python goatools使用

用david搞定了所有的GOterm后，接下来就是利用goslim处理这些term。

用的包是goatools，需要下载几个obo文件以及，fisher，pygraphviz以及graphviz等几个模块。

# -*- coding: utf-8 -*-
"""
Created on Fri Nov 21 20:06:42 2014

@author: hluo
"""

#!/usr/bin/python
# -*- coding: UTF-8 -*-

import os
import os.path as op
import sys
sys.path.insert(0, op.join(op.dirname(__file__), ".."))
from obo_parser import GODag
from mapslim import mapslim
import json
import re
#from goatools.mapslim import mapslim


# copied from find_enrichment.pydef get_goslim(term, godag, goslimdag):
    if not term in godag:
        return [None, None]
    else:
        direct_anc, all_anc = mapslim(term, godag, goslimdag)
        return [direct_anc, all_anc]
        

def mygofun(json_file):
    obo_file = '/home/hluo/Desktop/goslim/go-basic.obo'
    assert os.path.exists(obo_file), "file %s not found!" % obo_file

    slim_obo_file = '/home/hluo/Desktop/goslim/goslim_generic.obo'
    assert os.path.exists(slim_obo_file), "file %s not found!" % slim_obo_file

    # load DAGs
    go_dag = GODag(obo_file)
    goslim_dag = GODag(slim_obo_file)

    #json_file = 'NC_000913.gbk.json'
    myrecord = json.load(open(json_file))

    #re_obj = re.compile(r'GO:d+')
    re_obj = re.compile(r'(?<=$)S+(?=~)')
    #a =  re.match(re_Obj, text)

    #mylist = []
    for item in myrecord:
        mykey = filter(lambda x: x.startswith('GO'), item.keys())
        for k in mykey:
            tplist = [set(), set()]
            for text in item[k]:
                tplist1 = []
                goterm = re.findall(re_obj, text)[0]
                tplist1 = get_goslim(goterm, go_dag, goslim_dag)
                tplist[0] |= tplist1[0]
                tplist[1] |= tplist1[1]
            item[k + '_dslim'] = list(tplist[0])
            item[k + '_aslim'] = list(tplist[1])
    json.dump(myrecord, open('%s.txt' % json_file, 'w'), indent = 1)
        
if __name__ == '__main__':
    mygofun(NC_000913.gbk.json)

the script loads the json format file, and adds the new keys to every record in the file.

ps. dslim: direct slim. aslim: all slim.

Then I run a python batch script to process all the json files.

# -*- coding: utf-8 -*-
"""
Created on Mon Nov 24 17:37:24 2014

@author: hluo
"""

import os
import reimport sys
from mygoslim import mygofun
if __name__ == '__main__':
    mydir = '/home/hluo/Desktop/gbk'
    flist = os.listdir(mydir)
    re_obj = re.compile('.json$')
    #re_obj1 = re.compile('NC_d{6}.gbk')
    json_file_list = []
    for item in flist:
        re_item = re.findall(re_obj, item)
        if re_item:
            json_file_list.append(item)
    
    for item in json_file_list:
        mygofun('%s/%s' % (mydir, item))

In the script, use the 're'  and 'os' module to get all the json files.