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

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.

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


     >>> 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, 'header.psl', header=True)
<stdout> (1, 10, 19, 23)

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 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 | +================+=========================+===================================+ | QueryResutl | 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 fragment | | | query_gap_num | 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