def wiggleReader(f):
'''
Read wiggle (http://genome.ucsc.edu/goldenPath/help/wiggle) file of different styles.
Parameters
----------
f : file
file in wiggle format. Can be fixedStep, variableStep, or bed4
Yields
------
chrom, start, end, strand, score
'''
current_chrom = None
current_pos = None
current_step = None
# always for wiggle data
strand = '+'
mode = "bed"
for line in ireader.reader(f):
if line.isspace() or line.startswith(("track", "#", "browser")):
continue
elif line.startswith("variableStep"):
header = parse_header(line)
current_chrom = header['chrom']
current_pos = None
current_step = None
if 'span' in header: current_span = int(header['span'])
else: current_span = 1
mode = "variableStep"
elif line.startswith("fixedStep"):
header = parse_header(line)
current_chrom = header['chrom']
current_pos = int(header['start']) - 1
current_step = int(header['step'])
if 'span' in header: current_span = int(header['span'])
else: current_span = 1
mode = "fixedStep"
elif mode == "bed":
fields = line.split()
if len(fields) > 3:
if len(fields) > 5:
yield fields[0], int(fields[1]), int(
fields[2]), fields[5], float(fields[3])
else:
yield fields[0], int(fields[1]), int(
fields[2]), strand, float(fields[3])
elif mode == "variableStep":
fields = line.split()
pos = int(fields[0]) - 1
yield current_chrom, pos, pos + current_span, strand, float(
fields[1])
elif mode == "fixedStep":
yield current_chrom, current_pos, current_pos + current_span, strand, float(
line.split()[0])
current_pos += current_step
else:
raise "Unexpected input line: %s" % line.strip()
def read_chain_file(chain_file, print_table=False):
'''
Read chain file.
Parameters
----------
chain_file : file
Chain format file. Input chain_file could be either plain text, compressed file
(".gz",".Z", ".z", ".bz", ".bz2", ".bzip2"), or a URL pointing to the chain file
("http://","https://", "ftp://"). If url was used, chain file must be plain text.
print_table : bool, optional
Print mappings in human readable table.
Returns
-------
maps : dict
Dictionary with source chrom name as key, IntervalTree object as value. An
IntervalTree contains many intervals. An interval is a start and end position
and a value. eg. Interval(11, 12, strand="-", value = "abc")
target_chromSize : dict
Chromosome sizes of target genome
source_chromSize : dict
Chromosome sizes of source genome
'''
logging.info("Read the chain file \"%s\" " % chain_file)
maps = {}
target_chromSize = {}
source_chromSize = {}
if print_table:
blocks = []
for line in ireader.reader(chain_file):
# Example: chain 4900 chrY 58368225 + 25985403 25985638 chr5 151006098 - 43257292 43257528 1
if not line.strip():
continue
line = line.strip()
if line.startswith(('#', ' ')): continue
fields = line.split()
if fields[0] == 'chain' and len(fields) in [12, 13]:
#score = int(fields[1]) # Alignment score
source_name = fields[2] # E.g. chrY
source_size = int(fields[3]) # Full length of the chromosome
source_strand = fields[4] # Must be +
if source_strand != '+':
raise Exception(
"Source strand in a chain file must be +. (%s)" % line)
source_start = int(fields[5]) # Start of source region
#source_end = int(fields[6]) # End of source region
target_name = fields[7] # E.g. chr5
target_size = int(fields[8]) # Full length of the chromosome
target_strand = fields[9] # + or -
target_start = int(fields[10])
#target_end = int(fields[11])
target_chromSize[target_name] = target_size
source_chromSize[source_name] = source_size
if target_strand not in ['+', '-']:
raise Exception("Target strand must be - or +. (%s)" % line)
#chain_id = None if len(fields) == 12 else fields[12]
if source_name not in maps:
maps[source_name] = Intersecter()
sfrom, tfrom = source_start, target_start
# Now read the alignment chain from the file and store it as a list (source_from, source_to) -> (target_from, target_to)
elif fields[0] != 'chain' and len(fields) == 3:
size, sgap, tgap = int(fields[0]), int(fields[1]), int(fields[2])
if print_table:
if target_strand == '+':
blocks.append(
(source_name, sfrom, sfrom + size, source_strand,
target_name, tfrom, tfrom + size, target_strand))
elif target_strand == '-':
blocks.append(
(source_name, sfrom, sfrom + size, source_strand,
target_name, target_size - (tfrom + size),
target_size - tfrom, target_strand))
if target_strand == '+':
maps[source_name].add_interval(
Interval(
sfrom, sfrom + size,
(target_name, tfrom, tfrom + size, target_strand)))
elif target_strand == '-':
maps[source_name].add_interval(
Interval(sfrom, sfrom + size,
(target_name, target_size - (tfrom + size),
target_size - tfrom, target_strand)))
sfrom += size + sgap
tfrom += size + tgap
elif fields[0] != 'chain' and len(fields) == 1:
size = int(fields[0])
if print_table:
if target_strand == '+':
blocks.append(
(source_name, sfrom, sfrom + size, source_strand,
target_name, tfrom, tfrom + size, target_strand))
elif target_strand == '-':
blocks.append(
(source_name, sfrom, sfrom + size, source_strand,
target_name, target_size - (tfrom + size),
target_size - tfrom, target_strand))
if target_strand == '+':
maps[source_name].add_interval(
Interval(
sfrom, sfrom + size,
(target_name, tfrom, tfrom + size, target_strand)))
elif target_strand == '-':
maps[source_name].add_interval(
Interval(sfrom, sfrom + size,
(target_name, target_size - (tfrom + size),
target_size - tfrom, target_strand)))
else:
raise Exception("Invalid chain format. (%s)" % line)
#if (sfrom + size) != source_end or (tfrom + size) != target_end:
# raise Exception("Alignment blocks do not match specified block sizes. (%s)" % header)
if print_table:
for i in blocks:
print('\t'.join([str(n) for n in i]))
return (maps, target_chromSize, source_chromSize)
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_bed_file(mapping,
inbed,
outfile=None,
unmapfile=None,
cstyle='a'):
'''
Convert genome coordinates (in bed format) between assemblies.
BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
Parameters
----------
mapping : dict
Dictionary with source chrom name as key, IntervalTree object as value.
inbed : file
Input BED file.
outfile : str, optional
Prefix of output files.
unmapfile: str, optional
Name of file to save unmapped entries. This option will be ignored if outfile is None.
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.
'''
# check if 'outfile' was set. If not set, print to screen, if set, print to file
if outfile is not None:
FILE_OUT = open(outfile, 'w')
if unmapfile is not None:
UNMAP = open(unmapfile, 'w')
else:
UNMAP = open(outfile + '.unmap', 'w')
else:
pass
for line in ireader.reader(inbed):
if line.startswith(('#', 'track', 'browser')): continue
if not line.strip(): continue
line = line.strip()
fields = line.split()
strand = '+'
# filter out line less than 3 columns
if len(fields) < 3:
print("Less than 3 fields. skip " + line, file=sys.stderr)
if outfile:
print(line + '\tInvalidBedFormat', file=UNMAP)
continue
try:
int(fields[1])
except:
print("Start coordinate is not an integer. skip " + line,
file=sys.stderr)
if outfile:
print(line + '\tInvalidStartPosition', file=UNMAP)
continue
try:
int(fields[2])
except:
print("End coordinate is not an integer. skip " + line,
file=sys.stderr)
if outfile:
print(line + '\tInvalidEndPosition', file=UNMAP)
continue
if int(fields[1]) > int(fields[2]):
print(
"\"Start\" is larger than \"End\" coordinate is not an integer. skip "
+ line,
file=sys.stderr)
if outfile:
print(line + '\tStart>End', file=UNMAP)
continue
# deal with bed less than 12 columns
if len(fields) < 12:
# try to reset strand
try:
for f in fields:
if f in ['+', '-']:
strand = f
except:
pass
chrom = fields[0]
start = int(fields[1])
end = int(fields[2])
a = map_coordinates(mapping,
chrom,
start,
end,
strand,
chrom_style=cstyle)
try:
if (a is None) or (len(a) % 2 != 0):
if outfile is None:
print(line + '\tUnmap')
else:
print(line + '\tUnmap', file=UNMAP)
continue
if len(a) == 2:
#reset fields
fields[0] = a[1][0]
fields[1] = a[1][1]
fields[2] = a[1][2]
for i in range(
0, len(fields)): #update the strand information
if fields[i] in ['+', '-']:
fields[i] = a[1][3]
if outfile is None:
print(line + '\t->\t' +
'\t'.join([str(i) for i in fields]))
else:
print('\t'.join([str(i) for i in fields]),
file=FILE_OUT)
if len(a) > 2:
count = 0
for j in range(1, len(a), 2):
count += 1
fields[0] = a[j][0]
fields[1] = a[j][1]
fields[2] = a[j][2]
for i in range(
0,
len(fields)): #update the strand information
if fields[i] in ['+', '-']:
fields[i] = a[j][3]
if outfile is None:
print(line + '\t' + '(split.' + str(count) + ':' +
':'.join([str(i) for i in a[j - 1]]) +
')\t' + '\t'.join([str(i) for i in fields]))
else:
print('\t'.join([str(i) for i in fields]),
file=FILE_OUT)
except:
if outfile is None:
print(line + '\tFail')
else:
print(line + '\tFail', file=UNMAP)
continue
# deal with bed12 and bed12+8 (genePred format)
if len(fields) == 12 or len(fields) == 20:
strand = fields[5]
if strand not in ['+', '-']:
raise Exception("Unknown strand: %s. Can only be '+' or '-'." %
strand)
fail_flag = False
exons_old_pos = annoGene.getExonFromLine(
line) #[[chr,st,end],[chr,st,end],...]
#print exons_old_pos
exons_new_pos = []
for e_chr, e_start, e_end in exons_old_pos:
# a has two elements, first is query, 2nd is target. # [('chr1', 246974830, 246974833,'+'), ('chr1', 248908207, 248908210,'+')]
a = map_coordinates(mapping,
e_chr,
e_start,
e_end,
strand,
chrom_style=cstyle)
if a is None:
fail_flag = True
break
if len(a) == 2:
exons_new_pos.append(a[1])
else:
fail_flag = True
break
if not fail_flag:
# check if all exons were mapped to the same chromosome and the same strand
chr_id = set()
exon_strand = set()
for e_chr, e_start, e_end, e_strand in exons_new_pos:
chr_id.add(e_chr)
exon_strand.add(e_strand)
if len(chr_id) != 1 or len(exon_strand) != 1:
fail_flag = True
if not fail_flag:
# build new bed
cds_start_offset = int(fields[6]) - int(fields[1])
cds_end_offset = int(fields[2]) - int(fields[7])
new_chrom = exons_new_pos[0][0]
new_chrom_st = exons_new_pos[0][1]
new_chrom_end = exons_new_pos[-1][2]
new_name = fields[3]
new_score = fields[4]
new_strand = exons_new_pos[0][3]
new_thickStart = new_chrom_st + cds_start_offset
new_thickEnd = new_chrom_end - cds_end_offset
new_ittemRgb = fields[8]
new_blockCount = len(exons_new_pos)
new_blockSizes = ','.join(
[str(o - n) for m, n, o, p in exons_new_pos])
new_blockStarts = ','.join([
str(n - new_chrom_st) for m, n, o, p in exons_new_pos
])
new_bedline = '\t'.join(
str(i)
for i in (new_chrom, new_chrom_st, new_chrom_end,
new_name, new_score, new_strand,
new_thickStart, new_thickEnd, new_ittemRgb,
new_blockCount, new_blockSizes,
new_blockStarts))
if check_bed12(new_bedline) is False:
fail_flag = True
else:
if outfile is None:
print(line + '\t->\t' + new_bedline)
else:
print(new_bedline, file=FILE_OUT)
if fail_flag:
if outfile is None:
print(line + '\tFail')
else:
print(line, file=UNMAP)
def crossmap_gff_file(mapping, ingff, outfile=None, cstyle='a'):
'''
Description
-----------
Convert genome coordinates (in GFF/GTF format) between assemblies.
GFF (General Feature Format) lines have nine required fields that must be Tab-separated:
1. seqname - The name of the sequence. Must be a chromosome or scaffold.
2. source - The program that generated this feature.
3. feature - The name of this type of feature. Some examples of standard feature types
are "CDS", "start_codon", "stop_codon", and "exon".
4. start - The starting position of the feature in the sequence. The first base is numbered 1.
5. end - The ending position of the feature (inclusive).
6. score - A score between 0 and 1000. If the track line useScore attribute is set to 1
for this annotation data set, the score value will determine the level of gray in
which this feature is displayed (higher numbers = darker gray). If there is no score
value, enter ".".
7. strand - Valid entries include '+', '-', or '.' (for don't know/don't care).
8. frame - If the feature is a coding exon, frame should be a number between 0-2 that
represents the reading frame of the first base. If the feature is not a coding exon,
the value should be '.'.
9. group - All lines with the same group are linked together into a single item.
GFF format: http://genome.ucsc.edu/FAQ/FAQformat.html#format3
GTF (Gene Transfer Format) is a refinement to GFF that tightens the specification. The
first eight GTF fields are the same as GFF. The group field has been expanded into a
list of attributes. Each attribute consists of a type/value pair. Attributes must end
in a semi-colon, and be separated from any following attribute by exactly one space.
GTF format: http://genome.ucsc.edu/FAQ/FAQformat.html#format4
We do NOT check if features (exon, CDS, etc) originally belonging to the same gene were
converted into the same chromosome/strand.
Parameters
----------
mapping : dict
Dictionary with source chrom name as key, IntervalTree object as value.
ingff : file
Input GFF/GTF file.
outfile : str, optional
Prefix of output files.
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 outfile is not None:
rand_str = ''.join(
random.choices(string.ascii_uppercase + string.digits, k=8))
FILE_OUT = open(outfile, 'w')
UNMAP = open(outfile + '.' + rand_str + '.unmap', 'w')
for line in ireader.reader(ingff):
if line.startswith(('#', 'track', 'browser', 'visibility')): continue
if not line.strip(): continue
line = line.strip()
fields = line.split('\t')
try:
start = int(fields[3]) - 1 #0-based
end = int(fields[4]) / 1
feature_size = end - start
except:
print('Cannot recognize \"start\" and \"end\" coordinates. Skip ' +
line,
file=sys.stderr)
if outfile:
print(line, file=UNMAP)
continue
if fields[6] not in ['+', '-', '.']:
print('Cannot recognize \"strand\". Skip ' + line, file=sys.stderr)
if outfile:
print(line, file=UNMAP)
continue
strand = '-' if fields[6] == '-' else '+'
chrom = fields[0]
a = map_coordinates(mapping,
chrom,
start,
end,
strand,
chrom_style=cstyle)
if a is None:
if outfile is None:
print(line + '\tfail (no match to target assembly)')
else:
print(line, file=UNMAP)
continue
if len(a) != 2:
if outfile is None:
print(line + '\tfail (multpile match to target assembly)')
else:
print(line, file=UNMAP)
else:
if (int(a[1][2]) - int(
a[1][1])) != feature_size: # check if it is exact match
if outfile is None:
print(line + '\tfail (not exact match)')
else:
print(line, file=UNMAP)
fields[0] = a[1][0] # chrom
fields[3] = int(a[1][1]) + 1 # start, 1-based
fields[4] = int(a[1][2])
fields[6] = a[1][3]
if outfile is None:
print(line + '\t->\t' + '\t'.join([str(i) for i in fields]))
else:
print('\t'.join([str(i) for i in fields]), file=FILE_OUT)
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, 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_region_file(mapping,
inbed,
outfile=None,
min_ratio=0.85,
cstyle='a'):
'''
Convert large genomic regions (in bed format) between assemblies.
BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
Parameters
----------
mapping : dict
Dictionary with source chrom name as key, IntervalTree object as value.
inbed : file
Input BED file.
outfile : str, optional
Prefix of output files.
min_ratio : float, optional
Minimum ratio of query bases that must remap
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.
'''
# check if 'outfile' was set. If not set, print to screen, if set, print to file
if outfile is not None:
FILE_OUT = open(outfile, 'w')
UNMAP = open(outfile + '.unmap', 'w')
else:
pass
for line in ireader.reader(inbed):
if line.startswith(('#', 'track', 'browser')): continue
if not line.strip(): continue
line = line.strip()
fields = line.split()
strand = '+'
# filter out line less than 3 columns
if len(fields) < 3:
print("Less than 3 fields. skip " + line, file=sys.stderr)
if outfile:
print(line + '\tInvalidBedFormat', file=UNMAP)
continue
try:
int(fields[1])
except:
print("Start coordinate is not an integer. skip " + line,
file=sys.stderr)
if outfile:
print(line + '\tInvalidStartPosition', file=UNMAP)
continue
try:
int(fields[2])
except:
print("End coordinate is not an integer. skip " + line,
file=sys.stderr)
if outfile:
print(line + '\tInvalidEndPosition', file=UNMAP)
continue
if int(fields[1]) > int(fields[2]):
print(
"\"Start\" is larger than \"End\" coordinate is not an integer. skip "
+ line,
file=sys.stderr)
if outfile:
print(line + '\tStart>End', file=UNMAP)
continue
# try to reset strand
try:
for f in fields:
if f in ['+', '-']:
strand = f
except:
pass
chrom = fields[0]
start = int(fields[1])
end = int(fields[2])
total_query_length = end - start #used to calculate q_map_ratio
a = map_coordinates(mapping,
chrom,
start,
end,
strand,
chrom_style=cstyle)
# input: 'chr1',246974830,247024835
# output: [('chr1', 246974830, 246974833, '+' ), ('chr1', 248908207, 248908210, '+' ), ('chr1', 247024833, 247024835, '+'), ('chr1', 249058210, 249058212,'+')]
# [('chr1', 246974830, 246974833), ('chr1', 248908207, 248908210)]
if (a is None) or (len(a) % 2 != 0):
if outfile is None:
print(line + '\tFail\tUnmap')
else:
print(line + '\tFail\tUnmap', file=UNMAP)
continue
#when a == 2, there is one-to-one match (i.e. 100% match)
if len(a) == 2:
#reset fields to target assembly
fields[0] = a[1][0]
fields[1] = a[1][1]
fields[2] = a[1][2]
for i in range(0, len(fields)): #update the strand information
if fields[i] in ['+', '-']:
fields[i] = a[1][3]
if outfile is None:
print(line + '\t->\t' + '\t'.join([str(i) for i in fields]) +
"\tmap_ratio=1.0000")
else:
print('\t'.join([str(i)
for i in fields]) + "\tmap_ratio=1.0000",
file=FILE_OUT)
#when a is an even number but bigger than 2, each segment is 100% match,
# but the whole region is not. In this case, check *min_ratio* of the query
if len(a) > 2:
a_query = a[::
2] #EVEN: [('chr1', 246974830, 246974833, '+'), ('chr1', 247024833, 247024835, '+')]
a_query_mapped_nt = sum([i[2] - i[1]
for i in a_query]) #sum([3,2])
a_target = a[
1::
2] #ODDS: [('chr1', 248908207, 248908210, '+'), ('chr1', 249058210, 249058212, '+')]
a_target_chroms = set([i[0] for i in a_target])
a_target_chroms = set([i[0] for i in a_target])
a_target_starts = [i[1] for i in a_target]
a_target_ends = [i[2] for i in a_target]
#print (a_target_ends)
map_ratio = a_query_mapped_nt / total_query_length
#map_ratio > cutoff
if map_ratio >= min_ratio:
if len(a_target_chroms) == 1:
t_chrom = a_target_chroms.pop()
fields[0] = t_chrom
fields[1] = min(a_target_starts)
fields[2] = max(a_target_ends)
if outfile is None:
print(line + '\t->\t' +
'\t'.join([str(i) for i in fields]) +
("\tmap_ratio=%.4f" % map_ratio))
else:
print('\t'.join([str(i) for i in fields]) +
("\tmap_ratio=%.4f" % map_ratio),
file=FILE_OUT)
else:
if outfile is None: print(line + '\tFail\tCrossChroms')
else: print(line + '\tFail\tCrossChroms', file=UNMAP)
# map_ratio > 0 but < cutoff
elif map_ratio > 0 and map_ratio < min_ratio:
if outfile is None:
print(line + '\tFail' + ("\tmap_ratio=%.4f" % map_ratio))
else:
print(line + '\tFail' + ("\tmap_ratio=%.4f" % map_ratio),
file=UNMAP)
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)])
def crossmap_wig_file(mapping,
in_file,
out_prefix,
taget_chrom_size,
in_format,
binSize=100000):
'''
Description
-----------
Convert genome coordinates (in wiggle/bigwig format) between assemblies.
wiggle format: http://genome.ucsc.edu/goldenPath/help/wiggle.html
bigwig format: http://genome.ucsc.edu/goldenPath/help/bigWig.html
Parameters
----------
mapping : dict
Dictionary with source chrom name as key, IntervalTree object as value.
in_file : file
Input file in wig or bigwig format. Both "variableStep" and "fixedStep" wiggle
lines are supported.
out_prefix : str
Prefix of output files.
taget_chrom_size : dict
Chromosome size of the target genome assembly. Key is chromosome ID, value is the
length of the chromosome. Note, the chromosome ID and length information were
extracted from the chain file, therefore, the chrom_IDs can be with or without
the leading "chr".
in_format : str
Either "wiggle" or "bigwig"
binSize : int
The chunk size when reading bigwig file in each iteration.
'''
OUT_FILE1 = open(out_prefix + '.bgr', 'w') # original bgr file
OUT_FILE2 = open(out_prefix + '.sorted.bgr', 'w') # sorted bgr file
OUT_FILE3 = pyBigWig.open(out_prefix + '.bw', "w") # bigwig file
chrom_style = 'chr1'
if in_format.upper() == "WIGGLE":
logging.info("Liftover wiggle file \"%s\" to bedGraph file \"%s\"" %
(in_file, out_prefix + '.bgr'))
for chrom, start, end, strand, score in wiggleReader(in_file):
chrom_style = chrom
maps = map_coordinates(mapping, chrom, start, end, '+')
if maps is None:
continue
if len(maps) == 2:
print('\t'.join([
str(i)
for i in [maps[1][0], maps[1][1], maps[1][2], score]
]),
file=OUT_FILE1)
else:
continue
maps[:] = []
OUT_FILE1.close()
logging.info("Merging overlapped entries in bedGraph file")
for (chrom, start, end, score) in bgrMerge.merge(out_prefix + '.bgr'):
print('\t'.join([str(i) for i in (chrom, start, end, score)]),
file=OUT_FILE2)
OUT_FILE2.close()
os.remove(out_prefix + '.bgr') #remove .bgr, keep .sorted.bgr
# make bigwig header
target_chroms_sorted = []
for k in sorted(taget_chrom_size.keys()):
i_chrom = update_chromID(chrom_style, k)
i_value = taget_chrom_size[k]
target_chroms_sorted.append((i_chrom, i_value))
# add bigwig header
logging.info("Writing header to \"%s\" ..." % (out_prefix + '.bw'))
OUT_FILE3.addHeader(target_chroms_sorted)
# add entries to bigwig file
logging.info("Writing entries to \"%s\" ..." % (out_prefix + '.bw'))
for line in ireader.reader(out_prefix + '.sorted.bgr'):
r_chr, r_st, r_end, r_value = line.split()
OUT_FILE3.addEntries([r_chr], [int(r_st)],
ends=[int(r_end)],
values=[float(r_value)])
OUT_FILE3.close()
elif in_format.upper() == "BIGWIG":
logging.info("Liftover bigwig file %s to bedGraph file %s:" %
(in_file, out_prefix + '.bgr'))
for chrom, start, end, score in bigwigReader(in_file):
chrom_style = chrom
maps = map_coordinates(mapping, chrom, start, end, '+')
try:
if maps is None: continue
if len(maps) == 2:
print('\t'.join([
str(i)
for i in [maps[1][0], maps[1][1], maps[1][2], score]
]),
file=OUT_FILE1)
else:
continue
except:
continue
maps[:] = []
OUT_FILE1.close()
logging.info("Merging overlapped entries in bedGraph file")
for (chrom, start, end, score) in bgrMerge.merge(out_prefix + '.bgr'):
print('\t'.join([str(i) for i in (chrom, start, end, score)]),
file=OUT_FILE2)
OUT_FILE2.close()
os.remove(out_prefix + '.bgr') #remove .bgr, keep .sorted.bgr
logging.info("Writing header to \"%s\" ..." % (out_prefix + '.bw'))
# make bigwig header
target_chroms_sorted = []
for k in sorted(taget_chrom_size.keys()):
i_chrom = update_chromID(chrom_style, k)
i_value = taget_chrom_size[k]
target_chroms_sorted.append((i_chrom, i_value))
# add bigwig header
OUT_FILE3.addHeader(target_chroms_sorted)
# add entries to bigwig file
logging.info("Writing entries to \"%s\" ..." % (out_prefix + '.bw'))
for line in ireader.reader(out_prefix + '.sorted.bgr'):
r_chr, r_st, r_end, r_value = line.split()
OUT_FILE3.addEntries([r_chr], [int(r_st)], [int(r_end)],
[float(r_value)])
OUT_FILE3.close()
else:
raise Exception("Unknown foramt. Must be 'wiggle' or 'bigwig'")
