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 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:
(1)64 (2)PF (3)PF3D7_1468700 | organism=Plasmodium_falciparum_3D7 | product=eukaryotic initiation factor 4A (eIF4A) | location=Pf3D7_14_v3:2825370-2826918(+) | length=398 | sequence_SO=chromosome | SO=protein_coding