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prepareLodFiles.py
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#!/usr/bin/env python3
#Copyright (C) 2013 by Ngan Nguyen
# Copyright (C) 2012-2019 by UCSC Computational Genomics Lab
#
#Released under the MIT license, see LICENSE.txt
"""Take care of Level-of-detail files
"""
import os
from sonLib.bioio import system
from optparse import OptionGroup
def fixLodFilePath(lodtxtfile, localHalfile, outdir):
#fix the path of the original hal file to point to the created
#link relative to the output directory
relPath = os.path.relpath(localHalfile, start=outdir)
lodTxtBuf = ''
for line in open(lodtxtfile):
tokens = line.split()
if len(tokens) == 2 and tokens[0] == '0':
lodTxtBuf += '0 %s\n' % relPath
else:
lodTxtBuf += line
with open(lodtxtfile, 'w') as lodFile:
lodFile.write(lodTxtBuf)
def getLodFiles(localHalfile, options, outdir):
lodtxtfile = os.path.join(outdir, "lod.txt") #outdir/lod.txt
loddir = os.path.join(outdir, "lod") #outdir/lod
if options.lodtxtfile and options.loddir: #if lod files were given, then just make soft links to them
if os.path.exists(lodtxtfile):
if os.path.abspath(lodtxtfile) != os.path.abspath(options.lodtxtfile):
system("rm %s" %lodtxtfile)
system("ln -s %s %s" %(os.path.abspath(options.lodtxtfile), lodtxtfile))
else:
system("ln -s %s %s" %(os.path.abspath(options.lodtxtfile), lodtxtfile))
if os.path.exists(loddir):
if os.path.abspath(loddir) != os.path.abspath(options.loddir):
if os.path.islink(loddir):
system("rm %s" %loddir)
else:
system("rm -Rf %s" %loddir)
loddir = os.path.join(outdir, os.path.basename(options.loddir))
system("ln -s %s %s" %(os.path.abspath(options.loddir), loddir))
else:
system("ln -s %s %s" %(os.path.abspath(options.loddir), loddir))
else: #if lod files were not given, create them using halLodInterpolate.py
system("halLodInterpolate.py %s %s --outHalDir %s %s" %(localHalfile, lodtxtfile, loddir, options.lodOpts))
fixLodFilePath(lodtxtfile, localHalfile, outdir)
return lodtxtfile, loddir
def getLod(options, localHalfile, outdir):
#Create lod files if useLod is specified
lodtxtfile = ''
loddir = ''
options.lodOpts = ''
if options.lodMaxBlock is not None:
options.lodOpts += '--maxBlock %d ' % options.lodMaxBlock
if options.lodScale is not None:
options.lodOpts += '--scale %f ' % options.lodScale
if options.lodMaxDNA is not None:
options.lodOpts += '--maxDNA %d ' % options.lodMaxDNA
if options.lodInMemory is True:
options.lodOpts += '--inMemory '
if options.lodMinSeqFrac is not None:
options.lodOpts += '--minSeqFrac %f ' % options.lodMinSeqFrac
if options.lodMinCovFrac is not None:
options.lodOpts += '--minCovFrac %f ' % options.lodMinCovFrac
if options.lodChunk is not None:
options.lodOpts += '--chunk %d ' % options.lodChunk
if options.maxCores and int(options.maxCores) > 1 and (options.lod or len(options.lodOpts) > 0):
options.lodOpts += '--numProc %d ' % int(options.maxCores)
if len(options.lodOpts) > 0:
print(options.lodOpts)
options.lod = True
if options.lod:
lodtxtfile, loddir = getLodFiles(localHalfile, options, outdir)
return lodtxtfile, loddir
def getLodLowestLevel(lodtxtfile):
"""Gets the lowest level at which an LOD hal is used instead of the
base-level hal file."""
f = open(lodtxtfile, 'r')
line = f.readline()
level = int(line.split()[0])
while line and level == 0:
line = f.readline()
if len(line.strip()) == 0:
continue
fields = line.strip().split()
if len(fields) == 2 and fields[1] != "max":
level = int(line.split()[0])
f.close()
return level
def addLodOptions(parser):
group = parser.add_argument_group("LEVEL OF DETAILS", "Level-of-detail (LOD) options.")
group.add_argument('--lod', dest='lod', action="store_true", default=False, help='If specified, create "level of detail" (lod) hal files and will put the lod.txt at the bigUrl instead of the original hal file. ')
group.add_argument('--lodTxtFile', dest='lodtxtfile', help='"hal Level of detail" lod text file. If specified, will put this at the bigUrl instead of the hal file. ')
group.add_argument('--lodDir', dest='loddir', help='"hal Level of detail" lod dir. If specified, will put this at the bigUrl instead of the hal file. ')
group.add_argument('--lodMaxBlock', dest='lodMaxBlock', type=int, help='Maximum number of blocks to display in a hal level of detail (see halLodInterpolate.py --help for the default value).', default=None)
group.add_argument('--lodScale', dest='lodScale', type=float, help='Scaling factor between two successive levels of detail (see halLodInterpolate.py --help for the default value).', default=None)
group.add_argument('--lodMaxDNA', dest='lodMaxDNA', type=int, help='Maximum query length such that its hal level of detail will contain nucleotide information. (see halLodInterpolate.py --help for the default value).', default=None)
group.add_argument('--lodInMemory', dest='lodInMemory', action='store_true', help='Load entire hal file into memory when generating levels of detail instead of using hdf5 cache. Could result in drastic speedup. .', default=False)
group.add_argument('--lodMinSeqFrac', dest='lodMinSeqFrac', type=float, help='Minumum sequence length to sample as fraction of step size for level of detail generation: ie sequences with length <= floor(minSeqFrac * step) are ignored (see halLodExtract --help for default value).', default=None)
group.add_argument('--lodMinCovFrac', dest='lodMinCovFrac', type=float, help='Minimum fraction of a genome that must be covered by sequences that exceed --minSeqFrac * step. LODs that would violate this threshold will not be generated (or displayed in the browser). This is seen a better than the alternative, which is to produce unreasonably sparse LODs because half the sequences were not sampled (see halLodInterpolate.py --help for default value).', default=None)
group.add_argument('--lodChunk', dest='lodChunk', type=int, help='HDF5 chunk size for generated levels of detail (see halLodExtract --help for default value).', default=None)
#group.add_argument('--snpwidth', dest='snpwidth', type=int, default=5000, help='Maximum window size to display SNPs. ')
group = parser.add_argument_group(group)