- SUPPORT AND BUGS
Bio::Community::Tools::IdConverter - Various methods to convert member ID
use Bio::Community::Tools::IdConverter; # Add member description to its ID my $converter = Bio::Community::Tools::IdConverter->new( -metacommunity => $meta, -member_attr => 'desc', -conversion_method => 'append', ); my $meta_by_otu = $converter->get_converted_meta; # Replace by IDs given in a file $converter = Bio::Community::Tools::IdConverter->new( -metacommunity => $meta, -cluster_file => 'gg_99_otu_map.txt', ); $meta_by_otu = $converter->get_converted_meta;
Convert the ID of members given in a metacommunity based on another member attribute, such as its description, or based on IDs provided in a file. This file can be a Greengenes OTU cluster file, a BLAST file, or a QIIME taxonomic assignment file. A new metacommunity containing members with converted IDs is returned.
Note that when given a files, this script expects high-quality results. No quality processing is done and only the first match assigned to a member is kept.
Florent Angly email@example.com
User feedback is an integral part of the evolution of this and other Bioperl modules. Please direct usage questions or support issues to the mailing list, firstname.lastname@example.org, rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
If you have found a bug, please report it on the BioPerl bug tracking system to help us keep track the bugs and their resolution: https://redmine.open-bio.org/projects/bioperl/
Copyright 2011-2014 by Florent Angly <email@example.com>
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.10.1 or, at your option, any later version of Perl 5 you may have available.
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Function: Create a new Bio::Community::Tool::IdConverter object Usage : my $converter = Bio::Community::Tool::IdConverter->new( -metacommunity => $meta, -member_attr => 'desc', ); # or my $converter = Bio::Community::Tool::IdConverter->new( -metacommunity => $meta, -cluster_file => '99_otu_map.txt', ); # or my $converter = Bio::Community::Tool::IdConverter->new( -metacommunity => $meta, -blast_file => 'blast_res.tab', ); # or my $converter = Bio::Community::Tool::IdConverter->new( -metacommunity => $meta, -taxassign_file => 'rep_set_tax_assignments.txt', ); Args : -metacommunity : See metacommunity(). And ones of: -member_attr : See member_attr(). -cluster_file : See cluster_file(). -blast_file : See blast_file(). -taxassign_file : See taxassign_file(). Returns : a Bio::Community::Tools::IdConverter object
Function: Get/set communities, given as metacommunity, to summarize. Usage : my $meta = $converter->metacommunity; Args : A Bio::Community::Meta object Returns : A Bio::Community::Meta object
Function: Get / set whether member ID should be converted using the value of another attribute, e.g. the member's description. Replacing member ID by its description is useful when importing data from formats that do not explicitly represent member ID, e.g. from 'generic' to 'qiime'. Usage : $converter->member_attr('id'); Args : member attribute, e.g. 'desc' (see C<Bio::Community::Member>) Returns : member attribute
Function: Get / set the tab-delimited file that defines the OTU clusters. The columns are: OTU ID, ID of the representative sequence, IDs of the other sequences in the OTU. For example: 0 367523 1 187144 2 544886 544649 3 310669 4 355095 310677 347705 563209 The OTU files distributed by Greengenes use this format (e.g., 99_otu_map.txt). Usage : $converter->cluster_file('99_otu_map.txt'); Args : OTU cluster file name Returns : OTU cluster file name
Function: Get / set the tab-delimited BLAST file that defines the best similarity. This type of file generally has 12 columns and the first two should be the member ID and the ID of sequence with the best similarity. For example: OTU_4 JN647692.1.1869 99.6 250 1 0 1 250 1 250 * * OTU_12 655879 94.4 250 14 0 1 250 1 250 * * Usage : $converter->blast_file('blastn_res.tab'); Args : BLAST file name Returns : BLAST file name
Function: Get / set the tab-delimited file that defines the OTU taxonomic assignemts. The first four columns (out of 12) should be: OTU ID, taxonomic string, E-value, taxonomic ID. For example: 345 k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Propionibacteriaceae; g__Propionibacterium; s__acnes 5e-138 1042485 95.67 300 13 0 1 300 878 579 346 k__Bacteria; p__Firmicutes; c__Bacilli; o__; f__; g__; s__ 8e-134 1064834 99.59 245 1 0 1 245 909 665 347 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pseudomonadales; f__Pseudomonadaceae; g__Pseudomonas; s__ 2e-103 959954 98.99 198 2 0 103 300 718 521 The taxonomic assignment files generated by QIIME (rep_set_tax_assignments.txt) follow this format. Usage : $converter->taxassign_file('rep_set_tax_assignments.txt'); Args : taxonomic assignment file name Returns : taxonomic assignment file name
Function: Get / set how to convert IDs, i.e. either replace the existing ID (the default), prepend in front of it, or append after it. Usage : $converter->conversion_method('prepend'); Args : conversion method, 'replace', 'prepend' or 'append' Returns : conversion method
Function: Get / set the string used to construct the ID when using the 'append' or 'prepend' conversion method, '_' by default Usage : $converter->conversion_separator(' '); Args : any string to use as conversion separator Returns : the string used as conversion method
Function: Convert the communities and return the corresponding metacommunity. Usage : my $meta_by_otu = $converter->get_converted_meta; Args : None Returns : A Bio::Community::Meta object