def build_index(self, filename, indexfile):
"""
Recipe from Brad Chapman's blog
<http://bcbio.wordpress.com/2009/07/26/sorting-genomic-alignments-using-python/>
"""
indexes = interval_index_file.Indexes()
in_handle = open(filename)
reader = maf.Reader(in_handle)
while True:
pos = reader.file.tell()
rec = next(reader)
if rec is None:
break
for c in rec.components:
indexes.add(
c.src,
c.forward_strand_start,
c.forward_strand_end,
pos,
max=c.src_size,
)
index_handle = open(indexfile, "w")
indexes.write(index_handle)
index_handle.close()
def main():
# Parse command line
options, args = doc_optparse.parse( __doc__ )
try:
maf_file = args[0]
# If it appears to be a bz2 file, attempt to open with table
if maf_file.endswith( ".bz2" ):
table_file = maf_file + "t"
if not os.path.exists( table_file ):
doc_optparse.exit( "To index bz2 compressed files first "
"create a bz2t file with bzip-table." )
# Open with SeekableBzip2File so we have tell support
maf_in = SeekableBzip2File( maf_file, table_file )
# Strip .bz2 from the filename before adding ".index"
maf_file = maf_file[:-4]
elif maf_file.endswith( ".lzo" ):
from bx.misc.seeklzop import SeekableLzopFile
table_file = maf_file + "t"
if not os.path.exists( table_file ):
doc_optparse.exit( "To index lzo compressed files first "
"create a lzot file with lzop_build_offset_table." )
# Open with SeekableBzip2File so we have tell support
maf_in = SeekableLzopFile( maf_file, table_file )
# Strip .lzo from the filename before adding ".index"
maf_file = maf_file[:-4]
else:
maf_in = open( maf_file )
# Determine the name of the index file
if len( args ) > 1:
index_file = args[1]
else:
index_file = maf_file + ".index"
if options.species:
species = options.species.split( "," )
else:
species = None
except:
doc_optparse.exception()
maf_reader = bx.align.maf.Reader( maf_in )
indexes = interval_index_file.Indexes()
# Need to be a bit tricky in our iteration here to get the 'tells' right
while 1:
pos = maf_reader.file.tell()
block = maf_reader.next()
if block is None: break
for c in block.components:
if species is not None and c.src.split('.')[0] not in species:
continue
indexes.add( c.src, c.forward_strand_start, c.forward_strand_end, pos, max=c.src_size )
out = open( index_file, 'w' )
indexes.write( out )
out.close()
def __init__( self, axt_filename, index_filename=None, keep_open=False, species1 = None, species2=None, species_to_lengths=None, support_ids=False ):
if index_filename is None: index_filename = axt_filename + ".index"
self.indexes = interval_index_file.Indexes( filename=index_filename )
self.axt_filename = axt_filename
# nota bene: (self.species1 = species1 or "species1") is incorrect if species1=""
self.species1 = species1
if (self.species1 == None): self.species1 = "species1"
self.species2 = species2
if (self.species2 == None): self.species2 = "species2"
self.species_to_lengths = species_to_lengths
self.support_ids = support_ids # for extra text at end of axt header lines
if keep_open:
self.f = open( axt_filename )
else:
self.f = None
def index(gff_file, index_file=None):
index = interval_index_file.Indexes()
with open(gff_file) as in_handle:
while 1:
pos = in_handle.tell()
line = in_handle.readline()
if not line:
break
if not line.startswith("#"):
parts = line.split("\t")
(seqid, gtype, source, start, end) = parts[:5]
index.add(seqid, int(start), int(end), pos)
if index_file is None:
index_file = gff_file + ".index"
with open(index_file, "w") as index_handle:
index.write(index_handle)
return index_file
def build_index(in_file, index_file):
indexes = interval_index_file.Indexes()
with open(in_file) as in_handle:
reader = maf.Reader(in_handle)
while 1:
pos = reader.file.tell()
rec = reader.next()
if rec is None:
break
for c in rec.components:
indexes.add(c.src,
c.forward_strand_start,
c.forward_strand_end,
pos,
max=c.src_size)
with open(index_file, "w") as index_handle:
indexes.write(index_handle)
def main():
# Parse command line
options, args = doc_optparse.parse(__doc__)
if options.version: return
try:
wiggle_file = args[0]
# If it appears to be a bz2 file, attempt to open with table
if wiggle_file.endswith(".bz2"):
table_file = wiggle_file + "t"
if not os.path.exists(table_file):
doc_optparse.exit("To index bz2 compressed files first "
"create a bz2t file with bzip-table.")
# Open with SeekableBzip2File so we have tell support
wiggle_in = SeekableBzip2File(wiggle_file, table_file)
# Strip .bz2 from the filename before adding ".index"
wiggle_file = wiggle_file[:-4]
elif wiggle_file.endswith(".lzo"):
from bx.misc.seeklzop import SeekableLzopFile
table_file = wiggle_file + "t"
if not os.path.exists(table_file):
doc_optparse.exit("To index lzo compressed files first "
"create a lzot file with bzip-table.")
# Open with SeekableBzip2File so we have tell support
wiggle_in = SeekableLzopFile(wiggle_file, table_file)
# Strip .lzo from the filename before adding ".index"
wiggle_file = wiggle_file[:-4]
else:
wiggle_in = open(wiggle_file)
# Determine the name of the index file
if len(args) > 1:
index_file = args[1]
else:
index_file = wiggle_file + ".index"
except:
doc_optparse.exception()
indexes = interval_index_file.Indexes()
# Can't use the iterator, as there is no next() and thus
# no way to access the positions. The following code is
# modified from wiggle.py
last_chrom = None
start = None
end = None
first_pos = None
# always for wiggle data
strand = '+'
mode = "bed"
while 1:
pos = wiggle_in.tell()
line = wiggle_in.readline()
if not line: break
if line.isspace() or line.startswith("track") or line.startswith(
"#") or line.startswith("browser"):
continue
elif line.startswith("bed"):
indexes.add(fields[0], int(fields[1]), int(fields[2]), pos)
elif line.startswith("variableStep") or line.startswith("fixedStep"):
if first_pos != None:
indexes.add(last_chrom, start, end, first_pos)
first_pos = pos
header = bx.wiggle.parse_header(line)
last_chrom = header['chrom']
start = int(header['start']) - 1
end = start
current_step = None
if 'span' in header:
current_span = int(header['span'])
else:
current_span = 1
if 'step' in header:
current_step = int(header['step'])
if line.startswith("variableStep"):
mode = "variableStep"
else:
mode = "fixedStep"
elif mode == "variableStep":
fields = line.split()
end = int(fields[0]) - 1 + current_span
elif mode == "fixedStep":
end += current_step
else:
raise "Unexpected input line: %s" % line.strip()
out = open(index_file, 'w')
indexes.write(out)
out.close()
