draft tsv to spec MF regulatorbranch

mf_reg_meta.tsv

mf_reg_meta_gen.py

import json
from tsv2pdm import tab
from  warnings import warn
import re


def key_hack(l, key, val):
    """Returns an object from a list of objects where one of the
    attributes shared by all object acts as a unique key.
    Warns and returns false if not unique key.
    """
    out = [x for x in l if x[key] == val]
    if len(out) == 1:
        return out[0]
    elif len(out) > 1:
        warn("%s is not a unique %s key in input" % (val, key))
        return False
    else:
        return False

def name_parser(name, nodes):
    rmapping = { 'regulator' : 'http://purl.obolibrary.org/obo/RO_0002578',
                 'activator' : 'http://purl.obolibrary.org/obo/RO_0002629',
                 'inhibitor' : 'http://purl.obolibrary.org/obo/RO_0002630'
                 }
        
    m = re.match("(.+) (regulator|activator|inhibitor) activity$", name)
    out = {}
    if m:
        reg_func = m.group(1)
        rel = m.group(2)
        if rel in rmapping:
            out['rel'] = rmapping[rel]
        else:
            out['rel'] = ''
            
        o =  key_hack(l = nodes, key = 'lbl' , val = reg_func + ' activity')
        if o:
            out['obj'] = o['id']
        else:
            out['obj'] = ''
    return out

out = tab(headers = ['id', 'name', 'xrefs', 'rel', 'reg_activity'])
'reg_activity'
gof = open('/repos/go_trunk_ont/extensions/go-plus.json', 'r')
gog = json.loads(gof.read())
go = gog['graphs'][0]
MF_regs_f = open('mf_regulator_activity-labels.txt', 'r')
mf_regs = MF_regs_f.readlines()
mfr = [fu.strip("'") for fu in [t.strip() for t in mf_regs]]

for t in mfr:
    node = key_hack(l = go['nodes'], key = 'lbl', val = t)
    logical_def = key_hack(go['logicalDefinitionAxioms'], 'definedClassId', node['id'])
    row = {}
    row['name'] = t
    row['id'] = node['id']
    row['xrefs'] = ','.join(node['meta']['definition']['xrefs'])
    if logical_def and len(logical_def['restrictions']) == 1:
        row['rel'] = logical_def['restrictions'][0]['propertyId']
        row['reg_activity'] = logical_def['restrictions'][0]['fillerId']
    else:
        auto_map = name_parser(nodes = go['nodes'], name = t)
        if auto_map:     
            row['rel'] = auto_map['rel']
            row['reg_activity'] = auto_map['obj']
        else:
            row['rel'] = ''
            row['reg_activity'] = ''
#    print(row)
    if out.validate_row(row):
        out.tab.append(row)

print out.print_tab(sort_keys = ['rel', 'name'], reverse = True)