[Bioperl-pipeline] Still working with biopipe....
matthieu CONTE
m_conte at hotmail.com
Wed Nov 26 08:26:10 EST 2003
I still have problem with my pipeline blast's program.....
"
Creating biopipe
Loading Schema...
Reading Data_setup xml : /home/conte/xml/newhope.xml
Doing DBAdaptor and IOHandler setup
Doing Transformers..
Doing Pipeline Flow Setup
Doing Analysis..
Doing Rules
Doing Job Setup...
Loading of pipeline biopipe completed
2 analysis found.
Running test and setup..
//////////// Analysis Test ////////////
Checking Analysis 1 DataMonger
-------------------- WARNING ---------------------
MSG: Skipping test for DataMonger
---------------------------------------------------
ok
Checking Analysis 2 Blast ok
Fetching Jobs...
Fetched 1 incomplete jobs
Running job /tmp//6/biopipe_DataMonger.1069852072.635.out
/tmp//6/biopipe_DataMonger.1069852072.635.err
"
I think there is a problem with the method "get_Seq_by_id"
I make a little bioperl program to test the use of the association of the
"get_all_ids" and "get_Seq_by_ids" it just return the ids and not sequences
only the method "seq" give the sequences but I didn't manage to use it in my
XML code!.....
use Bio::DB::Fasta;
my $index_file_name='oriz_mfasta.txt';
my $inx=Bio::DB::Fasta->new($index_file_name);
my @ids=$inx->get_all_ids();
foreach (@ids)
{
my $seq=$inx->seq($_);
print "$_!!!!$seq\n";
}
Matthieu CONTE
M. Sc. in Bioinformatics form SIB
00 33 06.68.90.28.70
m_conte at hotmail.com
>From: Shawn Hoon <shawnh at stanford.edu>
>To: "matthieu CONTE" <m_conte at hotmail.com>
>CC: bioperl-pipeline at bioperl.org
>Subject: Re: [Bioperl-pipeline] Still working with biopipe....
>Date: Fri, 21 Nov 2003 10:01:22 -0800
>
>Hi Mattieu,
> Thanks for trying this out.
>are you using the bioperl-pipeline bundle from the website? It looks like
>it and that is the correct version to use.
>There are some problems with you xml file mainly you need to put in the
>attribute ids for iohandler/analysis etc.
>I have attached a corrected version of your xml file. You should try and
>look at bioperl-pipeline/xml/examples/xml/blast_db_flat.xml
>in the examples directory and use that as a template.
>
>
>hope that helps
>
>shawn
><< test.xml >>
>
>
>On Friday, November 21, 2003, at 7:44AM, matthieu CONTE wrote:
>
>>Hi,
>>Still working with biopipe....
>>I’m now trying to create de novo a pipeline to find orthologues between
>>Oryza sativa (Os) and Arabidopsis thaliana (At) by BBMH (best blast mutal
>>hit) (before to develop something more efficient and more complicate !).
>>So I started by a simple blast between a prot from Os to At multifasta
>>prot using the Bio::DB::Fasta and all the bioperl methods needed (and
>>loop on all the Os proteins instead of a massive blast with a chunk of Os
>>proteins). I would like to take a sequence from oriz_mfasta.txt ( using
>>the get_Seq_by_id fonction) and blast it against arabido_mfasta.txt and
>>so on for all the seq of oryza.This is the first step. But, it's not
>>working !!! Probably because it's not really clear for me the function of
>>all the XML code I am working with (especially the <datamonger> tag !).
>>
>>You will find the code and the biopipe output below.
>>Thanks in advance
>>
>>
>>
>><pipeline_setup>
>>
>><!-- FILES -->
>><global
>> rootdir="/home/conte/test_blast"
>> datadir="$rootdir/datahope"
>> workdir="$rootdir/blasthope"
>> inputfile="$datadir/oriz_mfasta.txt"
>> blastpath = ""
>> blast_param1="-p blastp -e 1e-5"
>> blastdb1="$datadir/arabido_mfasta.txt"
>> resultdir1="$rootdir/resulthope/analysis1"
>>/>
>><pipeline_flow_setup>
>><!--CALL MODULES -->
>> <database_setup>
>> <streamadaptor>
>> <module>Bio::Pipeline::Dumper</module>
>> </streamadaptor>
>> <streamadaptor>
>> <module>Bio::DB::Fasta</module>
>> </streamadaptor>
>> </database_setup>
>>
>><!-- IOHANDLER PICK UP iDs-->
>> <iohandler_setup>
>> <iohandler>
>> <adaptor_id>2</adaptor_id>
>> <adaptor_type>STREAM</adaptor_type>
>> <iohandler_type>INPUT</iohandler_type>
>> <method>
>> <name>new</name>
>> <rank>1</rank>
>> <argument>
>> <value>$inputfile</value>
>> </argument>
>> </method>
>> <method>
>> <name>get_Seq_by_id</name>
>> <argument>
>> <value>INPUT</value>
>> </argument>
>> <rank>2</rank>
>> </method>
>> </iohandler>
>>
>> <iohandler>
>> <adaptor_id>2</adaptor_id>
>> <adaptor_type>STREAM</adaptor_type>
>> <iohandler_type>INPUT</iohandler_type>
>> <method>
>> <name>new</name>
>> <rank>1</rank>
>> <argument>
>> <value>$inputfile</value>
>> </argument>
>> </method>
>> <method>
>> <name>get_all_ids</name>
>> <rank>2</rank>
>> </method>
>> </iohandler>
>>
>><!-- PARAMETRES OUTPUT (DUMPER) -->
>> <iohandler>
>> <adaptor_id>1</adaptor_id>
>> <adaptor_type>STREAM</adaptor_type>
>> <iohandler_type>OUTPUT</iohandler_type>
>> <method>
>> <name>new</name>
>> <rank>1</rank>
>> <argument>
>> <tag>-dir</tag>
>> <value>$resultdir1</value>
>> SCALAR
>> <rank>1</rank>
>> </argument>
>> <argument>
>> <tag>-module</tag>
>> <value>generic</value>
>> SCALAR
>> <rank>1</rank>
>> </argument>
>> <argument>
>> <tag>-prefix</tag>
>> SCALAR
>> <value>INPUT</value>
>> <rank>2</rank>
>> </argument>
>> <argument>
>> <tag>-format</tag>
>> SCALAR
>> <value>gff</value>
>> <rank>3</rank>
>> </argument>
>> <argument>
>> <tag>-file_suffix</tag>
>> SCALAR
>> <value>gff</value>
>> <rank>4</rank>
>> </argument>
>> </method>
>> <method>
>> <name>dump</name>
>> <rank>2</rank>
>> <argument>
>> <value>OUTPUT</value>
>> ARRAY
>> <rank>1</rank>
>> </argument>
>> </method>
>> </iohandler>
>> </iohandler_setup>
>>
>><!-- ANALYSIS -->
>> <analysis>
>> <data_monger>
>> <initial></initial>
>> <input>
>> <name>protein_ids</name>
>> <iohandler>1</iohandler>
>> </input>
>> <input_create>
>> <module>setup_initial</module>
>> <rank>1</rank>
>> <argument>
>> <tag>protein_ids</tag>
>> <value>2</value>
>> </argument>
>> </input_create>
>></data_monger>
>><input_iohandler></input_iohandler>
>> </analysis>
>>
>><!-- BLAST-->
>> <analysis>
>> <logic_name>Blast</logic_name>
>> <runnable>Bio::Pipeline::Runnable::Blast</runnable>
>> <db>family</db>
>> <db_file>$blastdb1</db_file>
>> <program>blastall</program>
>>
>><!-- BLASTPATH-->
>> <program_file>$blastpath</program_file>
>> <analysis_parameters>$blast_param1</analysis_parameters>
>> <runnable_parameters>-formatdb 1 -result_dir
>>$resultdir1</runnable_parameters>
>>
>> <input_iohandler></input_iohandler>
>>
>> <output_iohandler></output_iohandler>
>> </analysis>
>>
>><!-- RULES -->
>><rule>
>> <current_analysis_id>1</current_analysis_id>
>> <next_analysis_id>2</next_analysis_id>
>> NOTHING
>>
>></rule>
>>
>></pipeline_flow_setup>
>><job_setup>
>></job_setup>
>>
>></pipeline_setup>
>>
>>
>>And I obtain:
>>“
>>Creating biopipe
>> Loading Schema...
>>Reading Data_setup xml : /home/conte/xml/newhope.xml
>>Doing DBAdaptor and IOHandler setup
>>Doing Pipeline Flow Setup
>>Doing Analysis..
>>
>>------------- EXCEPTION -------------
>>MSG: Need to store analysis first
>>STACK Bio::Pipeline::SQL::JobAdaptor::store
>>/usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/SQL/
>>JobAdaptor.pm:459
>>STACK Bio::Pipeline::XMLImporter::_create_initial_input_and_job
>>/usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/
>>XMLImporter.pm:837
>>STACK Bio::Pipeline::XMLImporter::run
>>/usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/
>>XMLImporter.pm:484
>>STACK toplevel PipelineManager:120
>>
>>
>>
>>
>>
>>
>>
>>
>>Matthieu CONTE
>>M. Sc. in Bioinformatics form SIB
>>CIRAD
>>00 33 06.68.90.28.70
>>m_conte at hotmail.com
>>
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