Scripting against a remote HTML blast server

## Scripting against the CN Solexa blast server:

## See "blast.form.html", the HTML dump generated by "blast.jsp". This

## file shows how the names for the various options.

## The blast server page

URL=http://.../blast.jsp

URL=http://.../blast.cgi

## Get this from firefox (Note, expires after about 5 min!)

JSESSIONID=

JSESSIONID=BE55C37071E8CE748053DBCC47FCA3F3

JSESSIONID=1D179D4B6EF55555D344E388D6ABEA19

JSESSIONID=8921525F177EE917E5A27D3FB0CC577D

## Sequence file to submit to the form

SEQFILE=test.seq

SEQFILE=C02HBa0008G02.seq

## All other settings will be default ...

## Don't forget to redirect the result somewhere sensible

curl \

--cookie JSESSIONID=$JSESSIONID \

--form SEQFILE=@$SEQFILE \

--form DATALIB=potato \

$URL \

> $SEQFILE.cn.blast

## Try grabbing (lots of) XML output

JSESSIONID=AE961CF9BF250CCF656832143701BE59

SEQFILE=test.seq

curl \

--cookie JSESSIONID=$JSESSIONID \

--form SEQFILE=@$SEQFILE \

--form DATALIB=potato \

--form ALIGNMENT_VIEW=7 \

--form DESCRIPTIONS=500 \

--form ALIGNMENTS=500 \

$URL \

> $SEQFILE.cn.blast.xml

## Test the XML format using BioPerl

perl -e 'use Bio::SearchIO;

while($r = Bio::SearchIO->

new(

-file=>"$SEQFILE.cn.blast.xml",

-format=>blastxml,

)->next_result){

print $r->query_name, "\n";

while( $h = $r->next_hit ) {

print "\t", $h->name, "\n";

}

}

'

## Looks good!