Bio.SearchIO.BlatIO module

Bio.SearchIO parser for BLAT output formats.

This module adds support for parsing BLAT outputs. BLAT (BLAST-Like Alignment Tool) is a sequence similarity search program initially built for annotating the human genome.

Bio.SearchIO.BlastIO was tested using standalone BLAT version 34, psLayout version 3. It should be able to parse psLayout version 4 without problems.

More information on BLAT is available from these sites:

• Publication: http://genome.cshlp.org/content/12/4/656

• User guide: http://genome.ucsc.edu/goldenPath/help/blatSpec.html

• Source download: http://www.soe.ucsc.edu/~kent/src

• Executable download: http://hgdownload.cse.ucsc.edu/admin/exe/

• Blat score calculation: http://genome.ucsc.edu/FAQ/FAQblat.html#blat4

Supported Formats

BlatIO supports parsing, indexing, and writing for both PSL and PSLX output formats, with or without header. To parse, index, or write PSLX files, use the ‘pslx’ keyword argument and set it to True.

>>> # blat-psl defaults to PSL files
>>> from Bio import SearchIO
>>> psl = 'Blat/psl_34_004.psl'
>>> qresult = SearchIO.read(psl, 'blat-psl')
>>> qresult
QueryResult(id='hg19_dna', 10 hits)

>>> # set the pslx flag to parse PSLX files
>>> pslx = 'Blat/pslx_34_004.pslx'
>>> qresult = SearchIO.read(pslx, 'blat-psl', pslx=True)
>>> qresult
QueryResult(id='hg19_dna', 10 hits)

For parsing and indexing, you do not need to specify whether the file has a header or not. For writing, if you want to write a header, you can set the ‘header’ keyword argument to True. This will write a ‘psLayout version 3’ header to your output file.

>>> from Bio import SearchIO
>>> qresult = SearchIO.read(psl, "blat-psl")
>>> SearchIO.write(qresult, "example.psl", "blat-psl", header=True)
(1, 10, 19, 23)
>>> import os
>>> os.remove("example.psl")

Note that the number of HSPFragments written may exceed the number of HSP objects. This is because in PSL files, it is possible to have single matches consisting of noncontiguous sequence fragments. This is where the HSPFragment object comes into play. These fragments are grouped into a single HSP because they share the same statistics (e.g. match numbers, BLAT score, etc.). However, they do not share the same sequence attributes, such as the start and end coordinates, making them distinct objects.

In addition to parsing PSL(X) files, BlatIO also computes the percent identities and scores of your search results. This is done using the calculation formula posted here: http://genome.ucsc.edu/FAQ/FAQblat.html#blat4. It mimics the score and percent identity calculation done by UCSC’s web BLAT service.

Since BlatIO parses the file in a single pass, it expects all results from the same query to be in consecutive rows. If the results from one query are spread in nonconsecutive rows, BlatIO will consider them to be separate QueryResult objects.

In most cases, the PSL(X) format uses the same coordinate system as Python (zero-based, half open). These coordinates are anchored on the plus strand. However, if the query aligns on the minus strand, BLAT will anchor the qStarts coordinates on the minus strand instead. BlatIO is aware of this, and will re-anchor the qStarts coordinates to the plus strand whenever it sees a minus strand query match. Conversely, when you write out to a PSL(X) file, BlatIO will reanchor qStarts to the minus strand again.

BlatIO provides the following attribute-column mapping:

Object	Attribute	Column Name, Value
QueryResult	id	Q name, query sequence ID
	seq_len	Q size, query sequence full length
Hit	id	T name, hit sequence ID
	seq_len	T size, hit sequence full length
HSP	hit_end	T end, end coordinate of the last hit fragment
	hit_gap_num	T gap bases, number of bases inserted in hit
	hit_gapopen_num	T gap count, number of hit gap inserts
	hit_span_all	blockSizes, sizes of each fragment
	hit_start	T start, start coordinate of the first hit fragment
	hit_start_all	tStarts, start coordinate of each hit fragment
	match_num	match, number of non-repeat matches
	mismatch_num	mismatch, number of mismatches
	match_rep_num	rep. match, number of matches that are part of repeats
	n_num	N’s, number of N bases
	query_end	Q end, end coordinate of the last
	query_gap_num	query fragment Q gap bases, number of bases inserted in query
	query_gapopen_num	Q gap count, number of query gap inserts
	query_span_all	blockSizes, sizes of each fragment
	query_start	Q start, start coordinate of the first query block
	query_start_all	qStarts, start coordinate of each query fragment
	len [1]	block count, the number of blocks in the alignment
HSPFragment	hit	hit sequence, if present
	hit_strand	strand, hit sequence strand
	query	query sequence, if present
	query_strand	strand, query sequence strand

In addition to the column mappings above, BlatIO also provides the following object attributes:

Object	Attribute	Value
HSP	gapopen_num	Q gap count + T gap count, total number of gap openings
	ident_num	matches + repmatches, total number of identical residues
	ident_pct	percent identity, calculated using UCSC’s formula
	query_is_protein	boolean, whether the query sequence is a protein
	score	HSP score, calculated using UCSC’s formula

Finally, the default HSP and HSPFragment properties are also provided. See the HSP and HSPFragment documentation for more details on these properties.

[1]

You can obtain the number of blocks / fragments in the HSP by invoking len on the HSP

class Bio.SearchIO.BlatIO.BlatPslParser(handle, pslx=False)

Bases: object

Parser for the BLAT PSL format.

__init__(handle, pslx=False)

Initialize the class.

__iter__()

Iterate over BlatPslParser, yields query results.

class Bio.SearchIO.BlatIO.BlatPslIndexer(filename, pslx=False)

Bases: SearchIndexer

Indexer class for BLAT PSL output.

__init__(filename, pslx=False)

Initialize the class.

__iter__()

Iterate over the file handle; yields key, start offset, and length.

get_raw(offset)

Return raw bytes string of a QueryResult object from the given offset.

__abstractmethods__ = frozenset({})

class Bio.SearchIO.BlatIO.BlatPslWriter(handle, header=False, pslx=False)

Bases: object

Writer for the blat-psl format.

__init__(handle, header=False, pslx=False)

Initialize the class.

write_file(qresults)

Write query results to file.