mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
84 lines
2.6 KiB
Python
84 lines
2.6 KiB
Python
#!/usr/bin/env python
|
|
#Guruprasad Ananda
|
|
"""
|
|
Converts coordinates from one build/assembly to another using liftOver binary and mapping files downloaded from UCSC.
|
|
"""
|
|
|
|
import os, string, subprocess, sys
|
|
import tempfile
|
|
import re
|
|
|
|
assert sys.version_info[:2] >= ( 2, 4 )
|
|
|
|
def stop_err(msg):
|
|
sys.stderr.write(msg)
|
|
sys.exit()
|
|
|
|
def safe_bed_file(infile):
|
|
"""Make a BED file with track and browser lines ready for liftOver.
|
|
|
|
liftOver will fail with track or browser lines. We can make it happy
|
|
by converting these to comments. See:
|
|
|
|
https://lists.soe.ucsc.edu/pipermail/genome/2007-May/013561.html
|
|
"""
|
|
fix_pat = re.compile("^(track|browser)")
|
|
(fd, fname) = tempfile.mkstemp()
|
|
in_handle = open(infile)
|
|
out_handle = open(fname, "w")
|
|
for line in in_handle:
|
|
if fix_pat.match(line):
|
|
line = "#" + line
|
|
out_handle.write(line)
|
|
in_handle.close()
|
|
out_handle.close()
|
|
return fname
|
|
|
|
if len( sys.argv ) < 9:
|
|
stop_err( "USAGE: prog input out_file1 out_file2 input_dbkey output_dbkey infile_type minMatch multiple <minChainT> <minChainQ> <minSizeQ>" )
|
|
|
|
infile = sys.argv[1]
|
|
outfile1 = sys.argv[2]
|
|
outfile2 = sys.argv[3]
|
|
in_dbkey = sys.argv[4]
|
|
mapfilepath = sys.argv[5]
|
|
infile_type = sys.argv[6]
|
|
gff_option = ""
|
|
if infile_type == "gff":
|
|
gff_option = "-gff "
|
|
minMatch = sys.argv[7]
|
|
multiple = int(sys.argv[8])
|
|
multiple_option = ""
|
|
if multiple:
|
|
minChainT = sys.argv[9]
|
|
minChainQ = sys.argv[10]
|
|
minSizeQ = sys.argv[11]
|
|
multiple_option = " -multiple -minChainT=%s -minChainQ=%s -minSizeQ=%s " %(minChainT,minChainQ,minSizeQ)
|
|
|
|
try:
|
|
assert float(minMatch)
|
|
except:
|
|
minMatch = 0.1
|
|
#ensure dbkey is set
|
|
if in_dbkey == "?":
|
|
stop_err( "Input dataset genome build unspecified, click the pencil icon in the history item to specify it." )
|
|
|
|
if not os.path.isfile( mapfilepath ):
|
|
stop_err( "%s mapping is not currently available." % ( mapfilepath.split('/')[-1].split('.')[0] ) )
|
|
|
|
safe_infile = safe_bed_file(infile)
|
|
cmd_line = "liftOver " + gff_option + "-minMatch=" + str(minMatch) + multiple_option + " " + safe_infile + " " + mapfilepath + " " + outfile1 + " " + outfile2 + " > /dev/null"
|
|
|
|
try:
|
|
# have to nest try-except in try-finally to handle 2.4
|
|
try:
|
|
proc = subprocess.Popen( args=cmd_line, shell=True, stderr=subprocess.PIPE )
|
|
returncode = proc.wait()
|
|
stderr = proc.stderr.read()
|
|
if returncode != 0:
|
|
raise Exception, stderr
|
|
except Exception, e:
|
|
raise Exception, 'Exception caught attempting conversion: ' + str( e )
|
|
finally:
|
|
os.remove(safe_infile)
|