mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-19 02:21:32 +08:00
78 lines
2.6 KiB
Python
78 lines
2.6 KiB
Python
#!/usr/bin/env python
|
|
# Dan Blankenberg
|
|
|
|
import os
|
|
import sys
|
|
|
|
assert sys.version_info[:2] >= (2, 6)
|
|
|
|
|
|
def __main__():
|
|
base_dir = os.path.join(os.getcwd(), "bacteria")
|
|
try:
|
|
base_dir = sys.argv[1]
|
|
except IndexError:
|
|
pass
|
|
|
|
organisms = {}
|
|
for result in os.walk(base_dir):
|
|
this_base_dir, sub_dirs, files = result
|
|
for file in files:
|
|
if file[-5:] == ".info":
|
|
tmp_dict = {}
|
|
info_file = open(os.path.join(this_base_dir, file))
|
|
info = info_file.readlines()
|
|
info_file.close()
|
|
for line in info:
|
|
fields = line.replace("\n", "").split("=")
|
|
tmp_dict[fields[0]] = "=".join(fields[1:])
|
|
if "genome project id" in tmp_dict.keys():
|
|
name = tmp_dict["genome project id"]
|
|
if "build" in tmp_dict.keys():
|
|
name = tmp_dict["build"]
|
|
if name not in organisms.keys():
|
|
organisms[name] = {"chrs": {}, "base_dir": this_base_dir}
|
|
for key in tmp_dict.keys():
|
|
organisms[name][key] = tmp_dict[key]
|
|
else:
|
|
if tmp_dict["organism"] not in organisms.keys():
|
|
organisms[tmp_dict["organism"]] = {"chrs": {}, "base_dir": this_base_dir}
|
|
organisms[tmp_dict["organism"]]["chrs"][tmp_dict["chromosome"]] = tmp_dict
|
|
|
|
for org_name, org in list(organisms.items()):
|
|
if "name" not in org:
|
|
del organisms[org_name]
|
|
|
|
orgs = list(organisms.keys())
|
|
# need to sort by name
|
|
swap_test = False
|
|
for i in range(0, len(orgs) - 1):
|
|
for j in range(0, len(orgs) - i - 1):
|
|
if organisms[orgs[j]]["name"] > organisms[orgs[j + 1]]["name"]:
|
|
orgs[j], orgs[j + 1] = orgs[j + 1], orgs[j]
|
|
swap_test = True
|
|
if swap_test is False:
|
|
break
|
|
|
|
print("||'''Organism'''||'''Kingdom'''||'''Group'''||'''Links to UCSC Archaea Browser'''||")
|
|
|
|
for org in organisms.values():
|
|
at_ucsc = False
|
|
# if no gpi, then must be a ncbi chr which corresponds to a UCSC org, w/o matching UCSC designation
|
|
try:
|
|
org["genome project id"]
|
|
except KeyError:
|
|
continue
|
|
if "build" in org:
|
|
at_ucsc = True
|
|
|
|
out_str = "||" + org["name"] + "||" + org["kingdom"] + "||" + org["group"] + "||"
|
|
if at_ucsc:
|
|
out_str = out_str + "Yes"
|
|
out_str = out_str + "||"
|
|
print(out_str)
|
|
|
|
|
|
if __name__ == "__main__":
|
|
__main__()
|