diff options
| -rwxr-xr-x | gatpub.py (renamed from get_addiction_sentences.py) | 92 | ||||
| -rw-r--r-- | server.py | 32 |
2 files changed, 89 insertions, 35 deletions
diff --git a/get_addiction_sentences.py b/gatpub.py index e24f122..6647e32 100755 --- a/get_addiction_sentences.py +++ b/gatpub.py @@ -5,16 +5,16 @@ import re import codecs import sys -gene=sys.argv[1] +#gene=sys.argv[1] ## turn dictionary (synonyms) to regular expression def undic(dic): - return "|".join(dic.keys())+"|"+"|".join(dic.values()) + return "|".join(dic.values()) def findWholeWord(w): return re.compile(r'\b({0})\b'.format(w), flags=re.IGNORECASE).search -def getSentences(query): +def getSentences(query, gene): abstracts = os.popen("esearch -db pubmed -query " + query + " | efetch -format uid |fetch-pubmed -path /run/media/hao/PubMed/Archive/ | xtract -pattern PubmedArticle -element MedlineCitation/PMID,ArticleTitle,AbstractText").read() out=str() for row in abstracts.split("\n"): @@ -26,18 +26,18 @@ def getSentences(query): for sent in sentences: if findWholeWord(gene)(sent): sent=re.sub(r'\b(%s)\b' % gene, r'<b>\1</b>', sent, flags=re.I) - out+=pmid+"\t"+sent+"\n" + out+=pmid+"\t"+sent+"<br>\n" return(out) def gene_addiction(gene): # search gene name & drug name in the context of addiction terms (i.e., exclude etoh affects cancer, or methods to extract cocaine) - q="\"(" + addiction.replace("|", " OR ") + ") AND (" + drugs.replace("|", " OR ", ) + ") AND " + gene + "\"" - sents=getSentences(q) + q="\"(" + addiction.replace("|", " OR ") + ") AND (" + drug.replace("|", " OR ", ) + ") AND " + gene + "\"" + sents=getSentences(q, gene) out=str() for sent in sents.split("\n"): - for drug0 in drugs_d: - if findWholeWord(drugs_d[drug0])(sent) : - sent=re.sub(r'\b(%s)\b' % drugs_d[drug0], r'<b>\1</b>', sent, flags=re.I) + for drug0 in drug_d: + if findWholeWord(drug_d[drug0])(sent) : + sent=re.sub(r'\b(%s)\b' % drug_d[drug0], r'<b>\1</b>', sent, flags=re.I) out+=gene+"\t"+"drug\t" + drug0+"\t"+sent+"\n" for add0 in addiction.split("|"): if findWholeWord(add0)(sent) : @@ -47,7 +47,7 @@ def gene_addiction(gene): def gene_anatomical(gene): q="\"(" + brain.replace("|", " OR ") + ") AND " + gene + "\"" - sents=getSentences(q) + sents=getSentences(q,gene) out=str() for sent in sents.split("\n"): for brain0 in brain_d: @@ -56,27 +56,50 @@ def gene_anatomical(gene): out+=gene+"\t"+"brain\t"+brain0+"\t"+sent+"\n" return(out) -def gene_biological(gene): - q="\"(" + biological.replace("|", " OR ") + ") AND " + gene + "\"" - sents=getSentences(q) +def gene_functional(gene): + q="\"(" + function.replace("|", " OR ") + ") AND " + gene + "\"" + sents=getSentences(q,gene) out=str() for sent in sents.split("\n"): - for bio0 in biological_d: - if findWholeWord(biological_d[bio0])(sent) : - sent=re.sub(r'\b(%s)\b' % biological_d[bio0], r'<b>\1</b>', sent, flags=re.I) + for bio0 in function_d: + if findWholeWord(function_d[bio0])(sent) : + sent=re.sub(r'\b(%s)\b' % function_d[bio0], r'<b>\1</b>', sent, flags=re.I) out+=gene+"\t"+"function\t"+bio0+"\t"+sent+"\n" return(out) -addiction="reward|reinforcement|sensitization|intake|addiction|drug abuse|relapse|self-administered|self-administration|reinstatement|binge|intoxication|withdrawal|conditioned place preference|aversion|aversive|CPP" +def generate_nodes(nodes_d): + # include all search terms even if there are no edges, just to show negative result + json0 =str() #"{ data: { id: '" + gene + "'} },\n" + for node in nodes_d: + json0 += "{ data: { id: '" + node + "'} },\n" + return(json0) -drugs_d = {"alcohol":"alcohol|alcoholism", +def generate_edges(data): + json0=str() + for line in data.split("\n"): + if len(line.strip())!=0: + (source, cat, target, pmid, sent) = line.split("\t") + edgeID=source+"_"+target + json0+="{ data: { id: \'" + edgeID + "\', source: \'" + source + "\', target: '" + target + "\' } },\n" + return(json0) + +addiction_d = {"reward":"reward|reinforcement|conditioned place preference|CPP|self-administration|self-administered", + "aversion":"aversion|aversive|conditioned taste aversion|CTA|withdrawal", + "relapse":"relapse|reinstatement|craving|drug seeking", + "sensitization":"sensitization", + "addiction":"addiction|drug abuse", + "intoxication":"intoxication|binge", + } +addiction=undic(addiction_d) + +drug_d = {"alcohol":"alcohol|alcoholism", "nicotine":"smoking|nicotine|tobacco", - "amphetamine":"methamphetamine|amphetamine", + "amphetamine":"methamphetamine|amphetamine|METH", "cocaine":"cocaine", "opioid":"opioid|fentanyl|oxycodone|oxycontin|heroin|morphine", - "cannabinoid":"marijuana|cannabinoid|Tetrahydrocannabinol|thc" + "cannabinoid":"marijuana|cannabinoid|tetrahydrocannabinol|thc|thc-9" } -drugs=undic(drugs_d) +drug=undic(drug_d) brain_d ={"cortex":"cortex|pfc|vmpfc|il|pl|prelimbic|infralimbic", "striatum":"striatum|STR", @@ -88,24 +111,23 @@ brain_d ={"cortex":"cortex|pfc|vmpfc|il|pl|prelimbic|infralimbic", # brain region has too many short acronyms to just use the undic function, so search PubMed using the following brain="cortex|accumbens|striatum|amygadala|hippocampus|tegmental|mesolimbic|infralimbic|prelimbic" -biological_d={"plasticity":"LTP|LTD|plasticity|synaptic|epsp|epsc", +function_d={"plasticity":"LTP|LTD|plasticity|synaptic|epsp|epsc", "neurotransmission": "neurotransmission|glutamate|GABA|cholinergic|serotoninergic", "signalling":"signalling|phosphorylation|glycosylation", # "regulation":"increased|decreased|regulated|inhibited|stimulated", "transcription":"transcription|methylation|histone|ribosome", } -biological=undic(biological_d) - -report=str() -out0=gene_addiction(gene) -report+=out0 -out1=gene_anatomical(gene) -report+=out1 -out2=gene_biological(gene) -report+=out2 -with codecs.open(gene+"_addiction_sentences.tab", "w", encoding='utf8') as writer: - writer.write(report) - writer.close() - +function=undic(function_d) +#out1=gene_anatomical(gene) +#out2=gene_functional(gene) +#report=out0+out1+out2 +#with codecs.open(gene+"_addiction_sentences.tab", "w", encoding='utf8') as writer: +# writer.write(report) +# writer.close() +n0=generate_nodes(function_d) +n1=generate_nodes(addiction_d) +n2=generate_nodes(drug_d) +n3=generate_nodes(brain_d) +default_nodes=n0+n1+n2+n3 diff --git a/server.py b/server.py new file mode 100644 index 0000000..907877a --- /dev/null +++ b/server.py @@ -0,0 +1,32 @@ +from flask import Flask, render_template, request, redirect +import simplejson as json +from gatpub import * + +app=Flask(__name__) +app.config['SECRET_KEY'] = '#DtfrL98G5t1dC*4' + +@app.route("/") +def root(): + return render_template('index.html') + +@app.route("/home") +def home(): + return render_template('index.html') + +@app.route("/network", methods=['GET', 'POST']) +def network(): + edges_list=[] + nodes_list=[] + if request.method == 'POST': + term = request.form + gene=term['query'] + nodes="{ data: { id: '" + gene + "'} },\n" + default_nodes + tmp0=gene_addiction(gene) + e0=generate_edges(tmp0) + tmp1=gene_functional(gene) + e1=generate_edges(tmp1) + tmp2=gene_anatomical(gene) + e2=generate_edges(tmp2) + return render_template('network.html', elements=nodes+e0+e1+e2) +if __name__ == '__main__': + app.run(debug=True) |