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# ABSTRACT: Front-end class for UCLUST parser |
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# CONTRIBUTOR: Amandine BERTRAND <amandine.bertrand@doct.uliege.be> |
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$Bio::FastParsers::Uclust::VERSION = '0.221230'; |
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use Moose; |
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use namespace::autoclean; |
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use autodie; |
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use Tie::IxHash; |
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extends 'Bio::FastParsers::Base'; |
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# public attributes (inherited) |
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with 'Bio::FastParsers::Roles::Clusterable'; |
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my $self = shift; |
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my $infile = $self->filename; |
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open my $in, '<', $infile; |
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tie my %members_for, 'Tie::IxHash'; |
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LINE: |
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while (my $line = <$in>) { |
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chomp $line; |
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my ($type, @fields) = split /\t/xms, $line; |
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# https://www.drive5.com/usearch/manual/opt_uc.html |
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# Field Description |
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# - Record type S, H, C or N (see table below). |
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# 0 Cluster number (0-based). |
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# 1 Sequence length (S, N and H) or cluster size (C). |
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# 2 For H records, percent identity with target. |
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# 3 For H records, the strand: + or - for nucleotides, . for proteins. |
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# 4 Not used, parsers should ignore this field. Included for backwards compatibility. |
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# 5 Not used, parsers should ignore this field. Included for backwards compatibility. |
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# 6 Compressed alignment or the symbol '=' (equals sign). The = indicates that the query is 100% identical to the target sequence (field 10). |
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# 7 Label of query sequence (always present). |
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# 8 Label of target sequence (H records only). |
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if ($type eq 'C') { |
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push @{ $members_for{ $fields[7] } }, (); |
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} |
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elsif ($type eq 'H') { |
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push @{ $members_for{ $fields[8] } }, $fields[7]; |
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} |
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} |
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# store representative and member sequence ids |
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$self->_set_members_for( \%members_for ); |
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return; |
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} |
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__PACKAGE__->meta->make_immutable; |
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1; |
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=pod |
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=head1 NAME |
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Bio::FastParsers::Uclust - Front-end class for UCLUST parser |
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=head1 VERSION |
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version 0.221230 |
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=head1 SYNOPSIS |
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use aliased 'Bio::FastParsers::Uclust'; |
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# open and parse UCLUST report |
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my $infile = 'test/uclust.uc'; |
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my $report = Uclust->new( file => $infile ); |
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# loop through representatives to get members |
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for my $repr ( $report->all_representatives ) { |
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my $members = $report->members_for($repr); |
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# ... |
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} |
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# get representatives ordered by descending cluster size |
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my @reprs = $report->all_representatives_by_cluster_size; |
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# create IdMapper |
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# Note: this requires Bio::MUST::Core |
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my $mapper = $report->clust_mapper(':'); |
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my @long_ids = $mapper->all_long_ids; |
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# ... |
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=head1 DESCRIPTION |
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This module implements a parser for the output file of the UCLUST program. It |
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provides methods for getting the ids of the representative sequences (either |
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sorted by descending cluster size or not) and for obtaining the members of any |
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cluster from the id of its representative. |
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It also has a method for facilitating the re-mapping of all the ids of every |
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cluster on a phylogenetic tree through a L<Bio::MUST::Core::IdMapper> object. |
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=head1 ATTRIBUTES |
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=head2 file |
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Path to UCLUST report file to be parsed |
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=head1 METHODS |
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=head2 all_representatives |
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Returns all the ids of the representative sequences of the clusters (not an |
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array reference). |
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# $report is a Bio::FastParsers::Uclust |
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for my $repr ( $report->all_representatives ) { |
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# process $repr |
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# ... |
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} |
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This method does not accept any arguments. |
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=head2 all_representatives_by_cluster_size |
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Returns all the ids of the representative sequences of the clusters (not an |
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array reference) sorted by descending cluster size (and then lexically by id). |
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# $report is a Bio::FastParsers::Uclust |
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for my $repr ( $report->all_representatives_by_cluster_size ) { |
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# process $repr |
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# ... |
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} |
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This method does not accept any arguments. |
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=head2 members_for |
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Returns all the ids of the member sequences of the cluster corresponding to |
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the id of the specified representative (as an array refrence). |
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# $report is a Bio::FastParsers::Uclust |
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for my $repr ( $report->all_representatives ) { |
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my $members = $report->members_for($repr); |
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# process $members ArrayRef |
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# ... |
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} |
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This method requires one argument: the id of the representative. |
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=head2 clust_mapper |
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Returns a L<Bio::MUST::Core::IdMapper> object associating representative |
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sequence ids to stringified full lists of their member sequence ids (including |
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the representatives themselves). |
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This method needs L<Bio::MUST::Core> to be installed on the computer. |
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# $report is a Bio::FastParsers::Uclust |
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my $mapper = $report->clust_mapper(':'); |
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The native methods from L<Bio::MUST::Core::IdMapper> can be applied on |
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C<$mapper>, e.g., C<all_long_ids> or C<long_id_for>. |
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This method accepts an optional argument: the id separator (default: C</>). |
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=head1 AUTHOR |
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Denis BAURAIN <denis.baurain@uliege.be> |
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=head1 CONTRIBUTOR |
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=for stopwords Amandine BERTRAND |
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Amandine BERTRAND <amandine.bertrand@doct.uliege.be> |
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=head1 COPYRIGHT AND LICENSE |
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This software is copyright (c) 2013 by University of Liege / Unit of Eukaryotic Phylogenomics / Denis BAURAIN. |
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This is free software; you can redistribute it and/or modify it under |
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the same terms as the Perl 5 programming language system itself. |
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=cut |