def main():
num_not_found_in_uniprot = 0
text = open('./ecoliparse.txt', 'r').read().replace('\'', '\"')
#print text
dict = json.loads(text)
#print dict
db.drop_collection('uniprot')
db.uniprot.insert(dict)
db.uniprot.create_index('gene_name')
gene_exist_list = []
gene_multi_exit_list = []
rna_gene_list = []
for enzyme in db.node.find({'TYPE': 'Enzyme'}):
for gene in enzyme['GENES']:
if gene not in gene_exist_list:
gene_exist_list.append(gene)
elif gene not in gene_multi_exit_list:
gene_multi_exit_list.append(gene)
for RNA in db.product.find({'TYPE': {'$ne': 'Protein'}}):
gene = RNA['Gene']
if gene not in rna_gene_list:
rna_gene_list.append(gene)
print 'existed gene list has been built'
fp.write('coding_gene_list\n\n')
fp.write(str(gene_exist_list))
fp.write('\n\ngene which product RNA\n\n')
fp.write(str(rna_gene_list))
fp.write('\n\n gene which product multi enzyme\n\n')
fp.write(str(gene_multi_exit_list))
#print gene_exist_list
saved_count = 0
cursor = db.node.find({'TYPE': 'Gene'}, timeout=False)
for gene in cursor:
fp.write(gene['NAME'] + ' ')
if not search_exists(gene['NAME'], gene_exist_list, rna_gene_list):
uniprot_name = gene['NAME'].replace('-', '').split('_')[0]
log = db.uniprot.find_one({'gene_name': uniprot_name})
if not log:
fp.write('can\'t be found in uniprot\n')
fp_not_found.write(gene['NAME'] + '\n')
num_not_found_in_uniprot += 1
continue
fp.write(' should be saved\n')
saved_count += 1
cursor.close()
print str(saved_count) + ' protein has been download'
fp.write('\n\nnum_with_TF: ' + str(num_with_TF) + '\n')
fp.write('num_with_Enzyme: ' + str(num_with_Enzyme) + 'compare: ' + str(len(gene_exist_list)) + '\n')
fp.write('num of gene which product RNA: ' + str(num_with_RNA) +'\n')
fp.write('num of gene with multi enzyme: ' + str(len(gene_multi_exit_list)) + '\n')
fp.write('num found in uniprot: ' + str(num_not_found_in_uniprot) + '\n')
fp.write('num of protein newly added: ' + str(saved_count))
fp.close()
fp_not_found.close()
def rebuild():
if OVERWRITE:
for collection in db.collection_names():
if collection not in ['system.indexes', 'system.users']:
db.drop_collection(collection)
print 'count log creating'
count()
print 'run regulondb importing from super manage.py'
regulondb()
print 'product importing '
product_process()
print 'run kegg_node importing from super manage.py'
kegg_node()
print 'run kegg_reaction importing from super manage.py'
kegg_reaction()
print 'run reaction connection from super manage.py'
db.node.create_index('NAME')
kegg_connect()
print 'run reaction function sort from super manage.py'
kegg_reaction_function_link()
print 'run link setting between gene and enzyme from super manage.py'
database_link()
print 'patch 1 built in August :adding alignment database'
patch1()
print 'working log creating'
log_create()
print 'uniprot updating'
uniprot_update()
print 'kegg rename'
rename_enzyme()
print '\nAdd Sysname to Gene'
gene_sysname()
print '\n Add sigma link'
sigma_link()
print 'Sort link type'
sort_link()
print 'BLAST database setup'
alignment_data()
print 'Fishing patch built in August 22'
patch2()
print 'Initial project information'
project_init()
def kegg_node(number=None):
basepath = './kegg/'
#paths = [basepath + 'compound.py', basepath + 'enzyme.py', basepath + 'module.py', basepath + 'protein.py']
#kind = {'0': 'Compound', '1': 'Enzyme', '2': 'Module', '3': 'Protein'}
paths = [basepath + 'compound.py', basepath + 'module.py', basepath + 'enzyme.py']
kind = {'0': 'Compound', '1': 'Module', '2': 'Enzyme'}
if number == None:
db.drop_collection('kegg_node')
for path in paths:
execfile(path, {})
else:
db.node.remove({'TYPE': kind[str(number)]})
execfile(paths[number], {})
def patch2():
db.drop_collection('node_ref')
db.drop_collection('link_ref')
path = './Patch/Fishing Patch.py'
execfile(path, {})
def kegg_reaction_function_link():
path = './kegg/mm_parse.py'
db.drop_collection('module__function_link')
#order = 'python ' + path
#os.system(order)
execfile(path, {})
def count():
db.drop_collection('count')
db.count.insert({'type': 'node', 'value': 0})
db.count.insert({'type': 'link', 'value': 0})
db.count.insert({'type': 'product', 'value': 0})
