diff options
| -rw-r--r-- | requirements.md | 48 | ||||
| -rwxr-xr-x | server.py | 7 | ||||
| -rw-r--r-- | utility/process_gwas.py (renamed from process_gwas.py) | 0 | ||||
| -rwxr-xr-x | utility/topGene_step0_extract_gene_alias_from_gene_info.sh (renamed from topGene_step0_extract_gene_alias_from_gene_info.sh) | 0 | ||||
| -rwxr-xr-x | utility/topGene_step1_cnt_abstracts.py (renamed from topGene_step1_cnt_abstracts.py) | 0 | ||||
| -rwxr-xr-x | utility/topGene_step2_cnt_sentences.py (renamed from topGene_step2_cnt_sentences.py) | 0 | ||||
| -rwxr-xr-x | utility/topGene_step3_generate_html.py (renamed from topGene_step3_generate_html.py) | 0 | ||||
| -rwxr-xr-x | utility/topGene_step4_get_pmids_for_all_top_genes.py (renamed from topGene_step4_get_pmids_for_all_top_genes.py) | 0 |
8 files changed, 11 insertions, 44 deletions
diff --git a/requirements.md b/requirements.md index a791b8c..80574c7 100644 --- a/requirements.md +++ b/requirements.md @@ -8,14 +8,10 @@ * Click==7.0 * itsdangerous==1.1.0 * Jinja2==2.10.3 - * MarkupSafe + * MarkupSafe==1.0 * Werkzeug==1.0.0 * SQLAlchemy==1.3.12 -* nltk==3.4.5 - * six==1.14.0 - - * Keras==2.3.1 * h5py==2.10.0 * numpy==1.18.1 @@ -34,8 +30,10 @@ * numpy==1.18.1 * six==1.14.0 +* nltk==3.4.5 + * six==1.14.0 -* tensorflow==2.1.0 +* tensorflow==1.14.0 * absl-py==0.9.0 * six==1.14.0 * astor==0.8.1 @@ -53,41 +51,13 @@ * numpy==1.18.1 * six==1.14.0 * numpy==1.18.1 - * opt-einsum==3.2.0 - * numpy==1.18.1 * protobuf==3.11.3 * setuptools==45.2.0 * six==1.14.0 - * scipy==1.4.1 - * numpy==1.18.1 * six==1.14.0 - * tensorboard==2.1.1 + * tensorboard==1.14.0 * absl-py==0.9.0 * six==1.14.0 - * google-auth==1.13.1 - * cachetools==4.1.0 - * pyasn1-modules==0.2.8 - * pyasn1==0.4.8 - * rsa==4.0 - * pyasn1==0.4.8 - * setuptools==45.2.0 - * six==1.14.0 - * google-auth-oauthlib==0.4.1 - * google-auth==1.13.1 - * cachetools==4.1.0 - * pyasn1-modules==0.2.8 - * pyasn1==0.4.8 - * rsa==4.0 - * pyasn1==0.4.8 - * setuptools==45.2.0 - * six==1.14.0 - * requests-oauthlib==1.3.0 - * oauthlib==3.1.0 - * requests==2.22.0 - * certifi==2019.11.28 - * chardet==3.0.4 - * idna==2.8 - * urllib3==1.25.8 * grpcio==1.27.2 * six==1.14.0 * Markdown==3.2.1 @@ -96,18 +66,14 @@ * protobuf==3.11.3 * setuptools==45.2.0 * six==1.14.0 - * requests==2.22.0 - * certifi==2019.11.28 - * chardet==3.0.4 - * idna==2.8 - * urllib3==1.25.8 * setuptools==45.2.0 * six==1.14.0 * Werkzeug==1.0.0 * wheel==0.34.2 - * tensorflow-estimator==2.1.0 + * tensorflow-estimator==1.14.0 * termcolor==1.1.0 * wheel==0.34.2 * wrapt==1.11.2 * python==3.6.9 + @@ -629,12 +629,13 @@ def sentences(): if(pmid+cat0 not in pmid_list): pmid_list.append(pmid+cat0) if(cat0=='stress'): - out_pred = "<li> "+ text + " <a href=\"https://www.ncbi.nlm.nih.gov/pubmed/?term=" + pmid +"\" target=_new>PMID:"+pmid+"<br></a>" out4 = predict_sent(text) if(out4 == 'pos'): - out_pos += out_pred + out_pred_pos = "<li> "+ text + " <a href=\"https://www.ncbi.nlm.nih.gov/pubmed/?term=" + pmid +"\" target=_new>PMID:"+pmid+"<br></a>" + out_pos += out_pred_pos else: - out_neg += out_pred + out_pred_neg = "<li>"+ text + " <a href=\"https://www.ncbi.nlm.nih.gov/pubmed/?term=" + pmid +"\" target=_new>PMID:"+pmid+"<br></a>" + out_neg += out_pred_neg out1="<h3>"+gene0 + " and " + cat0 + "</h3>\n" if len(pmid_list)>1: out2 = str(num_abstract) + ' sentences in ' + str(len(pmid_list)) + ' studies' + "<br><br>" diff --git a/process_gwas.py b/utility/process_gwas.py index eba59c0..eba59c0 100644 --- a/process_gwas.py +++ b/utility/process_gwas.py diff --git a/topGene_step0_extract_gene_alias_from_gene_info.sh b/utility/topGene_step0_extract_gene_alias_from_gene_info.sh index 4d3118b..4d3118b 100755 --- a/topGene_step0_extract_gene_alias_from_gene_info.sh +++ b/utility/topGene_step0_extract_gene_alias_from_gene_info.sh diff --git a/topGene_step1_cnt_abstracts.py b/utility/topGene_step1_cnt_abstracts.py index 420c9cf..420c9cf 100755 --- a/topGene_step1_cnt_abstracts.py +++ b/utility/topGene_step1_cnt_abstracts.py diff --git a/topGene_step2_cnt_sentences.py b/utility/topGene_step2_cnt_sentences.py index b05aa7a..b05aa7a 100755 --- a/topGene_step2_cnt_sentences.py +++ b/utility/topGene_step2_cnt_sentences.py diff --git a/topGene_step3_generate_html.py b/utility/topGene_step3_generate_html.py index 036325b..036325b 100755 --- a/topGene_step3_generate_html.py +++ b/utility/topGene_step3_generate_html.py diff --git a/topGene_step4_get_pmids_for_all_top_genes.py b/utility/topGene_step4_get_pmids_for_all_top_genes.py index adf527c..adf527c 100755 --- a/topGene_step4_get_pmids_for_all_top_genes.py +++ b/utility/topGene_step4_get_pmids_for_all_top_genes.py |