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from __future__ import absolute_import
from __future__ import print_function
__all__ = [ "openAlignmentFile",
"openIndexedAlignmentFile",
"entryPoint" ]
from pbcore.io import (IndexedFastaReader, FastaReader,
BaxH5Reader, BasH5Reader, BasH5Collection,
CmpH5Reader, BamReader, IndexedBamReader,
GffReader, FastqReader,
PacBioBamIndex, openDataSet)
def openIndexedAlignmentFile(fname, referenceFastaFname=None, sharedIndex=None):
"""
Factory function to get a handle to a reader for an alignment file
(cmp.h5 or BAM), requiring index capability (built-in for cmp.h5;
requires bam.pbi index for BAM
The reference FASTA, if provided, must have a FASTA index
(fasta.fai).
"""
if fname.endswith("cmp.h5"):
return CmpH5Reader(fname, sharedIndex=sharedIndex)
elif fname.endswith("bam"):
return IndexedBamReader(fname, referenceFastaFname=referenceFastaFname, sharedIndex=sharedIndex)
else:
raise ValueError("Invalid alignment file suffix")
def openAlignmentFile(fname, referenceFastaFname=None, sharedIndex=None):
"""
Factory function to get a handle to a reader for an alignment file
(cmp.h5 or BAM), not requiring index capability
(A `sharedIndex` can still be passed for opening a cmp.h5, for which
the index is compulsory.)
"""
if fname.endswith("cmp.h5"):
return CmpH5Reader(fname, sharedIndex=sharedIndex)
elif fname.endswith("bam"):
return BamReader(fname, referenceFastaFname)
def _openersFor(ext):
if ext == "gff": return (GffReader,)
elif ext in ("fq", "fastq"): return (FastqReader,)
elif ext in ("fa", "fasta"): return (IndexedFastaReader, FastaReader)
elif ext == "cmp.h5": return (CmpH5Reader,)
elif ext == "bas.h5": return (BasH5Reader,)
elif ext == "bax.h5": return (BaxH5Reader,)
elif ext == "fofn": return (BasH5Collection,)
elif ext == "bam": return (IndexedBamReader, BamReader)
elif ext == "pbi": return (PacBioBamIndex,)
elif ext == "xml": return (openDataSet,)
else:
raise ValueError("No known opener class for extension %s" % ext)
def _extension(fname):
parts = fname.split(".")
if parts[-1] == "h5":
return ".".join(parts[-2:])
else:
return parts[-1]
def _openAny(fname, *extraArgs):
ext = _extension(fname)
openers = _openersFor(ext)
lastException = None
for opener in openers:
try:
f = opener(fname, *extraArgs)
return f
except IOError as e:
lastException = e
else:
assert lastException is not None
raise lastException # pylint: disable=raising-bad-type
def entryPoint():
"""
This entry point (callable from the command line as ".open")
provides a convenient way to load up a data file for inspection.
"""
import sys, code, numpy as np
if len(sys.argv) < 2:
print("Requires at least one argument!")
return 1
fname = sys.argv[1]
extraArgs = sys.argv[2:]
f = _openAny(fname, *extraArgs)
banner = "Your file has been opened as object 'f'"
try:
from IPython import embed
embed(banner1=banner)
except ImportError:
code.InteractiveConsole(locals=locals()).interact(banner=banner)
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