def get_kegg_biomart_id(sp_latin):
kegg_map_dict = load_fn_to_obj(KEGG_ORGANISM_JSON)
kegg_sp, biomart_sp = '', ''
if sp_latin in kegg_map_dict:
kegg_sp = kegg_map_dict[sp_latin]
sp_latin_list = sp_latin.split('_')
biomart_sp = '{0}{1}'.format(sp_latin_list[0][0], sp_latin_list[1])
return kegg_sp, biomart_sp
proj_name_list = args.proj_names.split(',')
with open(all_info_file) as all_info_file_if:
for n, eachline in enumerate(all_info_file_if):
if n != 0:
eachline_info = eachline.strip().split('\t')
if eachline_info[0] in proj_name_list:
wgc_id = eachline_info[1]
sample_id = eachline_info[4]
wgc_to_sample_dict[wgc_id] = sample_id
sample_to_wgc_dict[sample_id] = wgc_id
if os.path.isfile('rawdata_number.json') and os.stat(
'rawdata_number.json').st_size:
sample_number_dict = python_tools.load_fn_to_obj('rawdata_number.json')
else:
sample_number_dict = {}
sample_dict = {}
for each_num in data_dir_dict:
if args.ALL or each_num in seq_number_list:
each_dir_list = data_dir_dict[each_num]
for each_dir in each_dir_list:
rawdata_list = os.listdir(each_dir)
for each_rawdata_dir in rawdata_list:
each_fq_dir = os.path.join(each_dir, each_rawdata_dir)
if os.path.isdir(each_fq_dir):
if re.search(r'(WGC\d{6})', each_rawdata_dir):
wgc_id = re.search(r'(WGC\d{6})',
each_rawdata_dir).groups()[0]
import sys
import os
import python_tools
if not len(sys.argv) == 4:
print ' python ' + sys.argv[
0] + ' exp.table gene.interpro.annotate exp.annotate.table'
sys.exit(0)
exp_table = sys.argv[1]
interpro_json = sys.argv[2]
exp_anno = sys.argv[3]
interpro_dict = python_tools.load_fn_to_obj(interpro_json)
exp_anno_inf = open(exp_anno, 'w')
with open(exp_table) as exp_table_inf:
for n, eachline in enumerate(exp_table_inf):
eachline = eachline.strip()
if n == 0:
exp_anno_inf.write(
'%s\tGene_name\tInterpro_ID\tInterpro_description\n' %
eachline)
else:
eachline_inf = eachline.split('\t')
gene_id = eachline_inf[0]
annotate_list = ['--'] * 3
if gene_id in interpro_dict:
for m, each in enumerate(annotate_list):
if interpro_dict[gene_id][m]:
annotate_list[m] = ','.join(interpro_dict[gene_id][m])
annotate_out = '\t'.join(annotate_list)
import os
import python_tools
if not len(sys.argv) == 4:
print ' python ' + sys.argv[
0] + ' gene.interpro.id interpro.map gene.interpro.des'
sys.exit(0)
gene_interpro_id_file = sys.argv[1]
interpro_map = sys.argv[2]
gene_interpro_des_file = sys.argv[3]
interpro_map_dict = {}
if interpro_map.endswith('json'):
interpro_map_dict = python_tools.load_fn_to_obj(interpro_map)
else:
with open(interpro_map) as interpro_map_inf:
for eachline in interpro_map_inf:
eachline_inf = eachline.strip().split('\t')
interpro_map_dict[eachline_inf[0]] = eachline_inf[1]
interpro_map_json = '%s.json' % interpro_map
python_tools.write_obj_to_json(interpro_map_dict, interpro_map_json)
gene_inf_dict = {}
with open(gene_interpro_id_file) as gene_interpro_id:
for n, eachline in enumerate(gene_interpro_id):
if n != 0:
eachline_inf = eachline.strip().split(',')
gene_id = eachline_inf[0]
gene_name = eachline_inf[1]