flattenClusters 1.0

flattenClusters 1.0

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A utility to map original Fasta Headers to clusterReport and/or queryOrthoMCL output.

Notes:

Please visit Cluster Orthologs and Paralogs and Assemble Custom Gene Sets to see how this app fits into the larger workflow.
App adapted from PERL script originally written by Chih-Horng Kuo

Quick Start

To use flattenClusters you will need the .group file from either clusterReport and/or queryOrthoMCL and the Map file from the Cluster Orthologs and Paralogs and Assemble Custom Gene Sets workflow.

Test Data

Input test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> homolog_clustering -> 2_queryOrthoMCL_output
and
Community Data -> iplantcollaborative -> example_data -> homolog_clustering -> 4_Concatenate_Multiple_Files_output

Output test data for this app appears directly in the Discovery Environment in the Data window under:
Community Data -> iplantcollaborative -> example_data -> homolog_clustering -> 13_flattenClusters_output

Input File(s)

Use

Community Data -> iplantcollaborative -> example_data -> homolog_clustering -> 2_queryOrthoMCL_output -> Query.group

and

Community Data -> iplantcollaborative -> example_data -> homolog_clustering -> 4_Concatenate_Multiple_Files_output -> Map_Combined.txt

Parameters Used in App

There are no parameters for this app.

Output File(s)

Expect 1 output file:

A flattened.txt one sequence per line, each line with 3 tab-delimited fields:

(1)OrthoMCL cluster ID - (2)2-letter abbreviation from OrthoMCL v1.4 - (3)Original Fasta Header

Consider Community Data -> iplantcollaborative -> example_data -> homolog_clustering -> 13_flattenClusters_output -> flattened.txt line 3: