[Bioperl-pipeline] Still working with biopipe....
Shawn Hoon
shawnh at stanford.edu
Fri Nov 21 13:01:22 EST 2003
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
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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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