Short introduction to perl & gff

Short introduction to perl & gff Marcus Ronninger The Linnaeus Centre for Bioinformatics

Motivation • Bioinformatics yields lots of information • The information have to be mined • Build or modify text files • Small changes can take long time with lots of data • Example: Change every letter to lower case • With script programming this could be done in less than a second

perl • Practical extraction and report language • Scripts • Object oriented programming • Graphical web interface, CGI • Possibilities • BioPerl

Example Example of a very simple perl script, to_lower_case.pl #!/usr/bin/perl -w use strict; my $seqfile = $ARGV[0]; my $outfile = $ARGV[1]; open (SEQ, $seqfile) || die "Can't open file: $seqfile"; open (OUTFILE, "> $outfile"); while(<SEQ>){ if ($_ =~ /^\>.*\n/){ print OUTFILE $_; } else{ print OUTFILE lc ($_); } }

Useful tools for parsing files • Scalar $ • Array @ • Regular expression /.fasta/ • Split, @chars = split //, $word • Substitute s/old-regex/new-string/ • Upper and lower case: uc, lc • Escape characters: \n \t \s etc • sub

General feature format, gff • AKA “gene finding format” • A format for handling output from different feature finding programs • Processes can be decoupled but the result can still be put together • Makes it easy to include external algorithms

General feature format The construction of the format is very simple. The values are tab-delimited. SEQ1 EMBL atg 103 105 . + 0 SEQ1 EMBL exon 103 172 . + 0 1. 2. 3. 4. 5. 6. 7. 8. 1. Sequence name 2. Source of the feature 3. Feature type 4. Start 5. End 6. Score - most feature finding programs have some kind of score for the found motif 7. Strand - can either be + or - 8. Frame - 0, 1, 2, .

Small example A small script that transforms known transcription factor binding sites into a .gff file #Gfap #Known TFBS (Besnard et al 1991) #count backwards form the TSS #start -14 AP-2: ccccaccccc -101 NF-1: tgggctgcggccca -116 Hgcs: ctgggctgcggc -117

Example Basically the same procedure as the perl example above $seqlength = 5000; $gff = “”; while (<LIT>){ if ($_ =~ /^#start/){ $rel_start = $'; } elsif (!($_ =~ /^#/) && ($_ =~ /\w+/)){ make_gff($_, $rel_start, "Literature"); } }

Example while (<LIT>){ if ($_ =~ /^#start/){ $rel_start = $'; } elsif (!($_ =~ /^#/) && ($_ =~ /\w+/)){ make_gff($_, $rel_start, "Literature"); } } sub make_gff{ my $start; my $stop; (my $seq, my $rs, my $type) = @_; my @feature = split(/\s+/, $seq); # now the array has the feature information if($type eq "Literature"){ $start = $seqlength + $rs + $feature[2]; $stop = $start + length($feature[1]) -1; $sign = '.'; $gff .= "$feature[0]\t$type\t$feature[0]\t$start\t$stop\tundef\t$sign\t$sign\n"; } etc.

Example Output: a file named lit.gff with the following contents AP-2: Literature AP-2: 4886 4895 undef . . NF-1: Literature NF-1: 4871 4884 undef . . Hgcs: Literature Hgcs: 4870 4881 undef . . This can now be loaded into programs thatsupport the gff format, e.g. Apollo

Apollo • Gff files is boring to view as they are • Use graphical software • Apollo, a sequence annotation editor • Great for viewing gff files together with the sequence

References • Tisdall J.D, “Beginning Perl for Bioinformatics” 2001, O’Reilly • http://www.sanger.ac.uk/Software/formats/GFF/ • http://www.fruitfly.org/annot/apollo/.

Short introduction to perl & gff