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__all__ = ["openAlignmentFile",
"openIndexedAlignmentFile",
"entryPoint"]
from pbcore.io import (IndexedFastaReader, FastaReader,
BamReader, IndexedBamReader,
GffReader, FastqReader,
PacBioBamIndex, openDataSet)
def raise_no_h5():
raise NotImplementedError("hdf5 file support has been removed")
def openIndexedAlignmentFile(fname, referenceFastaFname=None, sharedIndex=None):
"""
Factory function to get a handle to a reader for an alignment file (BAM),
requires bam.pbi index
The reference FASTA, if provided, must have a FASTA index
(fasta.fai).
"""
if fname.endswith(".h5"):
raise_no_h5()
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 (BAM),
not requiring index capability
"""
if fname.endswith("cmp.h5"):
raise_no_h5()
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":
raise_no_h5()
elif ext == "bas.h5":
raise_no_h5()
elif ext == "bax.h5":
raise_no_h5()
elif ext == "fofn":
raise_no_h5()
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":
raise_no_h5()
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
import code
import 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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