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#!/usr/bin/python3
"""
Application to convert AXT file to MAF file. Reads an AXT file from standard
input and writes a MAF file to standard out; some statistics are written to
standard error.
axt_to_maf primary:lengths_file secondary:lengths_file < axt_file > maf_file
--silent: prevents stats report
Lengths files provide the length of each chromosome (maf format needs this
information but axt file does not contain it). The format is a series of
lines of the form:
<chromosome name> <length>
The chromosome field in each axt block must match some <chromosome name> in
the lengths file.
"""
__author__ = "Bob Harris (rsharris@bx.psu.edu)"
import copy
import sys
import bx.align.axt
import bx.align.maf
def usage(s=None):
message = __doc__
if s is None:
sys.exit(message)
else:
sys.exit(f"{s}\n{message}")
def main():
global debug
##########
# parse the command line
##########
primary = None
secondary = None
silent = False
# pick off options
args = sys.argv[1:]
while len(args) > 0:
arg = args.pop(0)
val = None
fields = arg.split("=", 1)
if len(fields) == 2:
arg = fields[0]
val = fields[1]
if val == "":
usage(f"missing a value in {arg}=")
if (arg == "--silent") and (val is None):
silent = True
elif (primary is None) and (val is None):
primary = arg
elif (secondary is None) and (val is None):
secondary = arg
else:
usage(f"unknown argument: {arg}")
if primary is None:
usage("missing primary species")
if secondary is None:
usage("missing secondary species")
fields = primary.split(":")
if len(fields) != 2:
usage("bad primary species (must be species:lengths_file")
primary = fields[0]
primaryLengths = fields[1]
fields = secondary.split(":")
if len(fields) != 2:
usage("bad secondary species (must be species:lengths_file")
secondary = fields[0]
secondaryLengths = fields[1]
##########
# read the lengths
##########
speciesToLengths = {}
speciesToLengths[primary] = read_lengths(primaryLengths)
speciesToLengths[secondary] = read_lengths(secondaryLengths)
##########
# read the alignments
##########
out = bx.align.maf.Writer(sys.stdout)
axtsRead = 0
axtsWritten = 0
for axtBlock in bx.align.axt.Reader(
sys.stdin, species_to_lengths=speciesToLengths, species1=primary, species2=secondary
):
axtsRead += 1
p = axtBlock.get_component_by_src_start(primary)
if p is None:
continue
s = axtBlock.get_component_by_src_start(secondary)
if s is None:
continue
mafBlock = bx.align.Alignment(axtBlock.score, axtBlock.attributes)
mafBlock.add_component(clone_component(p))
mafBlock.add_component(clone_component(s))
out.write(mafBlock)
axtsWritten += 1
if not silent:
sys.stderr.write("%d blocks read, %d written\n" % (axtsRead, axtsWritten))
def clone_component(c):
return bx.align.Component(c.src, c.start, c.size, c.strand, c.src_size, copy.copy(c.text))
def read_lengths(fileName):
chromToLength = {}
f = open(fileName)
for lineNumber, line in enumerate(f):
line = line.strip()
if line == "":
continue
if line.startswith("#"):
continue
fields = line.split()
if len(fields) != 2:
raise ValueError("bad lengths line (%s:%d): %s" % (fileName, lineNumber, line))
chrom = fields[0]
try:
length = int(fields[1])
except ValueError:
raise ValueError("bad lengths line (%s:%d): %s" % (fileName, lineNumber, line))
if chrom in chromToLength:
raise ValueError("%s appears more than once (%s:%d): %s" % (chrom, fileName, lineNumber, line))
chromToLength[chrom] = length
f.close()
return chromToLength
if __name__ == "__main__":
main()
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