[BioRuby] Remote Blast
Anthony Underwood
email2ants at gmail.com
Fri Jul 4 15:22:06 UTC 2008
Hello Naohisa
Thanks for your full and clear response. Unfortunately I really do
need to query the nr nucleotide database.
I am currently working on a exec_ncbi method. Might be a chance to
test the github forking and merging process!
Thanks again
Anthony
On 4 Jul 2008, at 15:05, Naohisa GOTO wrote:
> Hi,
>
> On Fri, 4 Jul 2008 13:13:45 +0100
> Anthony Underwood <email2ants at gmail.com> wrote:
>
>> Hi all, is remote blast broken for bioruby?
>
> No.
> Below script works fine with both bioruby-1.2.1 and CVS HEAD.
> #---------------------------------------------------
> require 'bio'
>
> seq = Bio::Sequence::NA.new(
> "atgcagctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacg
> gtcgcccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtc
> gtgctcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggag
> gccctgactaccctggaagtagcaggccgcatgcttggaggtaaagtccatggttccctg
> gcccgtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaag
> aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg
> cccacctttggcaagaagaagggccccaatgccaactcttaa")
>
> p "-m 7"
>
> remote = Bio::Blast.remote('blastn', 'genes-nt', '-e 0.01')
> blobj = remote.query(seq)
> blobj.each_hit do |hit|
> puts "#{hit.target_def} #{hit.evalue}"
> end
>
> p "-m 8"
>
> remote8 = Bio::Blast.remote('blastn', 'genes-nt', '-m 8 -e 0.01')
> blobj = remote8.query(seq)
> blobj.each_hit do |hit|
> puts "#{hit.target_def} #{hit.evalue}"
> end
> #---------------------------------------------------
>
>> I have some code
>>
>> fasta_sequences.each do |seq_obj|
>> blast_report = remote_blast(seq_obj.seq, 'blastn', 'nr-nt')
>> ..........
>> end
>>
>> this calls the method
>>
>> def remote_blast(seq_obj, program, db = 'nr-nt', options = '', server
>> = 'genomenet')
>> # create BLAST factory object
>> factory = Bio::Blast.remote(program, db, '-m 8' + options, server)
>> report = factory.query(seq_obj)
>> end
>>
>> This fails to return anything - just times out
>
> BLAST search with database 'nr-nt' usually takes very very long time.
> In Bio::Blast#exec_genomenet method, timeout is extended to 600 sec,
> but if the calculation time is longer, timeout error will happen.
>
> The timeout can be shorter than above value depend on your network,
> because administrators of your network can limit maximum timeout
> value in their router and/or proxy.
>
>> If I include the -V option to limit the number of hits returned
>>
>> blast_report = remote_blast(seq_obj.seq, 'blastn', 'nr-nt', "-V
>> 10")
>
> '-V' option in blastall means:
> | -V Force use of the legacy BLAST engine [T/F] Optional
> | default = F"
> (taken from blatall help message)
>
> '-v' and '-b' can be used. Be careful they are case sensitive.
> | -v Number of database sequences to show one-line descriptions
> for (V) [Integer]
> | default = 500
> | -b Number of database sequence to show alignments for (B)
> [Integer]
> | default = 250
>
> In addition, using '-e' option to limit e-value is better,
> because default e-value (10.0) is generally too big.
>
>> I get no hits , or a message "RuntimeError: cannot understand
>> response" which I think is due to the "holding page" that occurs when
>> a job is running
>
> Perhaps because unrecognized option was specified.
>
>> Does anybody know a fix for this? Should I start to try and get a
>> ncbi remote blast working. Is there anybody who would like to help
>> with this?
>>
>> Thanks
>>
>> Anthony
>> _______________________________________________
>> BioRuby mailing list
>> BioRuby at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioruby
>
>
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
>
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
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