Search results for "distribution:Bio-Community GAAS"
Bio::Community::IO::Driver::gaas - Driver to read and write files in the GAAS format
This Bio::Community::IO::Driver::gaas driver reads and writes files in the format generated by GAAS (http://sourceforge.net/projects/gaas/). GAAS creates one such file per community. Here is an example: # tax_name tax_id rel_abund Streptococcus pyoge...
FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 UTC
Bio::Community::IO - Read and write files that describe communities
A Bio::Community::IO object implement methods to read and write communities in formats used by popular programs such as BIOM, GAAS, QIIME, Unifrac, or as generic tab-separated tables. The format should be automatically detected though it can be manua...
FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 UTC
bc_rarefy - Rarefy communities
This script reads a file containing biological communities and performs rarefaction, i.e. repeatedly takes a random subset of the community members, in order to normalize communities by member count. Rarefaction is useful to simulate an identical sam...
FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 UTC
bc_get_info - Get information about a community file
This script reads a file containing biological communities and retrieves basic information from it, such as the names of the communities it contains and their counts, the ID of members and their description, or the file format. The information is dis...
FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 UTC
bc_summarize - Summarize community composition
This script reads a file containing biological communities and summarizes it. In practice, this means transforming community member counts into relative abundance (taking into account any weights that members could have) and merging members that have...
FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 UTC
bc_accumulate - Create species accumulation curves (collector or rarefaction)
This script reads files containing biological communities generates an accumulation curve, either collector or rarefaction. In a rarefaction curve, an increasing number of randomly drawn members is sampled from the given communities and alpha diversi...
FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 UTC
bc_convert_ids - Convert member ID from member attribute or file
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...
FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 UTC
bc_add_taxonomy - Add a taxonomic lineage to community members
This script takes communities in which members have IDs reflecting their position in a taxonomic system and add the taxonomic lineage information to each member. The string 'unidentified' is given to members for which no taxonomic lineage is found....
FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 UTC
bc_measure_beta - Measure beta diversity between communities
This script reads files containing biological communities and calculates how dissimilar they are (beta diversity). The output is a tab-delimited file containing the beta diversity between all pairs of communities. The columns of this file contain the...
FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 UTC
bc_convert_files - Merge/split community files and convert between formats
This script reads files containing biological communities and converts them to another format. It also several community files into a single one or splits a single file into multiple files with a single community in each. Incidentally, this scripts a...
FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 UTC
bc_measure_alpha - Measure alpha diversity of communities
This script reads files containing biological communities and calculates their alpha diversity. The output is a tab-delimited file containing the alpha diversity for each community, with the community names in the first column, and their alpha divers...
FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 UTC
bc_manage_members - Delete or rename community members
This script reads files containing biological communities and includes, deletes merges, sorts or renames the specified communities. See Bio::Community for more information....
FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 UTC
Bio::Community::IO::FormatGuesser - Determine the format used by a community file
Given a file containing one or several communities, try to guess the file format used by examining the file content (not by looking at the file name). The guess() method will examine the data, line by line, until it finds a line that is specific to a...
FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 UTC
bc_clean_shrapnel - Remove low-count, low-prevalence community members
This script takes communities, removes shrapnel (low abundance, low prevalence members that are likely to be the result of sequencing errors) and saves the resulting communities in output files. By default, the cleaner removes only singletons, i.e. c...
FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 UTC
bc_manage_samples - Include, delete, merge, sort or rename samples
This script reads files containing biological communities and includes, deletes merges, sorts or renames the specified communities. See Bio::Community for more information....
FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 UTC
bc_relative_to_absolute - Convert relative abundances into absolute
This script reads files containing biological communities and a file of abundance for these communities. The relative abundance of each member is multiplied by the total abundance for its community and rounded (if requested) to obtain the absolute ab...
FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 UTC
bc_correct_mis_assignments - Try fixing incorrect taxonomic assignments, using a reference community
This script reads a community file that contains reference communities. For every non-reference community in the file, find if the expected members are also found in the reference community. If not, use taxonomic information try to find which member ...
FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 UTC