def crossmap_vcf_file(mapping,
infile,
outfile,
liftoverfile,
refgenome,
noCompAllele=False,
compress=False):
'''
Convert genome coordinates in VCF format.
Parameters
----------
mapping : dict
Dictionary with source chrom name as key, IntervalTree object as value.
infile : file
Input file in VCF format. Can be a regular or compressed (*.gz, *.Z,*.z, *.bz,
*.bz2, *.bzip2) file, local file or URL (http://, https://, ftp://) pointing to
remote file.
outfile : str
prefix of output files.
liftoverfile : file
Chain (https://genome.ucsc.edu/goldenPath/help/chain.html) format file. Can be a
regular or compressed (*.gz, *.Z,*.z, *.bz, *.bz2, *.bzip2) file, local file or
URL (http://, https://, ftp://) pointing to remote file.
refgenome : file
The genome sequence file of 'target' assembly in FASTA format.
noCompAllele : bool
A logical value indicates whether to compare ref_allele to alt_allele after
liftover. If True, the variant will be marked as "unmap" if
ref_allele == alt_allele.
'''
if noCompAllele:
printlog(
["Keep variants [reference_allele == alternative_allele] ..."])
else:
printlog([
"Filter out variants [reference_allele == alternative_allele] ..."
])
#index refegenome file if it hasn't been done
if not os.path.exists(refgenome + '.fai'):
printlog(["Creating index for", refgenome])
pysam.faidx(refgenome)
refFasta = pysam.Fastafile(refgenome)
FILE_OUT = open(outfile, 'w')
UNMAP = open(outfile + '.unmap', 'w')
total = 0
fail = 0
withChr = False # check if the VCF data lines use 'chr1' or '1'
for line in ireader.reader(infile):
if not line.strip():
continue
line = line.strip()
#deal with meta-information lines.
#meta-information lines needed in both mapped and unmapped files
if line.startswith('##fileformat'):
print(line, file=FILE_OUT)
print(line, file=UNMAP)
elif line.startswith('##INFO'):
print(line, file=FILE_OUT)
print(line, file=UNMAP)
elif line.startswith('##FILTER'):
print(line, file=FILE_OUT)
print(line, file=UNMAP)
elif line.startswith('##FORMAT'):
print(line, file=FILE_OUT)
print(line, file=UNMAP)
elif line.startswith('##ALT'):
print(line, file=FILE_OUT)
print(line, file=UNMAP)
elif line.startswith('##SAMPLE'):
print(line, file=FILE_OUT)
print(line, file=UNMAP)
elif line.startswith('##PEDIGREE'):
print(line, file=FILE_OUT)
print(line, file=UNMAP)
#meta-information lines needed in unmapped files
elif line.startswith('##assembly'):
print(line, file=UNMAP)
elif line.startswith('##contig'):
print(line, file=UNMAP)
if 'ID=chr' in line:
withChr = True
#update contig information
elif line.startswith('#CHROM'):
printlog(["Updating contig field ... "])
target_gsize = dict(
list(zip(refFasta.references, refFasta.lengths)))
for chr_id in sorted(target_gsize):
if chr_id.startswith('chr'):
if withChr is True:
print("##contig=<ID=%s,length=%d,assembly=%s>" %
(chr_id, target_gsize[chr_id],
os.path.basename(refgenome)),
file=FILE_OUT)
else:
print("##contig=<ID=%s,length=%d,assembly=%s>" %
(chr_id.replace('chr', ''), target_gsize[chr_id],
os.path.basename(refgenome)),
file=FILE_OUT)
else:
if withChr is True:
print("##contig=<ID=%s,length=%d,assembly=%s>" %
('chr' + chr_id, target_gsize[chr_id],
os.path.basename(refgenome)),
file=FILE_OUT)
else:
print("##contig=<ID=%s,length=%d,assembly=%s>" %
(chr_id, target_gsize[chr_id],
os.path.basename(refgenome)),
file=FILE_OUT)
print(
"##liftOverProgram=<CrossMap,version=%s,website=https://sourceforge.net/projects/crossmap>"
% __version__,
file=FILE_OUT)
print("##liftOverChainFile=<%s>" % liftoverfile, file=FILE_OUT)
print("##originalFile=<%s>" % infile, file=FILE_OUT)
print("##targetRefGenome=<%s>" % refgenome, file=FILE_OUT)
print("##liftOverDate=<%s>" %
datetime.date.today().strftime("%B%d,%Y"),
file=FILE_OUT)
print(line, file=FILE_OUT)
print(line, file=UNMAP)
printlog(["Lifting over ... "])
else:
if line.startswith('#'): continue
fields = str.split(line, maxsplit=7)
total += 1
chrom = fields[0]
start = int(fields[1]) - 1 # 0 based
end = start + len(fields[3])
a = map_coordinates(mapping, chrom, start, end, '+')
if a is None:
print(line + "\tFail(Unmap)", file=UNMAP)
fail += 1
continue
if len(a) == 2:
# update chrom
target_chr = str(
a[1][0]
) #target_chr is from chain file, could be 'chr1' or '1'
target_start = a[1][1]
target_end = a[1][2]
fields[0] = target_chr
# update start coordinate
fields[1] = target_start + 1
# update ref allele
target_chr = update_chromID(refFasta.references[0], target_chr)
try:
fields[3] = refFasta.fetch(target_chr, target_start,
target_end).upper()
except:
print(line + "\tFail(KeyError)", file=UNMAP)
fail += 1
continue
# update END if any
fields[7] = re.sub('END\=\d+', 'END=' + str(target_end),
fields[7])
if a[1][3] == '-':
fields[4] = revcomp_DNA(fields[4], True)
# check if ref_allele is the same as alt_allele
if noCompAllele:
print('\t'.join(map(str, fields)), file=FILE_OUT)
else:
if fields[3] != fields[4]:
print('\t'.join(map(str, fields)), file=FILE_OUT)
else:
print(line + "\tFail(REF==ALT)", file=UNMAP)
fail += 1
else:
print(line + "\tFail(Multiple_hits)", file=UNMAP)
fail += 1
continue
FILE_OUT.close()
UNMAP.close()
printlog(["Total entries:", str(total)])
printlog(["Failed to map:", str(fail)])
if compress:
try:
printlog(["Compressing \"%s\" ..." % outfile])
subprocess.call("gzip " + outfile, shell=True)
except:
pass
def crossmap_bam_file(mapping,
chainfile,
infile,
outfile_prefix,
chrom_size,
IS_size=200,
IS_std=30.0,
fold=3,
addtag=True):
'''
Description
-----------
Convert genome coordinates (in BAM/SAM format) between assemblies.
BAM/SAM format: http://samtools.sourceforge.net/
chrom_size is target chromosome size
Parameters
----------
mapping : dict
Dictionary with source chrom name as key, IntervalTree object as value.
chainfile : file
Input chain format file.
infile : file
Input BAM, SAM or CRAM foramt file.
outfile_prefix : str
Output prefix.
chrom_size : dict
Chromosome size of the *target* assembly, used to build bam header.
IS_size : int
Average insert size of pair-end sequencing.
IS_std : float
Stanadard deviation of insert size.
fold : float
A mapped pair is considered as \"proper pair\" if both ends mapped to
different strand and the distance between them is less then fold * stdev
from the mean.
addtag : bool
if addtag is set to True, will add tags to each alignmnet:
Q = QC (QC failed)
N = unmapped (originally unmapped or originally mapped but failed
to liftover to new assembly)
M = multiple mapped (alignment can be liftover to multiple places)
U = unique mapped (alignment can be liftover to only 1 place)
tags for pair-end sequencing include:
QF: QC failed
NN: both read1 and read2 unmapped
NU: read1 unmapped, read2 unique mapped
NM: read1 unmapped, multiple mapped
UN: read1 uniquely mapped, read2 unmap
UU: both read1 and read2 uniquely mapped
UM: read1 uniquely mapped, read2 multiple mapped
MN: read1 multiple mapped, read2 unmapped
MU: read1 multiple mapped, read2 unique mapped
MM: both read1 and read2 multiple mapped
tags for single-end sequencing include:
QF: QC failed
SN: unmaped
SM: multiple mapped
SU: uniquely mapped
'''
# determine the input file format (BAM, CRAM or SAM)
file_type = ''
if infile.lower().endswith('.bam'):
file_type = 'BAM'
comments = ['ORIGINAL_BAM_FILE=' + infile]
samfile = pysam.Samfile(infile, 'rb')
if len(samfile.header) == 0:
print("BAM file has no header section. Exit!", file=sys.stderr)
sys.exit(1)
elif infile.lower().endswith('.cram'):
file_type = 'CRAM'
comments = ['ORIGINAL_CRAM_FILE=' + infile]
samfile = pysam.Samfile(infile, 'rc')
if len(samfile.header) == 0:
print("CRAM file has no header section. Exit!", file=sys.stderr)
sys.exit(1)
elif infile.lower().endswith('.sam'):
file_type = 'SAM'
comments = ['ORIGINAL_SAM_FILE=' + infile]
samfile = pysam.Samfile(infile, 'r')
if len(samfile.header) == 0:
print("SAM file has no header section. Exit!", file=sys.stderr)
sys.exit(1)
else:
print(
"Unknown file type! Input file must have suffix '.bam','.cram', or '.sam'.",
file=sys.stderr)
sys.exit(1)
comments.append('CHAIN_FILE=' + chainfile)
sam_ori_header = samfile.header.to_dict()
# chromosome ID style of the original BAM file
chrom_style = sam_ori_header['SQ'][0]['SN'] # either 'chr1' or '1'
# update chrom_size of target genome
target_chrom_sizes = {}
for n, l in chrom_size.items():
target_chrom_sizes[update_chromID(chrom_style, n)] = l
(new_header, name_to_id) = sam_header.bam_header_generator(
orig_header=sam_ori_header,
chrom_size=target_chrom_sizes,
prog_name="CrossMap",
prog_ver=__version__,
format_ver=1.0,
sort_type='coordinate',
co=comments)
# write to file
if outfile_prefix is not None:
if file_type == 'BAM':
OUT_FILE = pysam.Samfile(outfile_prefix + '.bam',
"wb",
header=new_header)
printlog(
["Liftover BAM file:", infile, '==>', outfile_prefix + '.bam'])
elif file_type == 'CRAM':
OUT_FILE = pysam.Samfile(outfile_prefix + '.bam',
"wb",
header=new_header)
printlog([
"Liftover CRAM file:", infile, '==>', outfile_prefix + '.bam'
])
elif file_type == 'SAM':
OUT_FILE = pysam.Samfile(outfile_prefix + '.sam',
"wh",
header=new_header)
printlog(
["Liftover SAM file:", infile, '==>', outfile_prefix + '.sam'])
else:
print(
"Unknown file type! Input file must have suffix '.bam','.cram', or '.sam'.",
file=sys.stderr)
sys.exit(1)
# write to screen
else:
if file_type == 'BAM':
OUT_FILE = pysam.Samfile('-', "wb", header=new_header)
printlog(["Liftover BAM file:", infile])
elif file_type == 'CRAM':
OUT_FILE = pysam.Samfile('-', "wb", header=new_header)
printlog(["Liftover CRAM file:", infile])
elif file_type == 'SAM':
OUT_FILE = pysam.Samfile('-', "w", header=new_header)
printlog(["Liftover SAM file:", infile])
else:
print(
"Unknown file type! Input file must have suffix '.bam','.cram', or '.sam'.",
file=sys.stderr)
sys.exit(1)
QF = 0
NN = 0
NU = 0
NM = 0
UN = 0
UU = 0
UM = 0
MN = 0
MU = 0
MM = 0
SN = 0
SM = 0
SU = 0
total_item = 0
try:
while (1):
total_item += 1
old_alignment = next(samfile)
new_alignment = pysam.AlignedRead() # create AlignedRead object
new_alignment.query_name = old_alignment.query_name # 1st column. read name.
new_alignment.query_sequence = old_alignment.query_sequence # 10th column. read sequence. all bases.
new_alignment.query_qualities = old_alignment.query_qualities # 11th column. read sequence quality. all bases.
new_alignment.set_tags(old_alignment.get_tags()) # 12 - columns
# by default pysam will change RG:Z to RG:A, which can cause downstream failures with GATK and freebayes
# Thanks Wolfgang Resch <*****@*****.**> identified this bug and provided solution.
try:
rg, rgt = old_alignment.get_tag("RG", with_value_type=True)
except KeyError:
pass
else:
new_alignment.set_tag("RG", str(rg), rgt)
## Pair-end sequencing
if old_alignment.is_paired:
new_alignment.flag = 0x1 #pair-end in sequencing
if old_alignment.is_read1:
new_alignment.flag = new_alignment.flag | 0x40
elif old_alignment.is_read2:
new_alignment.flag = new_alignment.flag | 0x80
if old_alignment.is_qcfail:
new_alignment.flag = new_alignment.flag | 0x200
new_alignment.reference_id = -1 #3
new_alignment.reference_start = 0 #4
new_alignment.mapping_quality = 255 #5
new_alignment.cigartuples = old_alignment.cigartuples #6
new_alignment.next_reference_id = -1 #7
new_alignment.next_reference_start = 0 #8
new_alignment.template_length = 0 #9
QF += 1
if addtag: new_alignment.set_tag(tag="QF", value=0)
OUT_FILE.write(new_alignment)
continue
#==================================
# R1 originally unmapped
#==================================
elif old_alignment.is_unmapped:
new_alignment.flag = new_alignment.flag | 0x4 #2
new_alignment.reference_id = -1 #3
new_alignment.reference_start = 0 #4
new_alignment.mapping_quality = 255 #5
new_alignment.cigartuples = old_alignment.cigartuples #6
# R1 & R2 originally unmapped
if old_alignment.mate_is_unmapped:
new_alignment.next_reference_id = -1 #7
new_alignment.next_reference_start = 0 #8
new_alignment.template_length = 0 #9
NN += 1
if addtag: new_alignment.set_tag(tag="NN", value=0)
OUT_FILE.write(new_alignment)
continue
# R1 unmap, R2 is mapped
else:
try:
read2_chr = samfile.get_reference_name(
old_alignment.next_reference_id)
read2_strand = '-' if old_alignment.mate_is_reverse else '+'
read2_start = old_alignment.next_reference_start
read2_end = read2_start + 1
read2_maps = map_coordinates(
mapping, read2_chr, read2_start, read2_end,
read2_strand)
except:
read2_maps = None
#------------------------------------
# R1 unmapped, R2 failed to liftover
#------------------------------------
if read2_maps is None:
new_alignment.next_reference_id = -1 #7
new_alignment.next_reference_start = 0 #8
new_alignment.template_length = 0 #9
NN += 1
if addtag: new_alignment.set_tag(tag="NN", value=0)
OUT_FILE.write(new_alignment)
continue
#------------------------------------
# R1 unmapped, R2 unique
#------------------------------------
elif len(read2_maps) == 2:
# 2-9
if read2_maps[1][3] == '-':
new_alignment.flag = new_alignment.flag | 0x20
new_alignment.reference_id = name_to_id[
read2_maps[1]
[0]] #recommend to set the RNAME of unmapped read to its mate's
new_alignment.reference_start = read2_maps[1][
1] #recommend to set the POS of unmapped read to its mate's
new_alignment.mapping_quality = old_alignment.mapping_quality
new_alignment.cigartuples = old_alignment.cigartuples
new_alignment.next_reference_id = name_to_id[
read2_maps[1][0]]
new_alignment.next_reference_start = read2_maps[1][
1]
new_alignment.template_length = 0
NU += 1
if addtag: new_alignment.set_tag(tag="NU", value=0)
OUT_FILE.write(new_alignment)
continue
#------------------------------------
# R1 unmapped, R2 multiple
#------------------------------------
else:
if read2_maps[1][3] == '-':
new_alignment.flag = new_alignment.flag | 0x20
# 2-9
new_alignment.flag = new_alignment.flag | 0x100
new_alignment.reference_id = name_to_id[
read2_maps[1][0]]
new_alignment.reference_start = read2_maps[1][1]
new_alignment.mapping_quality = old_alignment.mapping_quality
new_alignment.cigartuples = old_alignment.cigartuples
new_alignment.next_reference_id = name_to_id[
read2_maps[1][0]]
new_alignment.next_reference_start = read2_maps[1][
1]
new_alignment.template_length = 0
NM += 1
if addtag: new_alignment.set_tag(tag="NM", value=0)
OUT_FILE.write(new_alignment)
continue
#==================================
# R1 is originally mapped
#==================================
else:
try:
read1_chr = samfile.get_reference_name(
old_alignment.reference_id)
read1_strand = '-' if old_alignment.is_reverse else '+'
read1_start = old_alignment.reference_start
read1_end = old_alignment.reference_end
read1_maps = map_coordinates(mapping, read1_chr,
read1_start, read1_end,
read1_strand)
except:
read1_maps = None
if not old_alignment.mate_is_unmapped:
try:
read2_chr = samfile.get_reference_name(
old_alignment.next_reference_id)
read2_strand = '-' if old_alignment.mate_is_reverse else '+'
read2_start = old_alignment.next_reference_start
read2_end = read2_start + 1
read2_maps = map_coordinates(
mapping, read2_chr, read2_start, read2_end,
read2_strand)
except:
read2_maps = None
#------------------------------------
# R1 failed to liftover
#------------------------------------
if read1_maps is None:
# read2 is unmapped or failed to convertion
if old_alignment.mate_is_unmapped or (read2_maps is
None):
# col2 - col9
new_alignment.flag = new_alignment.flag | 0x4 #2
new_alignment.reference_id = -1 #3
new_alignment.reference_start = 0 #4
new_alignment.mapping_quality = 255 #5
new_alignment.cigartuples = old_alignment.cigartuples #6
new_alignment.next_reference_id = -1 #7
new_alignment.next_reference_start = 0 #8
new_alignment.template_length = 0 #9
if addtag: new_alignment.set_tag(tag="NN", value=0)
NN += 1
OUT_FILE.write(new_alignment)
continue
# read2 is unique mapped
elif len(read2_maps) == 2:
# col2 - col9
if read2_maps[1][3] == '-':
new_alignment.flag = new_alignment.flag | 0x20
new_alignment.reference_id = name_to_id[
read2_maps[1]
[0]] #recommend to set the RNAME of unmapped read to its mate's
new_alignment.reference_start = read2_maps[1][
1] #recommend to set the POS of unmapped read to its mate's
new_alignment.mapping_quality = old_alignment.mapping_quality
new_alignment.cigartuples = old_alignment.cigartuples
new_alignment.next_reference_id = name_to_id[
read2_maps[1][0]]
new_alignment.next_reference_start = read2_maps[1][
1] #start
new_alignment.template_length = 0
NU += 1
if addtag: new_alignment.set_tag(tag="NU", value=0)
OUT_FILE.write(new_alignment)
continue
# read2 is multiple mapped
else:
# col2 - col9
if read2_maps[1][3] == '-':
new_alignment.flag = new_alignment.flag | 0x20
new_alignment.flag = new_alignment.flag | 0x100
new_alignment.reference_id = name_to_id[
read2_maps[1][0]]
new_alignment.reference_start = read2_maps[1][1]
new_alignment.mapping_quality = 255 # mapq not available
new_alignment.cigartuples = old_alignment.cigartuples
new_alignment.next_reference_id = name_to_id[
read2_maps[1][0]]
new_alignment.next_reference_start = read2_maps[1][
1] #start
new_alignment.template_length = 0
NM += 1
if addtag: new_alignment.set_tag(tag="NM", value=0)
OUT_FILE.write(new_alignment)
continue
#------------------------------------
# R1 uniquely mapped
#------------------------------------
elif len(read1_maps) == 2:
# col2 - col5
if read1_maps[1][3] == '-':
new_alignment.flag = new_alignment.flag | 0x10
new_alignment.reference_id = name_to_id[read1_maps[1]
[0]]
new_alignment.reference_start = read1_maps[1][1]
new_alignment.mapping_quality = old_alignment.mapping_quality
if read1_maps[0][3] != read1_maps[1][
3]: # opposite strand
# 6
new_alignment.cigartuples = old_alignment.cigartuples[::
-1] #reverse cigar tuple
# 10
new_alignment.query_sequence = revcomp_DNA(
old_alignment.query_sequence
) #reverse complement read sequence
# 11
new_alignment.query_qualities = old_alignment.query_qualities[::
-1] #reverse quality string
elif read1_maps[0][3] == read1_maps[1][
3]: # same strand
# 6
new_alignment.cigartuples = old_alignment.cigartuples
# R2 unmapped before or after conversion
if (old_alignment.mate_is_unmapped) or (read2_maps is
None):
#2,7-9
new_alignment.flag = new_alignment.flag | 0x8
new_alignment.next_reference_id = name_to_id[
read1_maps[1][0]]
new_alignment.next_reference_start = read1_maps[1][
1]
new_alignment.template_length = 0
UN += 1
if addtag: new_alignment.set_tag(tag="UN", value=0)
OUT_FILE.write(new_alignment)
continue
# R2 is unique mapped
elif len(read2_maps) == 2:
# 2,7-9
if read2_maps[1][3] == '-':
new_alignment.flag = new_alignment.flag | 0x20
new_alignment.next_reference_id = name_to_id[
read2_maps[1][0]] #chrom
new_alignment.next_reference_start = read2_maps[1][
1]
new_alignment.template_length = abs(
new_alignment.reference_start -
new_alignment.next_reference_start
) + old_alignment.reference_length
# 2
if (read2_maps[1][3] != read1_maps[1][3]) and (
new_alignment.template_length <=
IS_size + fold * IS_std) and (
new_alignment.template_length >=
IS_size - fold * IS_std):
new_alignment.flag = new_alignment.flag | 0x2
UU += 1
if addtag: new_alignment.set_tag(tag="UU", value=0)
OUT_FILE.write(new_alignment)
continue
# R2 is multiple mapped
else:
# 2 (strand)
if read2_maps[1][3] == '-':
new_alignment.flag = new_alignment.flag | 0x20
# 2 (secondary alignment)
new_alignment.flag = new_alignment.flag | 0x100
#7-9
new_alignment.next_reference_id = name_to_id[
read2_maps[1][0]]
new_alignment.next_reference_start = read2_maps[1][
1]
new_alignment.template_length = 0
UM += 1
if addtag: new_alignment.set_tag(tag="UM", value=0)
OUT_FILE.write(new_alignment)
continue
#------------------------------------
# R1 multiple mapped
#-----------------------------------
elif len(read1_maps) > 2 and len(read1_maps) % 2 == 0:
# 2
new_alignment.flag = new_alignment.flag | 0x100
if read1_maps[1][3] == '-':
new_alignment.flag = new_alignment.flag | 0x10
# 3-5
new_alignment.tid = name_to_id[read1_maps[1]
[0]] #chrom
new_alignment.pos = read1_maps[1][1] #start
new_alignment.mapq = 255
if read1_maps[0][3] != read1_maps[1][
3]: # opposite strand
# 6
new_alignment.cigartuples = old_alignment.cigartuples[::
-1] #reverse cigar tuple
# 10
new_alignment.query_sequence = revcomp_DNA(
old_alignment.query_sequence
) #reverse complement read sequence
# 11
new_alignment.query_qualities = old_alignment.query_qualities[::
-1] #reverse quality string
elif read1_maps[0][3] == read1_maps[1][
3]: # same strand
# 6
new_alignment.cigartuples = old_alignment.cigartuples
# (1) R2 is unmapped
if (old_alignment.mate_is_unmapped) or (read2_maps is
None):
#2,7-9
new_alignment.flag = new_alignment.flag | 0x8
new_alignment.next_reference_id = name_to_id[
read1_maps[1][0]]
new_alignment.next_reference_start = read1_maps[1][
1]
new_alignment.template_length = 0
MN += 1
if addtag: new_alignment.set_tag(tag="MN", value=0)
OUT_FILE.write(new_alignment)
continue
# (2) read2 is unique mapped
elif len(read2_maps) == 2:
# 2,7-9
if read2_maps[1][3] == '-':
new_alignment.flag = new_alignment.flag | 0x20
new_alignment.next_reference_id = name_to_id[
read2_maps[1][0]] #chrom
new_alignment.next_reference_start = read2_maps[1][
1]
new_alignment.template_length = 0
MU += 1
if addtag: new_alignment.set_tag(tag="MU", value=0)
OUT_FILE.write(new_alignment)
continue
# (3) R2 is multiple mapped
else:
# 2,7-9
if read2_maps[1][3] == '-':
new_alignment.flag = new_alignment.flag | 0x20
# 2 (secondary alignment)
new_alignment.flag = new_alignment.flag | 0x100
new_alignment.next_reference_id = name_to_id[
read2_maps[1][0]] #chrom
new_alignment.next_reference_start = read2_maps[1][
1]
new_alignment.template_length = 0
MM += 1
if addtag: new_alignment.set_tag(tag="MM", value=0)
OUT_FILE.write(new_alignment)
continue
# Singel end sequencing
else:
# 7-9
new_alignment.next_reference_id = -1
new_alignment.next_reference_start = 0
new_alignment.template_length = 0
# (1) originally unmapped
if old_alignment.is_unmapped:
# 2-6
new_alignment.flag = new_alignment.flag | 0x4
new_alignment.reference_id = -1
new_alignment.reference_start = 0
new_alignment.mapping_quality = 255
new_alignment.cigartuples = old_alignment.cigartuples
SN += 1
if addtag: new_alignment.set_tag(tag="SN", value=0)
OUT_FILE.write(new_alignment)
continue
else:
new_alignment.flag = 0x0
read_chr = samfile.get_reference_name(
old_alignment.reference_id)
read_strand = '-' if old_alignment.is_reverse else '+'
read_start = old_alignment.reference_start
read_end = old_alignment.reference_end
read_maps = map_coordinates(mapping, read_chr, read_start,
read_end, read_strand)
# (2) unmapped afte liftover
if read_maps is None:
new_alignment.flag = new_alignment.flag | 0x4
new_alignment.reference_id = -1
new_alignment.reference_start = 0
new_alignment.mapping_quality = 255
SN += 1
if addtag: new_alignment.set_tag(tag="SN", value=0)
OUT_FILE.write(new_alignment)
continue
# (3) unique mapped
if len(read_maps) == 2:
if read_maps[1][3] == '-':
new_alignment.flag = new_alignment.flag | 0x10
if read_maps[0][3] != read_maps[1][3]:
# 6
new_alignment.cigartuples = old_alignment.cigartuples[::
-1] #reverse cigar tuple
# 10
new_alignment.query_sequence = revcomp_DNA(
old_alignment.query_sequence
) #reverse complement read sequence
# 11
try:
new_alignment.query_qualities = old_alignment.query_qualities[::
-1] #reverse quality string
except:
new_alignment.query_qualities = []
else:
# 6
new_alignment.cigartuples = old_alignment.cigartuples
# 3-5
new_alignment.reference_id = name_to_id[read_maps[1]
[0]]
new_alignment.reference_start = read_maps[1][1]
new_alignment.mapping_quality = old_alignment.mapping_quality
SU += 1
if addtag: new_alignment.set_tag(tag="SU", value=0)
OUT_FILE.write(new_alignment)
continue
# (4) multiple mapped
if len(read_maps) > 2 and len(read_maps) % 2 == 0:
new_alignment.flag = new_alignment.flag | 0x100
if read_maps[1][3] == '-':
new_alignment.flag = new_alignment.flag | 0x10
if read_maps[0][3] != read_maps[1][3]:
# 6
new_alignment.cigartuples = old_alignment.cigartuples[::
-1] #reverse cigar tuple
# 10
new_alignment.query_sequence = revcomp_DNA(
old_alignment.query_sequence
) #reverse complement read sequence
# 11
new_alignment.query_qualities = old_alignment.query_qualities[::
-1] #reverse quality string
else:
# 6
new_alignment.cigartuples = old_alignment.cigartuples
# 3-5
new_alignment.tid = name_to_id[read_maps[1][0]]
new_alignment.pos = read_maps[1][1]
new_alignment.mapq = old_alignment.mapq
SM += 1
if addtag: new_alignment.set_tag(tag="SM", value=0)
OUT_FILE.write(new_alignment)
continue
except StopIteration:
printlog(["Done!"])
OUT_FILE.close()
if outfile_prefix is not None:
if file_type == "BAM" or file_type == "CRAM":
try:
printlog([
'Sort "%s" and save as "%s"' %
(outfile_prefix + '.bam', outfile_prefix + '.sorted.bam')
])
pysam.sort("-o", outfile_prefix + '.sorted.bam',
outfile_prefix + '.bam')
except:
printlog(["Warning: ", "output BAM file was NOT sorted"])
try:
printlog(['Index "%s" ...' % (outfile_prefix + '.sorted.bam')])
pysam.index(outfile_prefix + '.sorted.bam',
outfile_prefix + '.sorted.bam.bai')
except:
printlog(["Warning: ", "output BAM file was NOT indexed."])
print("Total alignments:" + str(total_item - 1))
print(" QC failed: " + str(QF))
if max(NN, NU, NM, UN, UU, UM, MN, MU, MM) > 0:
print(" Paired-end reads:")
print("\tR1 unique, R2 unique (UU): " + str(UU))
print("\tR1 unique, R2 unmapp (UN): " + str(UN))
print("\tR1 unique, R2 multiple (UM): " + str(UM))
print("\tR1 multiple, R2 multiple (MM): " + str(MM))
print("\tR1 multiple, R2 unique (MU): " + str(MU))
print("\tR1 multiple, R2 unmapped (MN): " + str(MN))
print("\tR1 unmap, R2 unmap (NN): " + str(NN))
print("\tR1 unmap, R2 unique (NU): " + str(NU))
print("\tR1 unmap, R2 multiple (NM): " + str(NM))
if max(SN, SU, SM) > 0:
print(" Single-end reads:")
print("\tUniquley mapped (SU): " + str(SU))
print("\tMultiple mapped (SM): " + str(SM))
print("\tUnmapped (SN): " + str(SN))
def crossmap_gvcf_file(mapping, infile, outfile, liftoverfile, refgenome, noCompAllele = False, compress = False, cstyle = 'a'):
'''
Convert genome coordinates in GVCF format.
Parameters
----------
mapping : dict
Dictionary with source chrom name as key, IntervalTree object as value.
infile : file
Input file in GVCF format. Can be a regular or compressed (*.gz, *.Z,*.z, *.bz,
*.bz2, *.bzip2) file, local file or URL (http://, https://, ftp://) pointing to
remote file.
outfile : str
prefix of output files.
liftoverfile : file
Chain (https://genome.ucsc.edu/goldenPath/help/chain.html) format file. Can be a
regular or compressed (*.gz, *.Z,*.z, *.bz, *.bz2, *.bzip2) file, local file or
URL (http://, https://, ftp://) pointing to remote file.
refgenome : file
The genome sequence file of 'target' assembly in FASTA format.
noCompAllele : bool
A logical value indicates whether to compare ref_allele to alt_allele after
liftover. If True, the variant will be marked as "unmap" if
ref_allele == alt_allele.
cstyle : str, optional
Chromosome ID style. Must be one of ['a', 's', 'l'], where
'a' : as-is. The chromosome ID of the output file is in the same style of the input file.
's' : short ID, such as "1", "2", "X.
'l' : long ID, such as "chr1", "chr2", "chrX.
'''
if noCompAllele:
logging.info("Keep variants [reference_allele == alternative_allele] ...")
else:
logging.info("Filter out variants [reference_allele == alternative_allele] ...")
#index refegenome file if it hasn't been done
if not os.path.exists(refgenome + '.fai'):
logging.info("Creating index for: %s" % refgenome)
pysam.faidx(refgenome)
if os.path.getmtime(refgenome + '.fai') < os.path.getmtime(refgenome):
logging.info("Index file is older than reference genome. Re-creating index for: %s" % refgenome)
pysam.faidx(refgenome)
refFasta = pysam.Fastafile(refgenome)
FILE_OUT = open(outfile ,'w')
UNMAP = open(outfile + '.unmap','w')
total_var = 0
failed_var = 0
total_region = 0
failed_region = 0
withChr = False # check if the VCF data lines use 'chr1' or '1'
for line in ireader.reader(infile):
if not line.strip():
continue
line=line.strip()
#deal with meta-information lines.
#meta-information lines needed in both mapped and unmapped files
if line.startswith('##fileformat'):
print(line, file=FILE_OUT)
print(line, file=UNMAP)
elif line.startswith('##INFO'):
print(line, file=FILE_OUT)
print(line, file=UNMAP)
elif line.startswith('##FILTER'):
print(line, file=FILE_OUT)
print(line, file=UNMAP)
elif line.startswith('##FORMAT'):
print(line, file=FILE_OUT)
print(line, file=UNMAP)
elif line.startswith('##ALT'):
print(line, file=FILE_OUT)
print(line, file=UNMAP)
elif line.startswith('##SAMPLE'):
print(line, file=FILE_OUT)
print(line, file=UNMAP)
elif line.startswith('##PEDIGREE'):
print(line, file=FILE_OUT)
print(line, file=UNMAP)
elif line.startswith('##GVCFBlock'):
print(line, file=FILE_OUT)
print(line, file=UNMAP)
elif line.startswith('##GATKCommandLine'):
print(line, file=FILE_OUT)
print(line, file=UNMAP)
elif line.startswith('##source'):
print(line, file=FILE_OUT)
print(line, file=UNMAP)
#meta-information lines needed in unmapped files
elif line.startswith('##assembly'):
print(line, file=UNMAP)
elif line.startswith('##contig'):
print(line, file=UNMAP)
if 'ID=chr' in line:
chr_template = 'chr1'
else:
chr_template = '1'
#update contig information
elif line.startswith('#CHROM'):
logging.info("Updating contig field ... ")
target_gsize = dict(list(zip(refFasta.references, refFasta.lengths)))
for chr_id in sorted(target_gsize):
if chr_id.startswith('chr'):
#if withChr is True:
print("##contig=<ID=%s,length=%d,assembly=%s>" % (update_chromID(chr_template, chr_id, cstyle), target_gsize[chr_id], os.path.basename(refgenome)), file=FILE_OUT)
print("##liftOverProgram=<CrossMap,version=%s,website=https://sourceforge.net/projects/crossmap>" % __version__, file=FILE_OUT)
print("##liftOverChainFile=<%s>" % liftoverfile, file=FILE_OUT)
print("##originalFile=<%s>" % infile, file=FILE_OUT)
print("##targetRefGenome=<%s>" % refgenome, file=FILE_OUT)
print("##liftOverDate=<%s>" % datetime.date.today().strftime("%B%d,%Y"), file=FILE_OUT)
print(line, file=FILE_OUT)
print(line, file=UNMAP)
logging.info("Lifting over ... ")
else:
if line.startswith('#'):continue
# process non-variant region
if 'END=' in line:
fields = str.split(line,maxsplit=8)
total_region += 1
chrom = fields[0]
start = int(fields[1])-1 # 0 based
try:
m = re.search(r"END\=(\d+)", line)
end = int(m[1])
except:
print (line + "\tFail(Unmap)", file=UNMAP)
failed_region += 1
continue
a = map_coordinates(mapping, chrom, start, end, '+', chrom_style = cstyle)
if a is None:
print (line + "\tFail(Unmap)", file=UNMAP)
failed_region += 1
continue
if len(a) == 2:
# update chrom
target_chr = str(a[1][0]) #target_chr is from chain file, could be 'chr1' or '1'
target_start = a[1][1]
target_end = a[1][2]
fields[0] = target_chr
# update start coordinate
fields[1] = target_start + 1
# update END
fields[7] = fields[7].replace(('END=' + str(end)), ('END=' + str(target_end)))
print('\t'.join(map(str, fields)), file=FILE_OUT)
# process variant line
else:
fields = str.split(line,maxsplit=7)
total_var += 1
chrom = fields[0]
start = int(fields[1])-1 # 0 based, ref_allele start
end = start + len(fields[3]) # ref_allele end
alt_allele = fields[4].replace(' ','').split(',')[0] # 20 10000598 . T A,<NON_REF> 1754.77 . DP=54;
a = map_coordinates(mapping, chrom, start, end, '+', chrom_style = cstyle)
if a is None:
print (line + "\tFail(Unmap)", file=UNMAP)
failed_var += 1
continue
if len(a) == 2:
# update chrom
target_chr = str(a[1][0]) #target_chr is from chain file, could be 'chr1' or '1'
target_start = a[1][1]
target_end = a[1][2]
fields[0] = target_chr
# update start coordinate
fields[1] = target_start + 1
# update ref allele
try:
target_chr = update_chromID(refFasta.references[0], target_chr)
fields[3] = refFasta.fetch(target_chr,target_start,target_end).upper()
except:
print(line+ "\tFail(No_targetRef)", file=UNMAP)
failed_var += 1
if a[1][3] == '-':
fields[4] = revcomp_DNA(alt_allele, True) + ',<NON_REF>'
# check if ref_allele is the same as alt_allele
if noCompAllele:
print('\t'.join(map(str, fields)), file=FILE_OUT)
else:
if fields[3] != fields[4]:
print('\t'.join(map(str, fields)), file=FILE_OUT)
else:
print (line + "\tFail(REF==ALT)", file=UNMAP)
failed_var += 1
else:
print (line + "\tFail(Multiple_hits)", file=UNMAP)
failed_var += 1
continue
FILE_OUT.close()
UNMAP.close()
logging.info ("Total variants: %d" % total_var)
logging.info ("Variants failed to map: %d" % failed_var)
logging.info ("Total non-variant regions: %d" % total_region)
logging.info ("Non-variant regions failed to map: %d" % failed_region)
if compress:
try:
logging.info("Compressing \"%s\" ..." % outfile)
subprocess.call("gzip " + outfile, shell=True)
except:
pass
def crossmap_maf_file(mapping, infile, outfile, liftoverfile, refgenome,
ref_name):
'''
Convert genome coordinates in MAF (mutation annotation foramt) format.
Parameters
----------
mapping : dict
Dictionary with source chrom name as key, IntervalTree object as value.
infile : file
Input file in VCF format. Can be a regular or compressed (*.gz, *.Z,*.z, *.bz,
*.bz2, *.bzip2) file, local file or URL (http://, https://, ftp://) pointing to
remote file.
outfile : str
prefix of output files.
liftoverfile : file
Chain (https://genome.ucsc.edu/goldenPath/help/chain.html) format file. Can be a
regular or compressed (*.gz, *.Z,*.z, *.bz, *.bz2, *.bzip2) file, local file or
URL (http://, https://, ftp://) pointing to remote file.
refgenome : file
The genome sequence file of 'target' assembly in FASTA format.
ref_name : str
The NCBI build name of the target assembly, for example, "GRCh37", "GRCh38".
'''
#index refegenome file if it hasn't been done
if not os.path.exists(refgenome + '.fai'):
logging.info("Creating index for: %s" % refgenome)
pysam.faidx(refgenome)
if os.path.getctime(refgenome + '.fai') < os.path.getctime(refgenome):
logging.info(
"Index file is older than reference genome. Re-creating index for: %s"
% refgenome)
pysam.faidx(refgenome)
refFasta = pysam.Fastafile(refgenome)
FILE_OUT = open(outfile, 'w')
UNMAP = open(outfile + '.unmap', 'w')
total = 0
fail = 0
for line in ireader.reader(infile):
if not line.strip():
continue
line = line.strip()
#meta-information lines needed in both mapped and unmapped files
if line.startswith('#'):
print(line, file=FILE_OUT)
print(line, file=UNMAP)
continue
elif line.startswith('Hugo_Symbol'):
print(
"#liftOver: Program=%sv%s, Time=%s, ChainFile=%s, NewRefGenome=%s"
% ("CrossMap", __version__,
datetime.date.today().strftime("%B%d,%Y"), liftoverfile,
refgenome),
file=FILE_OUT)
print(line, file=FILE_OUT)
print(line, file=UNMAP)
logging.info("Lifting over ... ")
else:
fields = str.split(line, sep='\t')
total += 1
fields[3] = ref_name
chrom = fields[4]
start = int(fields[5]) - 1 # 0 based
end = int(fields[6])
#strand = fields[7]
a = map_coordinates(mapping, chrom, start, end, '+')
if a is None:
print(line, file=UNMAP)
fail += 1
continue
if len(a) == 2:
target_chr = str(
a[1][0]
) #target_chr is from chain file, could be 'chr1' or '1'
target_start = a[1][1]
target_end = a[1][2]
# update chrom
fields[4] = target_chr
# update start coordinate
fields[5] = target_start + 1
# update end
fields[6] = target_end
# update ref allele
try:
target_chr = update_chromID(refFasta.references[0],
target_chr)
fields[10] = refFasta.fetch(target_chr, target_start,
target_end).upper()
except:
print(line, file=UNMAP)
fail += 1
continue
if a[1][3] == '-':
fields[10] = revcomp_DNA(fields[10], True)
print('\t'.join(map(str, fields)), file=FILE_OUT)
else:
print(line, file=UNMAP)
fail += 1
continue
FILE_OUT.close()
UNMAP.close()
logging.info("Total entries: %d", total)
logging.info("Failed to map: %d", fail)
def crossmap_gvcf_file(mapping, infile, outfile, liftoverfile, refgenome):
'''
Convert genome coordinates in GVCF format.
Parameters
----------
mapping : dict
Dictionary with source chrom name as key, IntervalTree object as value.
infile : file
Input file in GVCF format. Can be a regular or compressed (*.gz, *.Z,*.z, *.bz,
*.bz2, *.bzip2) file, local file or URL (http://, https://, ftp://) pointing to
remote file.
outfile : str
prefix of output files.
liftoverfile : file
Chain (https://genome.ucsc.edu/goldenPath/help/chain.html) format file. Can be a
regular or compressed (*.gz, *.Z,*.z, *.bz, *.bz2, *.bzip2) file, local file or
URL (http://, https://, ftp://) pointing to remote file.
refgenome : file
The genome sequence file of 'target' assembly in FASTA format.
'''
#index refegenome file if it hasn't been done
if not os.path.exists(refgenome + '.fai'):
printlog(["Creating index for", refgenome])
pysam.faidx(refgenome)
refFasta = pysam.Fastafile(refgenome)
FILE_OUT = open(outfile, 'w')
UNMAP = open(outfile + '.unmap', 'w')
total_var = 0
failed_var = 0
total_region = 0
failed_region = 0
withChr = False # check if the VCF data lines use 'chr1' or '1'
for line in ireader.reader(infile):
if not line.strip():
continue
line = line.strip()
#deal with meta-information lines.
#meta-information lines needed in both mapped and unmapped files
if line.startswith('##fileformat'):
print(line, file=FILE_OUT)
print(line, file=UNMAP)
elif line.startswith('##INFO'):
print(line, file=FILE_OUT)
print(line, file=UNMAP)
elif line.startswith('##FILTER'):
print(line, file=FILE_OUT)
print(line, file=UNMAP)
elif line.startswith('##FORMAT'):
print(line, file=FILE_OUT)
print(line, file=UNMAP)
elif line.startswith('##ALT'):
print(line, file=FILE_OUT)
print(line, file=UNMAP)
elif line.startswith('##SAMPLE'):
print(line, file=FILE_OUT)
print(line, file=UNMAP)
elif line.startswith('##PEDIGREE'):
print(line, file=FILE_OUT)
print(line, file=UNMAP)
elif line.startswith('##GVCFBlock'):
print(line, file=FILE_OUT)
print(line, file=UNMAP)
elif line.startswith('##GATKCommandLine'):
print(line, file=FILE_OUT)
print(line, file=UNMAP)
elif line.startswith('##source'):
print(line, file=FILE_OUT)
print(line, file=UNMAP)
#meta-information lines needed in unmapped files
elif line.startswith('##assembly'):
print(line, file=UNMAP)
elif line.startswith('##contig'):
print(line, file=UNMAP)
if 'ID=chr' in line:
withChr = True
#update contig information
elif line.startswith('#CHROM'):
printlog(["Updating contig field ... "])
target_gsize = dict(
list(zip(refFasta.references, refFasta.lengths)))
for chr_id in sorted(target_gsize):
if chr_id.startswith('chr'):
if withChr is True:
print("##contig=<ID=%s,length=%d,assembly=%s>" %
(chr_id, target_gsize[chr_id],
os.path.basename(refgenome)),
file=FILE_OUT)
else:
print("##contig=<ID=%s,length=%d,assembly=%s>" %
(chr_id.replace('chr', ''), target_gsize[chr_id],
os.path.basename(refgenome)),
file=FILE_OUT)
else:
if withChr is True:
print("##contig=<ID=%s,length=%d,assembly=%s>" %
('chr' + chr_id, target_gsize[chr_id],
os.path.basename(refgenome)),
file=FILE_OUT)
else:
print("##contig=<ID=%s,length=%d,assembly=%s>" %
(chr_id, target_gsize[chr_id],
os.path.basename(refgenome)),
file=FILE_OUT)
print(
"##liftOverProgram=<CrossMap,version=%s,website=https://sourceforge.net/projects/crossmap>"
% __version__,
file=FILE_OUT)
print("##liftOverChainFile=<%s>" % liftoverfile, file=FILE_OUT)
print("##originalFile=<%s>" % infile, file=FILE_OUT)
print("##targetRefGenome=<%s>" % refgenome, file=FILE_OUT)
print("##liftOverDate=<%s>" %
datetime.date.today().strftime("%B%d,%Y"),
file=FILE_OUT)
print(line, file=FILE_OUT)
print(line, file=UNMAP)
printlog(["Lifting over ... "])
else:
if line.startswith('#'): continue
# process non-variant region
if 'END=' in line:
fields = str.split(line, maxsplit=8)
total_region += 1
chrom = fields[0]
start = int(fields[1]) - 1 # 0 based
try:
m = re.search(r"END\=(\d+)", line)
end = int(m[1])
except:
print(line + "\tFail(Unmap)", file=UNMAP)
failed_region += 1
continue
a = map_coordinates(mapping, chrom, start, end, '+')
if a is None:
print(line + "\tFail(Unmap)", file=UNMAP)
failed_region += 1
continue
if len(a) == 2:
# update chrom
target_chr = str(
a[1][0]
) #target_chr is from chain file, could be 'chr1' or '1'
target_start = a[1][1]
target_end = a[1][2]
fields[0] = target_chr
# update start coordinate
fields[1] = target_start + 1
# update END
fields[7] = fields[7].replace(('END=' + str(end)),
('END=' + str(target_end)))
print('\t'.join(map(str, fields)), file=FILE_OUT)
# process variant line
else:
fields = str.split(line, maxsplit=7)
total_var += 1
chrom = fields[0]
start = int(fields[1]) - 1 # 0 based, ref_allele start
end = start + len(fields[3]) # ref_allele end
alt_allele = fields[4].replace(' ', '').split(
','
)[0] # 20 10000598 . T A,<NON_REF> 1754.77 . DP=54;
a = map_coordinates(mapping, chrom, start, end, '+')
if a is None:
print(line + "\tFail(Unmap)", file=UNMAP)
failed_var += 1
continue
if len(a) == 2:
# update chrom
target_chr = str(
a[1][0]
) #target_chr is from chain file, could be 'chr1' or '1'
target_start = a[1][1]
target_end = a[1][2]
fields[0] = target_chr
# update start coordinate
fields[1] = target_start + 1
# update ref allele
target_chr = update_chromID(refFasta.references[0],
target_chr)
fields[3] = refFasta.fetch(target_chr, target_start,
target_end).upper()
if a[1][3] == '-':
fields[4] = revcomp_DNA(alt_allele,
True) + ',<NON_REF>'
#ref_allele and alt_alele are different
if fields[3] != alt_allele:
print('\t'.join(map(str, fields)), file=FILE_OUT)
else:
print(line + "\tFail(REF==ALT)", file=UNMAP)
failed_var += 1
else:
print(line + "\tFail(Multiple_hits)", file=UNMAP)
failed_var += 1
continue
FILE_OUT.close()
UNMAP.close()
printlog(["Total variants:", str(total_var)])
printlog(["Variants failed to map:", str(failed_var)])
printlog(["Total non-variant regions:", str(total_region)])
printlog(["Non-variant regions failed to map:", str(failed_region)])
