def doPslCat(target, outDir, pslOptions=None, singleOutFname=None):
"""
concats psl files, creates one per query
Optionally sort by query and run pslCdnaFilter on it.
"""
pslDir = abspath(join(outDir, "psl", target))
pslCatFnames = []
if singleOutFname:
if isfile(singleOutFname):
open(singleOutFname, "w") # truncate to 0 bytes
else:
pslCatDir = abspath(join(outDir, "pslCat", target))
if not isdir(pslCatDir):
os.makedirs(pslCatDir)
for queryName in os.listdir(pslDir):
if singleOutFname:
pslCatName = singleOutFname
pipeOp = ">>"
else:
pslCatName = join(pslCatDir, queryName)
pipeOp = ">"
if not pslCatName.endswith(".psl"):
pslCatName += ".psl"
logging.info("Concatting psls for query %s to %s" %
(queryName, pslCatName))
queryPath = join(pslDir, queryName)
pslCatFnames.append(pslCatName)
sortCmd = ""
if pslOptions:
filtOpt = bigBlatJob.splitAddDashes(pslOptions)
sortCmd = " | sort -k10,10 | pslCDnaFilter %s stdin stdout " % (
filtOpt)
# yield job line:
# queryPath filtOpt pslCatName
cmd = "cat %(queryPath)s/* %(sortCmd)s %(pipeOp)s %(pslCatName)s" % locals(
)
runCommand(cmd)
def doPslCat(target, outDir, pslOptions=None, singleOutFname=None):
"""
concats psl files, creates one per query
Optionally sort by query and run pslCdnaFilter on it.
"""
pslDir = abspath(join(outDir, "psl", target))
pslCatFnames = []
if singleOutFname:
if isfile(singleOutFname):
open(singleOutFname, "w") # truncate to 0 bytes
else:
pslCatDir = abspath(join(outDir, "pslCat", target))
if not isdir(pslCatDir):
os.makedirs(pslCatDir)
for queryName in os.listdir(pslDir):
if singleOutFname:
pslCatName = singleOutFname
pipeOp = ">>"
else:
pslCatName = join(pslCatDir, queryName)
pipeOp = ">"
if not pslCatName.endswith(".psl"):
pslCatName += ".psl"
logging.info("Concatting psls for query %s to %s" % (queryName, pslCatName))
queryPath = join(pslDir, queryName)
pslCatFnames.append(pslCatName)
sortCmd = ""
if pslOptions:
filtOpt = bigBlatJob.splitAddDashes(pslOptions)
sortCmd = " | sort -k10,10 | pslCDnaFilter %s stdin stdout " % (filtOpt)
# yield job line:
# queryPath filtOpt pslCatName
cmd = "cat %(queryPath)s/* %(sortCmd)s %(pipeOp)s %(pslCatName)s" % locals()
runCommand(cmd)
#!/usr/bin/env python
# job script for bigBlat.py cat step
# concats and optionally sorts/filters all psl files of a query
# args: queryPslDirectory outputPslPath pslOptions (or string "None")
from sys import argv
from os import system
from bigBlatJob import splitAddDashes
args = argv[1:]
queryPath, pslCatName, pslOptions = args
sortCmd = ""
if pslOptions!="None":
filtOpt = splitAddDashes(pslOptions)
sortCmd = " | sort -k10,10 | pslCDnaFilter %s stdin stdout " % (filtOpt)
filtOptStr = splitAddDashes(pslOptions)
cmd = "cat %(queryPath)s/* %(sortCmd)s > %(pslCatName)s" % locals()
ret = system(cmd)
assert(ret==0)
#!/usr/bin/env python
# job script for bigBlat.py cat step
# concats and optionally sorts/filters all psl files of a query
# args: queryPslDirectory outputPslPath pslOptions (or string "None")
from sys import argv
from os import system
from bigBlatJob import splitAddDashes
args = argv[1:]
queryPath, pslCatName, pslOptions = args
sortCmd = ""
if pslOptions != "None":
filtOpt = splitAddDashes(pslOptions)
sortCmd = " | sort -k10,10 | pslCDnaFilter %s stdin stdout " % (filtOpt)
filtOptStr = splitAddDashes(pslOptions)
cmd = "cat %(queryPath)s/* %(sortCmd)s > %(pslCatName)s" % locals()
ret = system(cmd)
assert (ret == 0)
