baderlab/genemania_databuild_base repository overview

www.genemania.org⁠

repo - https://github.com/BaderLab/GeneMANIA_build⁠

July 2021- Issue with goatools library. the version that is install on this docker will not parse GAF 2.2 files. Manually make the below fix

reported issue to goatools git hub - https://github.com/tanghaibao/goatools/issues/207⁠

Manually went into /usr/local/lib/python2.7/dist-packages/goatools/anno/init/reader_gaf.py and updated the code to(line 151):

gaf_columns = {
    "2.2" : gafhdr + gafhdr2, # !gaf-version: 2.2
    "2.1" : gafhdr + gafhdr2, # !gaf-version: 2.1
    "2.0" : gafhdr + gafhdr2, # !gaf-version: 2.0
    "1.0" : gafhdr}           # !gaf-version: 1.0

# Expected numbers of columns for various versions
gaf_numcol = {
    "2.2" : 17,
    "2.1" : 17,
    "2.0" : 17,
    "1.0" : 15}

Manually updated v2.1 to contain this fix. Ideally we would be using the latest version of goatools but in the meantime we have a working docker.