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revision 1.10, Sun Oct 11 19:53:27 2009 UTC revision 1.11, Tue Oct 20 20:40:19 2009 UTC
# Line 1  Line 1 
1  #!/usr/bin/perl -w  #!/usr/bin/perl -w
2    
3    # This is a SAS component.
4    
5  #  #
6  # Copyright (c) 2003-2006 University of Chicago and Fellowship  # Copyright (c) 2003-2006 University of Chicago and Fellowship
7  # for Interpretations of Genomes. All Rights Reserved.  # for Interpretations of Genomes. All Rights Reserved.
# Line 25  Line 27 
27    
28      use base qw(Exporter);      use base qw(Exporter);
29    
30      our @EXPORT = qw(parse_fasta_record create_fasta_record rev_comp genome_of min max sims verify_dir);      our @EXPORT = qw(hypo parse_fasta_record create_fasta_record rev_comp genome_of min max sims verify_dir);
31    
32  =head1 SEED Utility Methods  =head1 SEED Utility Methods
33    
# Line 549  Line 551 
551  }  }
552    
553    
554    =head3 hypo
555    
556        my $flag = hypo($func);
557    
558    Return TRUE if the specified functional role is hypothetical, else FALSE.
559    Hypothetical functional roles are identified by key words in the text,
560    such as I<hypothesis>, I<predicted>, or I<glimmer> (among others).
561    
562    =over 4
563    
564    =item func
565    
566    Text of the functional role whose nature is to be determined.
567    
568    =item RETURN
569    
570    Returns TRUE if the role is hypothetical, else FALSE.
571    
572    =back
573    
574    =cut
575    
576    sub hypo {
577        my ($func) = @_;
578        if (! $func)                             { return 1 }
579        if ($func =~ /lmo\d+ protein/i)          { return 1 }
580        if ($func =~ /hypoth/i)                  { return 1 }
581        if ($func =~ /conserved protein/i)       { return 1 }
582        if ($func =~ /gene product/i)            { return 1 }
583        if ($func =~ /interpro/i)                { return 1 }
584        if ($func =~ /B[sl][lr]\d/i)             { return 1 }
585        if ($func =~ /^U\d/)                     { return 1 }
586        if ($func =~ /^orf[^_]/i)                { return 1 }
587        if ($func =~ /uncharacterized/i)         { return 1 }
588        if ($func =~ /pseudogene/i)              { return 1 }
589        if ($func =~ /^predicted/i)              { return 1 }
590        if ($func =~ /AGR_/)                     { return 1 }
591        if ($func =~ /similar to/i)              { return 1 }
592        if ($func =~ /similarity/i)              { return 1 }
593        if ($func =~ /glimmer/i)                 { return 1 }
594        if ($func =~ /unknown/i)                 { return 1 }
595        if (($func =~ /domain/i) ||
596            ($func =~ /^y[a-z]{2,4}\b/i) ||
597            ($func =~ /complete/i) ||
598            ($func =~ /ensang/i) ||
599            ($func =~ /unnamed/i) ||
600            ($func =~ /EG:/) ||
601            ($func =~ /orf\d+/i) ||
602            ($func =~ /RIKEN/) ||
603            ($func =~ /Expressed/i) ||
604            ($func =~ /[a-zA-Z]{2,3}\|/) ||
605            ($func =~ /predicted by Psort/) ||
606            ($func =~ /^bh\d+/i) ||
607            ($func =~ /cds_/i) ||
608            ($func =~ /^[a-z]{2,3}\d+[^:\+\-0-9]/i) ||
609            ($func =~ /similar to/i) ||
610            ($func =~ / identi/i) ||
611            ($func =~ /ortholog of/i) ||
612            ($func =~ /structural feature/i))    { return 1 }
613        return 0;
614    
615    }
616    
617    
618  1;  1;

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