diff options
Diffstat (limited to 'ratspub.py')
| -rwxr-xr-x | ratspub.py | 27 |
1 files changed, 7 insertions, 20 deletions
@@ -3,8 +3,9 @@ from nltk.tokenize import sent_tokenize import os import re from ratspub_keywords import * +from gene_synonyms import * -global function_d, brain_d, drug_d, addiction_d, brain_query_term, pubmed_path +global function_d, brain_d, drug_d, addiction_d, brain_query_term, pubmed_path, genes ## turn dictionary (synonyms) to regular expression def undic(dic): @@ -141,6 +142,8 @@ function=undic(function_d) addiction=undic(addiction_d) drug=undic(drug_d) +gene_s=undic(genes) + nodecolor={'function':"#A9CCE3", 'addiction': "#D7BDE2", 'drug': "#F9E79F", 'brain':"#A3E4D7", 'GWAS':"#AEB6BF", 'stress':"#EDBB99", 'psychiatric':"#F5B7B1"} #https://htmlcolorcodes.com/ third column down @@ -150,7 +153,7 @@ n2=generate_nodes(drug_d, 'drug') n3=generate_nodes(brain_d, 'brain') n4=generate_nodes(stress_d, 'stress') n5=generate_nodes(psychiatric_d, 'psychiatric') -n6=generate_nodes(psychiatric_d, 'GWAS') +n6='' nj0=generate_nodes_json(function_d, 'function') nj1=generate_nodes_json(addiction_d, 'addiction') @@ -158,23 +161,7 @@ nj2=generate_nodes_json(drug_d, 'drug') nj3=generate_nodes_json(brain_d, 'brain') nj4=generate_nodes_json(stress_d, 'stress') nj5=generate_nodes_json(psychiatric_d, 'psychiatric') -nj6=generate_nodes_json(psychiatric_d, 'GWAS') - - +nj6='' pubmed_path=os.environ["EDIRECT_PUBMED_MASTER"] -if ( not pubmed_path): - pubmed_path="~/Dropbox/ChenLab/Hakan/RatsPub/PubMed" -pubmed_path +="/Archive" -''' -print (pubmed_path) -host= os.popen('hostname').read().strip() -if host=="x1": - pubmed_path="/run/media/hao/PubMed/Archive/" -elif host=="hchen3": - pubmed_path="/media/hao/2d554499-6c5b-462d-85f3-5c49b25f4ac8/PubMed/Archive" -elif host=="penguin2": - pubmed_path="/export2/PubMed/Archive" -elif host=="hchen": - pubmed_path="~/Dropbox/ChenLab/Hakan/RatsPub/PubMed/Archive" -''' + |