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Introducing Bioperl

Toward the Bioinformatics Perl programmer's nirvana. Introducing Bioperl. What Is Bioperl?. http://www.bioperl.org. Bioperl's Relationship To Project Ensembl. http://www.ensembl.org. Installing Bioperl. $ tar -zxvf current_core_stable.tar.gz $ tar -zxvf current_run_stable.tar.gz

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Introducing Bioperl

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  1. Toward the Bioinformatics Perl programmer's nirvana Introducing Bioperl

  2. What Is Bioperl? http://www.bioperl.org

  3. Bioperl's Relationship To Project Ensembl http://www.ensembl.org

  4. Installing Bioperl $ tar -zxvf current_core_stable.tar.gz $ tar -zxvf current_run_stable.tar.gz $ perl Makefile.PL $ make $ make test $ su $ make install $ <Ctrl-D> $ su $ perl -MCPAN -e "shell" $ cpan> install Bundle::BioPerl $ cpan> quit $ <Ctrl-D>

  5. Using Bioperl: Fetching Sequences #! /usr/bin/perl -w # simple_get_sequence.pl - a simple Bioperl example program, which # downloads SWISS-PROT sequences. use strict; use Bio::Perl; my $ID = shift; my $Sequence = get_sequence( 'swiss', $ID ); write_sequence( ">./seqs/$ID.swp", 'swiss', $Sequence ); write_sequence( ">./seqs/$ID.fsa", 'fasta', $Sequence );

  6. Results of Fetching Sequences ... $ mkdir seqs $ chmod +x simple_get_sequence.pl $ ./simple_get_sequence.pl P00392 $ ./simple_get_sequence.pl P00392 $ ./simple_get_sequence.pl MERA_PSEAE $ diff seqs/P00392.fsa seqs/MERA_PSEAE.fsa $ diff seqs/P00392.swp seqs/MERA_PSEAE.swp $ perldoc Bio/Perl.pm

  7. The Multi_Seq_Get.pl program #! /usr/bin/perl -w # Multi_Seq_Get.pl - when provided with a list of IDs, download them. use strict; use Bio::Perl; while ( my $ID = <> ) { chomp( $ID ); print "Fetching Sequence: $ID.\n"; my $Sequence = get_sequence( 'swiss', $ID ); write_sequence( ">./seqs/$ID.swp", 'swiss', $Sequence ); write_sequence( ">./seqs/$ID.fsa", 'fasta', $Sequence ); }

  8. Fetching multiple sequences $ ./Multi_Seq_Get.pl Merp_IDs.lst $ ./Multi_Seq_Get.pl Mera_IDs.lst

  9. Don't reinvent the wheel. Use Bioperl whenever possible. Maxim 20.1

  10. Remote BLAST Searches $blast_result = blast_sequence( $seq ); write_blast( $filename, $blast_result );

  11. Combine Bioperl with other tools to get your work done Maxim 20.2

  12. A quick aside: the blastcl3 NetBlast client $ blastcl3 -i ./seqs/P00392.fsa -d swissprot -p blastp \ > Swiss-Prot.NetBlast_P00392.res

  13. The Blast_parse.pl program #! /usr/bin/perl -w # Blast_parse.pl - post-process/parse BLAST output. use strict; use Bio::SearchIO; my $bls_report = shift; my $in = new Bio::SearchIO( -format => 'blast', -file => $bls_report ); while ( my $result = $in->next_result ) { while( my $hit = $result->next_hit ) { print "Hit = ", $hit->name, "\n"; } }

  14. Parsing BLAST outputs $ ./Blast_parse.pl Swiss-Prot.NetBlast_P00392.res

  15. Results from Blast_parse.pl ... Hit = sp|P00392|MERA_PSEAE Hit = sp|P94702|MERA_ENTAG Hit = sp|Q52109|MERA_ACICA Hit = sp|P94188|MERA_ALCSP Hit = sp|P08332|MERA_SHIFL Hit = sp|Q51772|MERA_PSEFL Hit = sp|P17239|MERA_THIFE Hit = sp|Q54465|MERA_SHEPU Hit = sp||P08662_1 Hit = sp|P30341|MERA_STRLI

  16. Where To From Here

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