Snippet revisions — Bitbucket

+#!/usr/bin/env python

+# Denes Turei, Uniklinik RWTH Aachen 2018

+# turei.denes@gmail.com

+import datetime

+import pypath

+from pypath import ptm

+today = datetime.date.today().__str__()

+pa = pypath.PyPath()

+# building the human network

+pa.load_omnipath(kinase_substrate_extra = True)

+# exporting sif and tab

+pa.export_sif(outfile = 'omnipath_human_%s.sif' % today)

+pa.export_tab(outfile = 'omnipath_human_%s.tab' % today)

+# translating to mouse

+pa.orthology_translation(10090)

+pa.export_sif(outfile = 'omnipath_mouse_%s.sif' % today)

+pa.export_tab(outfile = 'omnipath_mouse_%s.tab' % today)

+# enzyme-substrate interactions

+human = ptm.PtmAggregator(map_by_homology_from = [])

+human.export_table(

+    fname = 'omnipath_human_enzyme-substrate_human_%s.tab' % today

+)

+# mouse direct

+mouse = ptm.PtmAggregator(

+    ncbi_tax_id = 10090,

+    map_by_homology_from = []

+)

+mouse.export_table(

+    fname = 'omnipath_mouse_enzyme-substrate_mouse_%s.tab' % today

+)

+# mouse orthology only

+mouse = ptm.PtmAggregator(

+    ncbi_tax_id = 10090,

+    map_by_homology_from = [9606, 10116],

+    nonhuman_direct_lookup = False

+)

+mouse.export_table(

+    fname = 'omnipath_mouse_enzyme-substrate_homology_%s.tab' % today

+)

+# mouse direct & orthology combined

+mouse = ptm.PtmAggregator(

+    ncbi_tax_id = 10090,

+    map_by_homology_from = [9606, 10116]

+)

+mouse.export_table(

+    fname = 'omnipath_mouse_enzyme-substrate_all_%s.tab' % today

+)

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