Snippets

Dénes Türei Export static tables of OmniPath data using pypath

Created by Dénes Türei
omnipath_static_tables.py
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#!/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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