Create JGI_genbank.py

JGI_genbank.py

@@ -0,0 +1,70 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#For batch downloading the tar bundles of IMG data which includes both annotation
+#and fasta files.
+
+#file is a .txt file containing IMG genome id's
+#username is your IMG username/email entered as a string in quotes
+#password is your IMG account password entered as a string in quotes
+
+def get_gbk(file, username, password):
+    import pycurl
+    from io import BytesIO
+    import urllib.parse
+    import re
+    import time
+    import os
+
+    with open(file) as f:
+        IMG_ids = f.read().splitlines()
+
+    not_in_Genome_Portal=[]
+    for id in IMG_ids:
+        available_files = BytesIO()
+        c = pycurl.Curl()
+        c.setopt(c.VERBOSE,1)
+        url='https://signon-old.jgi.doe.gov/signon/create'
+        params={'login':username,'password':password}
+        c.setopt(c.URL, url)
+        c.setopt(c.POSTFIELDS, urllib.parse.urlencode(params).encode())
+        c.setopt(c.COOKIEFILE, 'cookies')
+        c.perform()
+        id_to_search= 'IMG_'+str(id)
+        print(id_to_search)
+        c.setopt(c.URL,'https://genome.jgi.doe.gov/portal/ext-api/downloads/get-directory?organism='+id_to_search)
+        c.setopt(c.COOKIEJAR, 'cookies')
+        c.setopt(c.HTTPGET,1)
+        #file_handle = open("file.xml","wb")
+        c.setopt(c.WRITEDATA, available_files)
+        #c.setopt(c.WRITEDATA, file_handle)
+        c.perform()
+        available_files
+        body = available_files.getvalue()
+        x=body.decode('iso-8859-1')
+        print(x)
+        if x == 'Portal does not exist':
+            print(id_to_search+':'+ x)
+            not_in_Genome_Portal.append(id_to_search)
+        else:
+            labels=re.findall('(?<=file label=")(.*?)(?=")',x)[0]
+            labels=re.sub(' ','_',labels)
+            labels=re.sub('\(|\)','',labels)
+            labels=re.sub('-','_',labels)
+            name=re.findall('(?<=filename=")(.*assembled\.gbk)(?=" size)',x)
+            urls=re.findall('(?<=\;url=)(.*assembled\.gbk)(?=")',x)
+
+            name_of_file=labels+'_'+str(name[0])
+            print(name_of_file)
+
+            file_to_download= 'https://genome.jgi.doe.gov/portal/ext-api/downloads/get_tape_file?blocking=true&url='+str(urls[0])
+
+            c.setopt(c.URL,file_to_download)
+            c.setopt(c.COOKIEJAR, 'cookies')
+            c.setopt(c.HTTPGET,1)
+            file_handle2 = open(name_of_file,"wb")
+            c.setopt(c.WRITEDATA, file_handle2)
+            c.perform()
+            c.close()
+            time.sleep(3)
+        print('could not download '+str(len(not_in_Genome_Portal))+ ' Genome files:')
+        print(not_in_Genome_Portal)