NAME

bc_convert_ids - Convert member ID from member attribute or file

SYNOPSIS

  bc_convert_ids -input_files   my_communities.generic   \
                 -output_prefix my_converted_communities \
                 -member_attr   desc

or

  bc_convert_ids -input_files   my_communities.generic   \
                 -output_prefix my_converted_communities \
                 -cluster_file  gg_99_otu_map.txt

or

  bc_convert_ids -input_files   my_communities.generic   \
                 -output_prefix my_converted_communities \
                 -blast_file    blastn_res.tab

or

  bc_convert_ids -input_files    my_communities.generic      \
                 -output_prefix  my_converted_communities    \
                 -taxassign_file rep_set_tax_assignments.txt

DESCRIPTION

This script converts the ID of members given 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.

REQUIRED ARGUMENTS

-if <input_files>... | -input_files <input_files>...

Input file containing the communities to process. When providing communities in a format that supports only one community per file (e.g. gaas), you can provide multiple input files.

OPTIONAL ARGUMENTS

-ma <member_attr> | -member_attr <member_attr>

Replace member ID by the value of another member attribute, e.g. the member's description field ('desc'). Replacing a member's ID by its description is useful when importing data from formats that do not explicitly represent member ID, e.g. from 'generic' to 'qiime'.

-cf <cluster_file> | -cluster_file <cluster_file>

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).

-bf <blast_file> | -blast_file <blast_file>

The tab-delimited BLAST file that defines the best similarity. This type of file generally has 12 columns and the first two should contain OTU 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     *       *

Note that this script expects high-quality similarity results and that only the first similarity assigned to a member is kept.

-tf <taxassign_file> | -taxassign_file <taxassign_file>

The tab-delimited file that defines the OTU taxonomic assignments. 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.

-cm <conversion_method> | -conversion_method <conversion_method>

Choose to either 'replace' the existing ID, 'prepend' in front of it, or 'append' after it. Default: conversion_method.default

-cs <conversion_separator> | -conversion_separator <conversion_separator>

Set the string that will be used to construct the ID when using the 'append' or 'prepend' conversion method. Default: conversion_separator.default

-op <output_prefix> | -output_prefix <output_prefix>

Path and prefix for the output files. Default: output_prefix.default

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists.

Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.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.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

  http://bugzilla.open-bio.org/

AUTHOR - Florent Angly

Email florent.angly@gmail.com