Remove already internalized script

scripts/retrieve_enzyme.py

-#!/usr/bin/env python3
-
-import env
-import dbxref.config
-import dbxref.resolver
-import requests
-import logging
-import json
-import argparse
-import re
-import lxml.html as HTML
-
-logger = logging.getLogger(__name__)
-
-def main():
-	parser = argparse.ArgumentParser(description='Retrieve enzyme text documents for dbxrefs and convert them into json')
-	parser.add_argument('--basic', '-b', action='store_true', help='Include id, definition, name and synonyms')
-	parser.add_argument('--references', '-r', action='store_true', help='Include id, uniprot dbxrefs')
-	parser.add_argument('dbxrefs', nargs=argparse.REMAINDER)
-	args = parser.parse_args()
-	resolved = dbxref.resolver.resolve(args.dbxrefs, check_existence=False)
-	documents = []
-	for entry in resolved:
-		txt_url = entry['locations']['text'][0]
-		logger.debug('URL: %s', txt_url)
-		r = requests.get(txt_url)
-		logger.debug('Content: %s', r.text)
-		lines = r.text.split('\n')
-		output = {'dbxref': entry['dbxref']}
-		refs = []
-		comment = ""
-		reaction = ""
-		ls = r.text.replace('\n', ' ')
-		try:
-			html = HTML.document_fromstring(ls).head.text_content()
-			output['message'] = html
-			if output['message'] == ' 500 Internal Server Error ':
-				output['message'] = '500 Internal Server Error; probably invalid ID'
-		except:
-			for line in lines:
-				line_elements = line.strip().split('   ')
-				if line_elements[0] == 'DE':
-					output['name'] = line_elements[1]
-				if line_elements[0] == 'AN':
-					if 'alternative_names' in output:
-						output['alternative_names'].append(line_elements[1])
-					else:
-						output['alternative_names'] = [line_elements[1]]
-				if line_elements[0] == 'CA':
-					if re.match(re.compile('^\(\d+\) '), line_elements[1]):
-						if len(reaction) == 0:
-							reaction += line_elements[1][line_elements[1].find(' ')+1:]
-						else:
-							if 'reaction_catalyzed' in output:
-								output['reaction_catalyzed'].append(reaction)
-							else:
-								output['reaction_catalyzed'] = [reaction]
-							reaction = line_elements[1][line_elements[1].find(' ')+1:]
-					else:
-						if len(reaction) == 0:
-							reaction = line_elements[1]
-						else:
-							reaction = reaction + " " + line_elements[1]
-				if line_elements[0] == 'CF':
-					if 'cofactors' in output:
-						output['cofactors'].append(line_elements[1])
-					else:
-						output['cofactors'] = [line_elements[1]]
-				if line_elements[0] == 'CC':
-					if "-!-" in line_elements[1]:
-						if len(comment) == 0:
-							comment += line_elements[1][4:]
-						else:
-							if 'comments' in output:
-								output['comments'].append(comment)
-							else:
-								output['comments'] = [comment]
-							comment = line_elements[1][4:]
-					else:
-						comment += line_elements[2]
-				if line_elements[0] == 'PR':
-					link = line_elements[1].replace(';', '').split()
-					if 'prosite' in output:
-						output['prosite'].append(link[1])
-					else:
-						output['prosite'] = [link[1]]
-				if line_elements[0] == 'DR':
-					for i in range(1, len(line_elements)):
-						for e in line_elements[i].split(';  '):
-							if len(e) > 1:
-								l = e.split(', ')
-								l[1] = l[1].replace(' ', '')
-								l[1] = l[1].replace(';', '')
-								refs.append('UniProtKB/Swiss-Prot:' + l[0])
-				output['dbxrefs'] = refs
-			if len(reaction) > 0:
-				if 'reaction_catalyzed' in output:
-					output['reaction_catalyzed'].append(reaction)
-				else:
-					output['reaction_catalyzed'] = [reaction]
-			if len(comment) > 0:
-				if 'comments' in output:
-					output['comments'].append(comment)
-				else:
-					output['comments'] = [comment]
-		documents.append(format_output(output, args))
-	print(json.dumps(documents))
-
-def read_basic(d):
-	out = {}
-	definition = {}
-	if 'message' in d:
-		out['message'] = d['message']
-	if 'name' in d:
-		out['name'] = d['name']
-	if 'alternative_names' in d:
-		out['synonyms'] = d.pop('alternative_names')
-	if 'reaction_catalyzed' in d:
-		definition['reaction_catalyzed'] = d['reaction_catalyzed']
-	if 'cofactors' in d:
-		definition['cofactors'] = d['cofactors']
-	if 'comments' in d:
-		definition['comments'] = d['comments']
-	if len(definition) == 1:
-		out['definition'] = definition[0]
-	elif len(definition) > 1:
-		out['definition'] = definition
-	return (out)
-
-def format_output(d, args):
-	out = {'id': d['dbxref']}
-	if args.basic:
-		out.update(read_basic(d))
-	if args.references:
-		out['dbxrefs'] = d['dbxrefs']
-	if not args.basic and not args.references:
-		out.update(read_basic(d))
-		if 'dbxrefs' in d:
-			out['dbxrefs'] = d['dbxrefs']
-	return (out)
-
-main()