added python 3 version, renamed files, tested with Python 3.5.1 :: An…

…aconda 4.0.0 (x86_64)

query_enrichr_py3.py

@@ -0,0 +1,128 @@
+#!/usr/bin/env python
+
+# python 3
+# Author: Stephen Newhouse <[email protected]>
+# Date: June 2016
+# see: http://amp.pharm.mssm.edu/Enrichr/help#api for API docs
+#
+# Usage: python query_enrichr_v0.1.py <genelist> <listdesrciption> <enrichr_library> <enrichr_results>
+
+import json
+import requests
+import sys
+
+print("Enrichr API : Start")
+print("Enrichr API : Reading Command Options")
+## get command line args
+genelist = sys.argv[1]
+listdesrciption = sys.argv[2]
+enrichr_library = sys.argv[3]
+enrichr_results = sys.argv[4]
+
+# testing
+# genelist = "gene_list.txt"
+# enrichr_library = "KEGG_2016"
+# listdesrciption = "TEST"
+# enrichr_results = "example_enrichment_KEGG_2016"
+
+## Print options
+print('Enrichr API : Input file is:', genelist)
+print('Enrichr API : Analysis name: ', listdesrciption)
+print('Enrichr API : Enrichr Library: ', enrichr_library)
+print('Enrichr API : Enrichr Results File: ', enrichr_results)
+
+# get gene lits
+print("Enrichr API : Reading:",genelist)
+f = open(genelist)
+genes = f.read()
+
+## enrichr url
+ENRICHR_URL = 'http://amp.pharm.mssm.edu/Enrichr/addList'
+
+# stick gene list here
+genes_str = str(genes)
+
+# name of analysis or list
+description = str(listdesrciption)
+
+# payload
+payload = {
+  'list': (None, genes_str),
+  'description': (None, description)
+}
+
+# response
+print("Enrichr API : requests.post")
+response = requests.post(ENRICHR_URL, files=payload)
+
+if not response.ok:
+  raise Exception('Error analyzing gene list')
+
+job_id = json.loads(response.text)
+
+print('Enrichr API : Job ID:', job_id)
+
+################################################################################
+# View added gene list
+#
+ENRICHR_URL_A = 'http://amp.pharm.mssm.edu/Enrichr/view?userListId=%s'
+
+user_list_id = job_id['userListId']
+#print(user_list_id)
+
+response_gene_list = requests.get(ENRICHR_URL_A % str(user_list_id))
+
+if not response_gene_list.ok:
+    raise Exception('Error getting gene list')
+
+print('Enrichr API : View added gene list:', job_id)
+added_gene_list = json.loads(response_gene_list.text)
+print(added_gene_list)
+
+################################################################################
+# Get enrichment results
+#
+ENRICHR_URL = 'http://amp.pharm.mssm.edu/Enrichr/enrich'
+query_string = '?userListId=%s&backgroundType=%s'
+
+## get id data
+user_list_id = job_id['userListId']
+
+## Libraray
+gene_set_library = str(enrichr_library)
+
+response = requests.get(
+    ENRICHR_URL + query_string % (str(user_list_id), gene_set_library)
+ )
+if not response.ok:
+    raise Exception('Error fetching enrichment results')
+
+print('Enrichr API : Get enrichment results: Job Id:', job_id)
+data = json.loads(response.text)
+print(data)
+
+################################################################################
+## Download file of enrichment results
+#
+ENRICHR_URL = 'http://amp.pharm.mssm.edu/Enrichr/export'
+
+query_string = '?userListId=%s&filename=%s&backgroundType=%s'
+
+user_list_id = str(job_id['userListId'])
+
+filename = enrichr_results
+
+gene_set_library = str(enrichr_library)
+
+url = ENRICHR_URL + query_string % (user_list_id, filename, gene_set_library)
+
+response = requests.get(url, stream=True)
+
+print('Enrichr API : Downloading file of enrichment results: Job Id:', job_id)
+with open(filename + '.txt', 'wb') as f:
+    for chunk in response.iter_content(chunk_size=1024):
+        if chunk:
+            f.write(chunk)
+################################################
+print('Enrichr API : Results written to:', enrichr_results + ".txt")
+print("Enrichr API : Done")