Module:Bio::SearchIO
From BioPerl
| Pdoc documentation: Bio::SearchIO | CPAN documentation: Bio::SearchIO |
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This is a factory module for plugging in different parsers for pairwise alignment objects. It will produce Bio::Search::Result::ResultI compliant objects which in turn contain Bio::Search::Hit::HitI compliant objects and these contain Bio::Search::HSP::HSPI modules.
Supported formats
This module can parser many different pairwise alignment search algorithm results.
| Application | Bio::SearchIO module | sub-formats | comments |
| BLAST | Bio::SearchIO::blast | WU BLAST, NCBI BLAST, bl2seq, rpsblast, psiblast, phiblast, TimeLogic BLAST, UCSC BLAST-like | This supports many different BLAST flavors |
| Tabular BLAST | Bio::SearchIO::blasttable | -m9 and -m8 (NCBI) or -mformat 2 and -mformat 3 (WU-BLAST) tabular format | This is the tab-delimited column format from NCBI BLAST or WU BLAST |
| Megablast BLAST | Bio::SearchIO::megablast | Format 0 | Format 2 should be parseable as standard BLAST output. |
| XML BLAST | Bio::SearchIO::blastxml | NCBI XML format | NCBI's XML DTD |
| FASTA | Bio::SearchIO::fasta | -m 9 -d 0 OR the default -m 1 options | Default or compact formats |
| HMMER | Bio::SearchIO::hmmer | hmmsearch and hmmpfam output parsed | Domains are Hits and alignments fall into the HSP category. Note that query-subject relationship flips between hmmsearch and hmmpfam (i.e. the domain is subject in hmmpfam and query in hmmsearch) |
| Exonerate | Bio::SearchIO::exonerate | CIGAR and VULGAR formats | Only one of CIGAR or VULGAR should be parsed (provide the -vulgar =>1 or -cigar=>1 when initializing the object) |
| Genewise Genomewise | Bio::SearchIO::wise | -genesf output | This parses the -genesf or -genes output from Genewise and Genomewise |
| Sim4 | Bio::SearchIO::sim4 | A={0,1,3,4} output | Cannot parse LAV or 'exon file' formats (A=2 or A=5) |
| PSL alignment format BLAT UCSC tools | Bio::SearchIO::psl | psl format | with or without -noHead option |
| AXT alignment format BLAT UCSC tools | Bio::SearchIO::axt | Directly produced from blat or see the lavToAxt | If you run BLASTZ you can convert the LAV alignment format to AXT alignment format with lavToAxt |
| WABA | Bio::SearchIO::waba | This processes the waba output (not the human readable portion) | The format is a lot like AXT but has four lines per alignment block |
These objects represent the three components of a BLAST or FASTA pairwise database search result. The can be though of like
- Result - a container object for a given query sequence, there will be a Result for every query sequence in a database search
- Hit - a container object for each identified sequence found to be similar to the query sequence, it contains HSPs
