update scripts

Changes to be committed:
	modified:   lib/json2csv.py
	new file:   lib/linage.py
	modified:   lib/validate.py

Author: HadleyKing

lib/json2csv.py

@@ -1,3 +1,6 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
 import json, csv
 import argparse
 import jsonschema

lib/linage.py

@@ -0,0 +1,26 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import csv
+from Bio import Entrez
+
+bioproject = {}
+
+with open('test.csv', 'r') as file:
+    data = csv.reader(file)
+    header = next(data)
+    for row in data: 
+        bioproject[row[0]] = row[1:]
+print(bioproject)
+test_id = bioproject['GCA_013267415.1'][5]
+print(test_id)
+# print(",".join(assembly_ids))
+Entrez.email = "[email protected]"
+# print(Entrez.epost("assembly", id=",".join(assembly_ids)).read())
+handle = Entrez.esearch(db="taxonomy", term=test_id)
+record = Entrez.read(handle)
+handle.close()
+print(record['IdList'])
+handle2 = Entrez.efetch(db='taxonomy', id=record['IdList'][0])
+record2 = Entrez.read(handle2)
+print(record2[0]['Lineage'])

lib/validate.py

@@ -1,3 +1,6 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
 import json
 import argparse
 import jsonschema