Bioperl Training Exercise 11

• Write a standalone script that executes the following workflow:

1. input fasta protein (Google)

   Save the file File:Proteins.txt as proteins.fa.

2. launch EMBOSS' fuzzpro from your script to look for a pattern (e.g. potential N-glycosylation site). Output should be GFF and written to a temporary file. Hints:
   1. use Data::Dumper to figure out what kind of object your io object actually is
   2. use the methods script to find a method to create a temporary files.
   3. use perldoc to figure out how that method works
   4. the fuzzpro analysis run() method takes a hash as arguments. As keys, the actual EMBOSS fuzzpro should be used. Part of the possible keys can be obtained using the acd() method. However, the key to indicate the report format (GFF) is missing; it's -rformat2 (see fuzzpro EMBOSS documentation).
   5. The pattern for an N-glycosylation site is N-{P}-[ST]
3. Convert the GFF to features and add them to the sequence. Change every found feature:
   1. add note tag to indicate the used program (fuzzpro)
   2. add note tag to indicate the used pattern
   3. add label 'N-glycosylation'
   4. change the feature type to the Sequence Ontology term 'protein_match'
4. Write the annotated sequence to a genbank file

fuzzpro.pl

#!/usr/bin/perl use strict; use Bio::SeqIO; use Bio::Factory::EMBOSS; use Bio::Tools::GFF; use Data::Dumper;   # io object to read in the fasta from 'proteins.fa' my $in = Bio::SeqIO->new(-format => 'fasta', -file => '< proteins.fa');   # io object to write genbank to STDOUT my $out = Bio::SeqIO->new(-format => 'genbank', -fh => \*STDOUT);   # N-glycosylation pattern argument for fuzzpro my $pattern = 'N-{P}-[ST]';   # fuzzpro application object my $fuzzpro = Bio::Factory::EMBOSS->new->program('fuzzpro');   #print Data::Dumper->Dump([$fuzzpro->acd],['fuzzpro']);exit;   # for every sequence while (my $seq = $in->next_seq) { # create temporary file for fuzzpro output my ($fh, $gffile) = $in->tempfile;   # run fuzzpro $fuzzpro->run({ -sequence => $seq, -pattern => $pattern, -rformat => 'GFF', -outfile => $gffile });   # create reader/parser GFF object my $gffio = Bio::Tools::GFF->new(-fh => $fh, -gff_version => 2);   # loop over the feature stream while(my $feature = $gffio->next_feature()) { # attach feature to sequence $seq->add_SeqFeature($feature);   # change feature type $feature->primary_tag('protein_match');   # add notes $feature->add_tag_value(note => 'algorithm:fuzzpro'); $feature->add_tag_value(note => "pattern:$pattern");   # add label $feature->add_tag_value(label => 'N-glycosylation site'); } # close stream $gffio->close;   # write sequence to genbank $out->write_seq($seq); }