def main(argv=sys.argv[1:]):
"""Command-line program
Parameters
----------
argv : list, optional
A list of command-line arguments, which will be processed
as if the script were called from the command line if
:py:func:`main` is called directly.
Default: `sys.argv[1:]`. The command-line arguments, if the script is
invoked from the command line
"""
sp = SequenceParser()
bp = BaseParser()
parser = argparse.ArgumentParser(
description=format_module_docstring(__doc__),
formatter_class=argparse.RawDescriptionHelpFormatter,
parents=[bp.get_parser(), sp.get_parser()])
parser.add_argument("-k",
dest="read_length",
metavar="READ_LENGTH",
type=int,
default=29,
help="K-mer length to generate from input file. " +
"(Default: 29)")
parser.add_argument(
"--offset",
type=int,
default=14,
help=
"Offset from 5' end of plus-strand read at which to attribute score (Default: 14)"
)
parser.add_argument("--mismatches",
metavar="N",
type=int,
default=0,
help="Number of mismatches tolerated in alignment. " +
"(Default: 0)")
parser.add_argument(
"--bowtie",
dest="bowtie",
default="/usr/local/bin/bowtie",
type=str,
help="Location of bowtie binary (Default: ``/usr/local/bin/bowtie``)")
parser.add_argument("--have_kmers",default=False,action="store_true",
help="If specified, use k-mer files from previous run. "+\
" In this case 'sequence_file' should be the value "+\
"'outbase' from the k-mer files you want to use.")
parser.add_argument("--save_kmers",
default=False,
action="store_true",
help="Save k-mer files for reuse in a subsequent run.")
parser.add_argument(
"-p",
"--processes",
type=int,
default=2,
metavar="N",
help="Number of processes to use (should be <= number of chromosomes")
parser.add_argument(
"ebwt",
type=str,
help=
"Bowtie index of genome against which crossmap will be made. In most cases, should be generated from the same sequences that are in `sequence_file`."
)
parser.add_argument("outbase", type=str, help="Basename for output files")
args = parser.parse_args(argv)
bp.get_base_ops_from_args(args)
#filenames
base = "%s_%s_%s" % (args.outbase, args.read_length, args.mismatches)
bed_file = "%s_crossmap.bed" % base
#if not os.path.exists(args.sequence_file):
# printer.write("Could not find source file: %s" % args.sequence_file)
# printer.write("Exiting.")
# sys.exit(1)
if args.have_kmers == True:
import glob
kmer_files = glob.glob(args.sequence_file + "*kmers.fa")
seq_pat = re.compile(r".*_([^_]*)_kmers.fa")
seqs = {seq_pat.search(X).groups()[0]: X for X in kmer_files}
else:
seqs = sp.get_seqdict_from_args(args, index=True)
worker = functools.partial(chrom_worker, args=args)
chroms = seqs.items()
pool = multiprocessing.Pool(processes=args.processes)
bed_filenames = pool.map(worker, chroms, 1)
pool.close()
pool.join()
with open(bed_file, "w") as fout:
for f in sorted(bed_filenames):
shutil.copyfileobj(open(f, "r"), fout)
os.remove(f)
fout.close()
printer.write("Done.")
printer.write(
BigBedMessage.replace("OUTFILE", bed_file.replace(".bed", "")).replace(
"BOWTIE_INDEX", args.ebwt))
def main(argv=sys.argv[1:]):
"""Command-line program
Parameters
----------
argv : list, optional
A list of command-line arguments, which will be processed
as if the script were called from the command line if
:py:func:`main` is called directly.
Default: `sys.argv[1:]`. The command-line arguments, if the script is
invoked from the command line
"""
sp = SequenceParser()
bp = BaseParser()
parser = argparse.ArgumentParser(description=format_module_docstring(__doc__),
formatter_class=argparse.RawDescriptionHelpFormatter,
parents=[bp.get_parser(),sp.get_parser()])
parser.add_argument("-k",dest="read_length",metavar="READ_LENGTH",
type=int,default=29,
help="K-mer length to generate from input file. "+
"(Default: 29)")
parser.add_argument("--offset",type=int,default=14,
help="Offset from 5' end of plus-strand read at which to attribute score (Default: 14)")
parser.add_argument("--mismatches",metavar="N",
type=int,default=0,
help="Number of mismatches tolerated in alignment. "+
"(Default: 0)")
parser.add_argument("--bowtie",dest="bowtie",default="/usr/local/bin/bowtie",
type=str,
help="Location of bowtie binary (Default: ``/usr/local/bin/bowtie``)")
parser.add_argument("--have_kmers",default=False,action="store_true",
help="If specified, use k-mer files from previous run. "+\
" In this case 'sequence_file' should be the value "+\
"'outbase' from the k-mer files you want to use.")
parser.add_argument("--save_kmers",default=False,action="store_true",
help="Save k-mer files for reuse in a subsequent run.")
parser.add_argument("-p","--processes",type=int,default=2,metavar="N",
help="Number of processes to use (should be <= number of chromosomes")
parser.add_argument("ebwt",type=str,
help="Bowtie index of genome against which crossmap will be made. In most cases, should be generated from the same sequences that are in `sequence_file`.")
parser.add_argument("outbase",type=str,
help="Basename for output files")
args = parser.parse_args(argv)
bp.get_base_ops_from_args(args)
#filenames
base = "%s_%s_%s" % (args.outbase, args.read_length, args.mismatches)
bed_file = "%s_crossmap.bed" % base
#if not os.path.exists(args.sequence_file):
# printer.write("Could not find source file: %s" % args.sequence_file)
# printer.write("Exiting.")
# sys.exit(1)
if args.have_kmers == True:
import glob
kmer_files = glob.glob(args.sequence_file+"*kmers.fa")
seq_pat = re.compile(r".*_([^_]*)_kmers.fa")
seqs = { seq_pat.search(X).groups()[0] : X for X in kmer_files }
else:
seqs = sp.get_seqdict_from_args(args,index=True)
worker = functools.partial(chrom_worker,args=args)
chroms = seqs.items()
pool = multiprocessing.Pool(processes=args.processes)
bed_filenames = pool.map(worker,chroms,1)
pool.close()
pool.join()
with open(bed_file,"w") as fout:
for f in sorted(bed_filenames):
shutil.copyfileobj(open(f,"r"),fout)
os.remove(f)
fout.close()
printer.write("Done.")
printer.write(BigBedMessage.replace("OUTFILE",bed_file.replace(".bed","")).replace("BOWTIE_INDEX",args.ebwt))
def main(argv=sys.argv[1:]):
"""Command-line program
Parameters
----------
argv : list, optional
A list of command-line arguments, which will be processed
as if the script were called from the command line if
:py:func:`main` is called directly.
Default: `sys.argv[1:]`. The command-line arguments, if the script is
invoked from the command line
"""
sp = SequenceParser()
mp = MaskParser()
bp = BaseParser()
parser = argparse.ArgumentParser(description=format_module_docstring(__doc__),
formatter_class=argparse.RawDescriptionHelpFormatter,
parents=[bp.get_parser(),sp.get_parser(),mp.get_parser()],
)
parser.add_argument("--maxslide",type=int,default=10,
help="Maximum number of nt to search 5\' and 3\' of intron"+
" boundaries (Default: 10)")
parser.add_argument("--ref",type=str,metavar="ref.bed",default=None,
help="Reference file describing known splice junctions")
parser.add_argument("--slide_canonical",action="store_true",default=False,
help="Slide junctions to canonical junctions if present within equal support region")
parser.add_argument("infile",type=str,metavar="input.bed",
help="BED file describing discovered junctions")
parser.add_argument("outbase",type=str,
help="Basename for output files")
args = parser.parse_args(argv)
bp.get_base_ops_from_args(args)
printer.write("Opening genome from %s..." % args.sequence_file)
genome = sp.get_seqdict_from_args(args)
# load crossmap
cross_hash = mp.get_genome_hash_from_args(args)
# load ref junctions
if args.ref is not None:
printer.write("Loading reference junctions from %s" % args.ref)
known_hash = GenomeHash(list(BED_Reader(open(args.ref))),do_copy=False)
else:
known_hash = GenomeHash()
# set up variables
canonicals_plus = [("GT","AG"),
("GC","AG")
]
canonicals_minus = [("CT","AC"),
("CT","GC")
]
known_in_range = 0
canonical_in_range = 0
repetitive = 0
untouched = 0
c = 0
seen_already = []
outfiles = {
"repetitive" : "%s_repetitive.bed" % args.outbase,
"known" : "%s_shifted_known.bed" % args.outbase,
"canonical" : "%s_shifted_canonical.bed" % args.outbase,
"untouched" : "%s_untouched.bed" % args.outbase,
}
outfiles = { K : argsopener(V,args,"w") for K,V in outfiles.items() }
# process data
printer.write("Opening junctions from %s..." % args.infile)
for ivc in BED_Reader(CommentReader(opener(args.infile))):
processed = False
tup = None
if c % 1000 == 0 and c > 0:
printer.write("Processed: %s\tknown: %s\tshifted to canonical: %s\trepetitive: %s\tuntouched: %s" % \
(c, known_in_range, canonical_in_range, repetitive, untouched))
assert len(ivc) == 2
strand = ivc.strand
minus_range, plus_range = find_match_range(ivc,genome,args.maxslide)
# see if either end of splice junction +- match_range lands in repetitive areas of genome
if covered_by_repetitive(ivc,minus_range,plus_range,cross_hash):
repetitive += 1
outfiles["repetitive"].write(ivc.as_bed())
processed = True
# see if one or more known junctions in range
if processed == False and args.ref is not None:
# find_known_in_range(query_ivc,minus_range,plus_range,knownjunctions)
known_juncs = find_known_in_range(ivc,minus_range,plus_range,known_hash.get_nearby_features(ivc))
if len(known_juncs) > 0:
known_in_range += 1
for my_known in known_juncs:
tup = get_junction_tuple(my_known)
if tup not in seen_already:
outfiles["known"].write(my_known.as_bed())
seen_already.append(tup)
processed = True
# see if one or more canonical junctions in range
if processed == False and args.slide_canonical == True:
canonicals = canonicals_plus if strand == "+" else canonicals_minus
#find_canonicals_in_range(query_ivc,minus_range,plus_range,genome,canonicals)
canonical_juncs = find_canonicals_in_range(ivc,minus_range,plus_range,genome,canonicals)
if len(canonical_juncs) > 0:
canonical_in_range += 1
for can in canonical_juncs:
tup = get_junction_tuple(can)
if tup not in seen_already:
outfiles["canonical"].write(can.as_bed())
seen_already.append(tup)
processed = True
if processed == False:
outfiles["untouched"].write(ivc.as_bed())
untouched += 1
c += 1
# save output
printer.write("Totals: %s\tknown: %s\tshifted to canonical: %s\trepetitive: %s\tuntouched: %s" % \
(c, known_in_range, canonical_in_range, repetitive, untouched))
for v in outfiles.values():
v.close()
printer.write("Done.")
