On Wed, Nov 24, 2010 at 11:44 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
The BLAST+ suite actually lets you ask for certain other predefined columns in the tabular output. I am wondering about offering a "full" tabular output option in the BLAST+ wrappers - this seems simpler than making the user pick and choose which columns they want. e.g. for blastp:
The supported format specifiers are: qseqid means Query Seq-id qgi means Query GI qacc means Query accesion sseqid means Subject Seq-id sallseqid means All subject Seq-id(s), separated by a ';' sgi means Subject GI sallgi means All subject GIs sacc means Subject accession sallacc means All subject accessions qstart means Start of alignment in query qend means End of alignment in query sstart means Start of alignment in subject send means End of alignment in subject qseq means Aligned part of query sequence sseq means Aligned part of subject sequence evalue means Expect value bitscore means Bit score score means Raw score length means Alignment length pident means Percentage of identical matches nident means Number of identical matches mismatch means Number of mismatches positive means Number of positive-scoring matches gapopen means Number of gap openings gaps means Total number of gaps ppos means Percentage of positive-scoring matches frames means Query and subject frames separated by a '/' qframe means Query frame sframe means Subject frame
Note that calculating and recording of the above will add computation cost and IO load - so keeping the default std set of columns as the default in the Galaxy wrapper makes sense to me.
Potentially the BLAST XML output can be converted into this full tabular output too - I expect so but it may not be so easy.
I've started work on an extended 22 column tabular output option from the BLAST tools, covering what I consider to be all the important extra fields available, including the ability to convert from BLAST XML to this 22 column format. The work in progress is here if anyone wants to look: http://bitbucket.org/peterjc/galaxy-central/changeset/blastplus_nov25 Peter