EnsEMBL::IO meeting - Tue 20 May 14:00 Copper Room
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- Talked to Anne about possible work.
- Pointed me to Miguel, Compara might need some parsers.
- Miguel suggested BLAST parser, developed independently by different groups,
  pointed to Harpreet for web parser, told me what/where Compara and
  genebuilder use.
- Talked to Harpreet, checked out private sanger_plugins repository for
  NCBI BLAST parser used by web team.
- Created feature/blast_parser branch.
- Explored scope and contexts of existing BLAST parsers.

Web
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Use NCBIBLAST module in private sanger-plugins repo.
It simply parses the tab result file produced by the ncbi blast program "blast-formatter".

Output: a sequence of lines, each line/record composed of at least 13 fields:
0: qid (qseqid)
1: qstart (query start)
2: qend
3: tid (sseqid)
4: tstart (sstart)
5: tend (send)
6: score
7: evalue
8: pident
9: len (length)
10: aln
11: qframe
12: tframe (sframe)

Note: aln option doesn't seem to be a valid format specifier for blat-formatter of BLAST2.2.25.
Ouptut format used to produce test files is:
7 qseqid qstart qend sseqid sstart send score evalue pident length qframe sframe

Compara
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Parser is Bio::EnsEMBL::Compara::RunnableDB::BlastAndParsePAF.
Run ncbi_blastp and store the output into PeptideAlignFeature objects which are then stored
in the compara database.

blastp is run with -outfmt option (custom).

Output: a sequence of lines/records, each record composed of 14/16 fields

7 qacc sacc evalue score nident pident qstart qend sstart send length positive ppos [qseq sseq]
|
--> code meaning: "tabular with comment lines"

Genebuilders
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Use Bio::EnsEMBL::Analysis::Tools::BPlite, a port of bioperl 0.7 BPlite blast parser.
The description says:
"There are differences in the format of the various flavors of BLAST".
BPlite parses BLASTN, BLASTP, BLASTX, TBLASTN, TBLASTX reports from both high-perf
WU-BLAST and the more generic NCBI-BLAST.

BPlite have accompanying modules in Bio::EnsEMBL::Analysis::Tools::BPlite::[HSP,Iteration,Sbjct]
Iteration represents object for parsing a single iteration of a PSI-BLAST report.

and related Bio::EnsEMBL::Analysis::Tools::FilterBPlite.

BPlite inherits from Bio::Root::IO and Bio::SeqAnalysisParserI from Bioperl.
A subject is a BLAST hit, which may have several alignments (HSP, high scoring pairs) associated
with it.