def main(argv):
jamu_filepath = g_jamu_filepath
protein_dir = g_protein_dir
compound_dir = g_compound_dir
c2mapjamu_dir = g_c2mapjamu_dir
# Load a jamu formula
print('Loading jamu data from %s' % jamu_filepath)
jamu = {}
with open(jamu_filepath) as f:
jamu = yaml.load(f)
print(jamu)
# Load significant proteins
proteins = util.load_json_from_dir(protein_dir)
print('len(proteins)= %d' % len(proteins))
# Load narutal compound of jamu plants
compounds = util.load_json_from_dir(compound_dir)
print('len(compounds)= %d' % len(compounds))
# Construct the c2mapjamu
c2mapjamu = c2map.construct(proteins, compounds)
print c2mapjamu
# Visualize the c2mapjamu
# Generate random features and distance matrix.
n = 10
x = scipy.rand(n)
D = scipy.zeros([n, n])
for i in range(n):
for j in range(n):
D[i, j] = abs(x[i] - x[j])
# c2map.save_mat(D, c2mapjamu_dir+'/c2mapjamu.mat.png')
# c2map.save_mat(c2mapjamu, c2mapjamu_dir+'/c2mapjamu.mat.png')
c2map.save_graph(c2mapjamu, c2mapjamu_dir + '/c2mapjamu.graph.png')
def main(argv):
jamu_filepath = g_jamu_filepath
protein_dir = g_protein_dir
compound_dir = g_compound_dir
c2mapjamu_dir = g_c2mapjamu_dir
# Load a jamu formula
print('Loading jamu data from %s' % jamu_filepath)
jamu = {}
with open(jamu_filepath) as f:
jamu = yaml.load(f)
print(jamu)
# Load significant proteins
proteins = util.load_json_from_dir(protein_dir)
print('len(proteins)= %d' % len(proteins))
# Load narutal compound of jamu plants
compounds = util.load_json_from_dir(compound_dir)
print('len(compounds)= %d' % len(compounds))
# Construct the c2mapjamu
c2mapjamu = c2map.construct(proteins, compounds)
print c2mapjamu
# Visualize the c2mapjamu
# Generate random features and distance matrix.
n = 10
x = scipy.rand(n)
D = scipy.zeros([n,n])
for i in range(n):
for j in range(n):
D[i,j] = abs(x[i] - x[j])
# c2map.save_mat(D, c2mapjamu_dir+'/c2mapjamu.mat.png')
# c2map.save_mat(c2mapjamu, c2mapjamu_dir+'/c2mapjamu.mat.png')
c2map.save_graph(c2mapjamu, c2mapjamu_dir+'/c2mapjamu.graph.png')
def main(argv):
article_set_dir = '/home/tor/jamu/xprmnt/pubmed-article/06'
ori_compound_data_dir = '/home/tor/jamu/xprmnt/compound-data/ori'
ori_protein_data_dir = '/home/tor/jamu/xprmnt/protein-data/ori'
compound_data_dir = '/home/tor/jamu/xprmnt/compound-data/searched'
protein_data_dir = '/home/tor/jamu/xprmnt/protein-data/searched'
# get articles
article_filepaths = []
for filepath in glob.glob(os.path.join(article_set_dir, '*.xml')):
article_filepaths.append(filepath)
article_sets = read_article_sets(article_filepaths)
print '#article-sets=', len(article_sets)
n_articles = sum([len(i['data']) for i in article_sets])
print '#articles=', n_articles
# search for compounds
compounds = util.load_json_from_dir(ori_compound_data_dir)
print '#compounds=', len(compounds)
for c in compounds:
c['n_search_abstracts'] = [n_articles]
for article_set in article_sets:
for article_datum in article_set['data']:
if 'abstract' in article_datum:
abstract = article_datum['abstract'].lower()
c['pmid_of_containing_abstracts'] = []
if abstract.find(c['name'][0]) is not -1:
c['pmid_of_containing_abstracts'].append(
article_datum['pmid'])
compound_filepath = compound_data_dir + '/' + c['id'] + '.json'
with open(compound_filepath, 'w') as f:
json.dump(c, f)
# search for proteins
proteins = util.load_json_from_dir(ori_protein_data_dir)
print '#proteins=', len(proteins)
for p in proteins:
p['n_search_abstracts'] = [n_articles]
for article_set in article_sets:
for article_datum in article_set['data']:
if 'abstract' in article_datum:
abstract = article_datum['abstract'].lower()
p['pmid_of_containing_abstracts'] = []
if abstract.find(p['description'][0]) is not -1:
p['pmid_of_containing_abstracts'].append(
article_datum['pmid'])
if abstract.find(p['symbol'][0]) is not -1:
p['pmid_of_containing_abstracts'].append(
article_datum['pmid'])
p['pmid_of_containing_abstracts'] = list(
set(p['pmid_of_containing_abstracts']))
protein_filepath = protein_data_dir + '/' + p['id'] + '.json'
with open(protein_filepath, 'w') as f:
json.dump(p, f)
def main(argv):
article_set_dir = '/home/tor/jamu/xprmnt/pubmed-article/06'
ori_compound_data_dir = '/home/tor/jamu/xprmnt/compound-data/ori'
ori_protein_data_dir = '/home/tor/jamu/xprmnt/protein-data/ori'
compound_data_dir = '/home/tor/jamu/xprmnt/compound-data/searched'
protein_data_dir = '/home/tor/jamu/xprmnt/protein-data/searched'
# get articles
article_filepaths = []
for filepath in glob.glob(os.path.join(article_set_dir, '*.xml')):
article_filepaths.append(filepath)
article_sets = read_article_sets(article_filepaths)
print '#article-sets=', len(article_sets)
n_articles = sum([len(i['data']) for i in article_sets])
print '#articles=', n_articles
# search for compounds
compounds = util.load_json_from_dir(ori_compound_data_dir)
print '#compounds=', len(compounds)
for c in compounds:
c['n_search_abstracts'] = [n_articles]
for article_set in article_sets:
for article_datum in article_set['data']:
if 'abstract' in article_datum:
abstract = article_datum['abstract'].lower()
c['pmid_of_containing_abstracts'] = []
if abstract.find(c['name'][0]) is not -1:
c['pmid_of_containing_abstracts'].append(article_datum['pmid'])
compound_filepath = compound_data_dir+'/'+c['id']+'.json';
with open(compound_filepath,'w') as f:
json.dump(c, f)
# search for proteins
proteins = util.load_json_from_dir(ori_protein_data_dir)
print '#proteins=', len(proteins)
for p in proteins:
p['n_search_abstracts'] = [n_articles]
for article_set in article_sets:
for article_datum in article_set['data']:
if 'abstract' in article_datum:
abstract = article_datum['abstract'].lower()
p['pmid_of_containing_abstracts'] = []
if abstract.find(p['description'][0]) is not -1:
p['pmid_of_containing_abstracts'].append(article_datum['pmid'])
if abstract.find(p['symbol'][0]) is not -1:
p['pmid_of_containing_abstracts'].append(article_datum['pmid'])
p['pmid_of_containing_abstracts'] = list(set(p['pmid_of_containing_abstracts']))
protein_filepath = protein_data_dir+'/'+p['id']+'.json';
with open(protein_filepath,'w') as f:
json.dump(p, f)