/scripts/microbes/create_bacteria_table.py
Python | 79 lines | 72 code | 4 blank | 3 comment | 5 complexity | b263c164cd15bffd375bdffbed7f014b MD5 | raw file
1#!/usr/bin/env python
2#Dan Blankenberg
3
4import sys, os
5
6assert sys.version_info[:2] >= ( 2, 4 )
7
8def __main__():
9 base_dir = os.path.join( os.getcwd(), "bacteria" )
10 try:
11 base_dir = sys.argv[1]
12 except:
13 pass
14 #print "using default base_dir:", base_dir
15
16 organisms = {}
17 for result in os.walk(base_dir):
18 this_base_dir,sub_dirs,files = result
19 for file in files:
20 if file[-5:] == ".info":
21 dict = {}
22 info_file = open(os.path.join(this_base_dir,file),'r')
23 info = info_file.readlines()
24 info_file.close()
25 for line in info:
26 fields = line.replace("\n","").split("=")
27 dict[fields[0]]="=".join(fields[1:])
28 if 'genome project id' in dict.keys():
29 name = dict['genome project id']
30 if 'build' in dict.keys():
31 name = dict['build']
32 if name not in organisms.keys():
33 organisms[name] = {'chrs':{},'base_dir':this_base_dir}
34 for key in dict.keys():
35 organisms[name][key]=dict[key]
36 else:
37 if dict['organism'] not in organisms.keys():
38 organisms[dict['organism']] = {'chrs':{},'base_dir':this_base_dir}
39 organisms[dict['organism']]['chrs'][dict['chromosome']]=dict
40
41 orgs = organisms.keys()
42 for org in orgs:
43 if 'name' not in organisms[org]:del organisms[org]
44
45 orgs = organisms.keys()
46 #need to sort by name
47 swap_test = False
48 for i in range(0, len(orgs) - 1):
49 for j in range(0, len(orgs) - i - 1):
50 if organisms[orgs[j]]['name'] > organisms[orgs[j + 1]]['name']:
51 orgs[j], orgs[j + 1] = orgs[j + 1], orgs[j]
52 swap_test = True
53 if swap_test == False:
54 break
55
56
57
58
59 print "||'''Organism'''||'''Kingdom'''||'''Group'''||'''Links to UCSC Archaea Browser'''||"
60
61
62 for org in orgs:
63 org = organisms[org]
64 at_ucsc = False
65 #if no gpi, then must be a ncbi chr which corresponds to a UCSC org, w/o matching UCSC designation
66 try:
67 build = org['genome project id']
68 except: continue
69 if 'build' in org:
70 build = org['build']
71 at_ucsc = True
72
73 out_str = "||"+org['name']+"||"+org['kingdom']+"||"+org['group']+"||"
74 if at_ucsc:
75 out_str = out_str + "Yes"
76 out_str = out_str + "||"
77 print out_str
78
79if __name__ == "__main__": __main__()