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#!/usr/bin/python3
"""
Application to convert AXT file to LAV file. Reads an AXT file from standard
input and writes a LAV file to standard out; some statistics are written to
standard error.
usage: %prog primary_spec secondary_spec [--silent] < axt_file > lav_file
Each spec is of the form seq_file[:species_name]:lengths_file.
- seq_file should be a format string for the file names for the individual
sequences, with %s to be replaced by the alignment's src field. For
example, "hg18/%s.nib" would prescribe files named "hg18/chr1.nib",
"hg18/chr2.nib", etc.
- species_name is optional. If present, it is prepended to the alignment's
src field.
- Lengths files provide the length of each chromosome (lav 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 sys
import bx.align.axt
import bx.align.lav
def usage(s=None):
message = __doc__
if s is None:
sys.exit(message)
else:
sys.exit(f"{s}\n{message}")
def main():
global debug
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 file name and length")
if secondary is None:
usage("missing secondary file name and length")
try:
(primaryFile, primary, primaryLengths) = parse_spec(primary)
except Exception:
usage("bad primary spec (must be seq_file[:species_name]:lengths_file")
try:
(secondaryFile, secondary, secondaryLengths) = parse_spec(secondary)
except Exception:
usage("bad secondary spec (must be seq_file[:species_name]:lengths_file")
# read the lengths
speciesToLengths = {}
speciesToLengths[primary] = read_lengths(primaryLengths)
speciesToLengths[secondary] = read_lengths(secondaryLengths)
# read the alignments
out = bx.align.lav.Writer(sys.stdout, attributes={"name_format_1": primaryFile, "name_format_2": secondaryFile})
axtsRead = 0
axtsWritten = 0
for axtBlock in bx.align.axt.Reader(
sys.stdin, species_to_lengths=speciesToLengths, species1=primary, species2=secondary, support_ids=True
):
axtsRead += 1
out.write(axtBlock)
axtsWritten += 1
out.close()
if not silent:
sys.stderr.write("%d blocks read, %d written\n" % (axtsRead, axtsWritten))
def parse_spec(spec): # returns (seq_file,species_name,lengths_file)
fields = spec.split(":")
if len(fields) == 2:
return (fields[0], "", fields[1])
elif len(fields) == 3:
return (fields[0], fields[1], fields[2])
else:
raise ValueError
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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