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hallamlab / MetaPathways

A modular pipeline for constructing Pathway/Genome Databases from environmental sequence information
http://hallam.microbiology.ubc.ca/MetaPathways
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Pull list of pathways and reactions from created PGDBs #18

Closed nielshanson closed 11 years ago

nielshanson commented 11 years ago

After creating a PGDB, the Pipeline should run and extract pathway and gene lists from a PGDB. The completed files should be put in the results/pgdb folder for each output set.

i.e. results/pgdb/$sample_name.pwys.txt as tab separated file

Pathway_short_name Pathway_common_name   #Reactions #ORFs_found
PWY-XXXX Carbon Cycle 12 6

i.e. results/pgdb/$sample_name.rxns.txt

Pathway_short_name Pathway_long_name #Reactions #ORFs
$RXN)1 #ORFs
$RXN_2 #ORFs
...
$RXN_N #ORFs