reference: fasta filefile
:return: list of contigs in the format specified by PyCvf
:rtype: list
"""
contigs = []
reference_fai = str(reference) + ".fai"
if reference is not None and os.path.isfile(reference_fai):
with open(reference_fai) as fai_file:
for line in fai_file:
line_items = line.strip().split("\t")
name, length = line_items[0:2]
name = name.split(" ")[0]
contigs.append(_Contig(name, int(length)))
return contigs
def chromNum(chrom):
m = re.search(r"[cC]hr(?P<num>[\dXY]+)", chrom)
if m is not None:
if m.group('num') == 'X':
num = 100
elif m.group('num') == 'Y':
num = 101
else:
num = int(m.group('num'))
return num
else:
return chrom
def addContigInfosTovcf(vcffile, outvcffile, reference):
"""
Add contig infos to vcf
:param vcffile: input vcffile
:param outvcffile: output vcffile
:param reference: the reference genome fasta filefile
:type vcffile: file
:type outvcffile: vcffile
:type reference: fasta filefile
:return: nothing
"""
# compute contig information
contigs = get_contigs(reference)
filename, extension = os.path.splitext(outvcffile)
if extension == ".gz":
outputfile = filename
gzip = True
else:
outputfile = outvcffile
gzip = False
with open(outputfile, "w") as fout:
with smart_open(vcffile) as fd:
for line in fd:
if re.search(r"^##contig", line) is not None:
continue
if re.search(r"^#CHROM", line):
for ctg in sorted(contigs, key=lambda x: chromNum(x.name)):
fout.write('##contig=<ID=%s,length=%d>\n'
% (ctg.name, ctg.length))
fout.write(line)
# bgzip file
if gzip:
cmd = "bgzip -f "+outputfile
call(cmd, shell=True)
cmd = "tabix -p vcf " + outvcffile
call(cmd, shell=True)
def sorting(records, reference_contigs):
if reference_contigs:
contigs_order_dict = defaultdict()
for (index, contig) in enumerate(reference_contigs):
contigs_order_dict[contig.name] = index
records.sort(
key=lambda x: (contigs_order_dict[x.chrom], x.start))
else:
records.sort(key=lambda x: (x.chrom, x.start))
return records
def vcf_to_pybed(vcf_records):
"""
Convert vcf records to bed records
:param vcf_records: the vcf records
:type vcfrecords: a list of vcf records
:return: the corresponding betools records
:rtype: a bedtools object
"""
intervals = []
for record in vcf_records:
chrom = record.chrom
start = record.start - 1
end = record.end
name = record.id
interval_list = list(map(str, [chrom, start, end, name]))
intervals.append(create_interval_from_list(interval_list))
return BedTool(intervals).sort()
# A small wrapper to print to stderr
def eprint(*args, **kwargs):
if VERBOSE:
print(*args, file=sys.stderr, **kwargs)
def warn(*args, **kwargs):
print(*args, file=sys.stderr, **kwargs)
def log(objs):
print("-- log -- ", objs, file=sys.stderr)
def warning(*objs):
print("WARNING: ", *objs, file=sys.stderr)
def smart_open(file_name):
"""
Opening compressed or uncompressed file according to the extension (.gz)
:param file_name: the file to open
:type file_name: str
:return: the corresponding file handle
:rtype: a file handle
"""
if file_name is not None:
if file_name.endswith(".gz"):
file_fd = gzip.open(file_name, "rt")
else:
file_fd = open(file_name)
else:
file_fd = sys.stdin
return file_fd
def flatten(l):
for el in l:
if isinstance(el, collections.Iterable) and not isinstance(el, str):
for sub in flatten(el):
yield sub
else:
yield el