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pbcore.io
=========
The ``pbcore.io`` package provides a number of lightweight interfaces
to PacBio data files and other standard bioinformatics file formats.
Preferred usage is to import classes directly from the ``pbcore.io``
package.
The classes within ``pbcore.io`` adhere to a few conventions, in order
to provide a uniform API:
- Each data file type is thought of as a container of a `Record`
type; all `Reader` classes support streaming access by iterating on the
reader object, and `IndexedBarReader` additionally provides
random-access to alignments/reads.
For example::
from pbcore.io import *
with IndexedBamReader(filename) as f:
for r in f:
process(r)
To make scripts a bit more user friendly, a progress bar can be
easily added using the `tqdm` third-party package::
from pbcore.io import *
from tqdm import tqdm
with IndexedBamReader(filename) as f:
for r in tqdm(f):
process(r)
- The constructor argument needed to instantiate `Reader` and
`Writer` objects can be either a filename (which can be suffixed
by ".gz" for all file types) or an open file handle.
The reader/writer classes will do what you would expect.
BAM format
----------
The BAM format is a standard format described aligned and unaligned
reads. PacBio uses the BAM format exclusively.
For basic functionality, one should use :class:`BamReader`;
use :class:`IndexedBamReader` API for full index operation support,
which requires the auxiliary *PacBio BAM index file* (``bam.pbi`` file).
.. autoclass:: pbcore.io.BamAlignment
:members:
:undoc-members:
.. autoclass:: pbcore.io.BamReader
:members:
:undoc-members:
.. autoclass:: pbcore.io.IndexedBamReader
:members:
:undoc-members:
FASTA Format
------------
FASTA is a standard format for sequence data. We recommmend using the
`FastaTable` class, which provides random access to indexed FASTA
files (using the conventional SAMtools "fai" index).
.. autoclass:: pbcore.io.FastaTable
:members:
.. autoclass:: pbcore.io.FastaRecord
:members:
.. autoclass:: pbcore.io.FastaReader
:members:
.. autoclass:: pbcore.io.FastaWriter
:members:
FASTQ Format
------------
FASTQ is a standard format for sequence data with associated quality scores.
.. autoclass:: pbcore.io.FastqRecord
:members:
.. autoclass:: pbcore.io.FastqReader
:members:
.. autoclass:: pbcore.io.FastqWriter
:members:
GFF Format (Version 3)
----------------------
The GFF format is an open and flexible standard for representing genomic features.
.. autoclass:: pbcore.io.Gff3Record
:members:
.. autoclass:: pbcore.io.GffReader
:members:
.. autoclass:: pbcore.io.GffWriter
:members:
|
