From 4bd4005b3f66fa0836e33cae1b80e7dccfd57583 Mon Sep 17 00:00:00 2001
From: Karen DRUART <karen.druart@pasteur.fr>
Date: Thu, 6 Oct 2022 15:53:29 +0200
Subject: [PATCH] Upload New File
---
XML_Subsetter/extract_uniprot_XML.py | 183 +++++++++++++++++++++++++++
1 file changed, 183 insertions(+)
create mode 100644 XML_Subsetter/extract_uniprot_XML.py
diff --git a/XML_Subsetter/extract_uniprot_XML.py b/XML_Subsetter/extract_uniprot_XML.py
new file mode 100644
index 0000000..801b995
--- /dev/null
+++ b/XML_Subsetter/extract_uniprot_XML.py
@@ -0,0 +1,183 @@
+#!/usr/bin/python3
+# extract XML sequences from a subset fasta file OR extract XML and create a fasta file from a list of accessions id
+# usage from a fasta file ./extract_uniprot_XML.py -x uniprot.xml -f file.fasta -o output_name
+# usage from a list of accession ./extract_uniprot_XML.py -x uniprot.xml -l accessions.txt -o output_name
+# created Jan 22; KD
+
+
+#############################################################################
+# Author: Karen Druart -- karen.druart@pasteur.fr #
+# https://research.pasteur.fr/fr/member/karen-druart/ #
+# Copyright (c) 2022 Institut Pasteur #
+# #
+# #
+# Redistribution and use in source and binary forms, with or without #
+# modification, are permitted provided that the following conditions #
+# are met: #
+# #
+# 1. Redistributions of source code must retain the above copyright #
+# notice, this list of conditions and the following disclaimer. #
+# 2. Redistributions in binary form must reproduce the above copyright #
+# notice, this list of conditions and the following disclaimer in the #
+# documentation and/or other materials provided with the distribution. #
+# 3. Neither the name of the copyright holder nor the names of its #
+# contributors may be used to endorse or promote products derived from #
+# this software without specific prior written permission. #
+# #
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS #
+# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT #
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR #
+# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT #
+# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, #
+# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT #
+# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, #
+# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY #
+# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT #
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE #
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. #
+# #
+# This program is free software: you can redistribute it and/or modify #
+# #
+#############################################################################
+
+
+
+
+
+
+
+import re
+import sys
+import getopt
+
+
+
+def define_db(database):
+ if database=="Swiss-Prot":
+ return 'sp'
+ elif database=="TrEMBL":
+ return 'tr'
+
+def wrap(seq, size):
+ cmp=0
+ seqout=""
+ for i in range(0,len(seq)):
+ if i - cmp *size == size:
+ cmp=cmp+1
+ seqout=seqout+"\n"
+ seqout=seqout+seq[i]
+ return seqout
+
+
+from optparse import OptionParser
+
+parser = OptionParser()
+parser.add_option("-f", "--fasta", dest="fasta_name", help="fasta file containing the list of proteins of interest")
+parser.add_option("-l", "--list", dest="list_name", help="file containing the list of accessions of interest")
+parser.add_option("-x", "--xml", dest="xml_file", help="XML file to extract proteins of interest")
+parser.add_option("-o", "--output", dest="output_name", help="the name of the outputfile. If empty, the name of the fasta or list file will be used")
+parser.epilog="For more help on 'extract_uniprot_XML' see the README."
+
+(options, args) = parser.parse_args()
+
+if not options.xml_file: # if filename is not given
+ parser.error('XML file not given\n')
+if not options.fasta_name and not options.list_name: # if filename is not given
+ parser.error('Please give a fasta file or a list of accessions to extract from the XML file\n')
+
+isFasta=0
+if not options.list_name:
+ filename=options.fasta_name
+ isFasta=1
+elif not options.fasta_name:
+ filename=options.list_name
+if not options.output_name:
+ output_name=filename.split(".")[0]
+
+
+
+
+
+
+
+l_acc=[]
+with open(filename) as filin:
+ lines=filin.readlines()
+if isFasta:
+ for line in lines:
+ if line.startswith(">"):
+ acc=line.split("|")[1]
+ l_acc.append(acc)
+ print("\n")
+ print("Number of sequence in fasta file: "+str(len(l_acc))+"\n")
+else:
+ for line in lines:
+ l_acc.append(line[:-1])
+ print("\n")
+ print("Number of accessions in file: "+str(len(l_acc))+"\n")
+
+
+
+xmlo=open(options.output_name+".xml","w")
+if isFasta==0:
+ fastao=open(options.output_name+".fasta","w")
+
+
+with open(options.xml_file) as filin:
+ xml_lines=filin.readlines()
+
+flag_entry=0
+temp_entry=[]
+toprint=1
+for line in xml_lines:
+ if line.startswith("<entry"):
+ acc=[]
+ seq=[]
+ name=""
+ fullname=""
+ database=line.split('dataset="')[1].split('"')[0]
+ temp_entry=[line]
+ flag_entry=1
+ toprint=1
+ elif line.startswith("<accession"):
+ acc.append(re.split(">|<",line)[2])
+ temp_entry.append(line)
+ elif line.startswith("<sequence"):
+ temp_entry.append(line)
+ if line.find("</sequence>"):
+ seq=re.split(">|<",line)[2]
+ elif line.startswith("<name>"):
+ temp_entry.append(line)
+ name=re.split(">|<",line)[2]
+ elif line.startswith("<fullName>"):
+ temp_entry.append(line)
+ if fullname=="":
+ fullname=re.split(">|<",line)[2]
+ elif line.startswith('</entry'):
+ temp_entry.append(line)
+ flag_entry=0
+ # we test if we have to keep this proteoform
+ for a in acc:
+ if a in l_acc:
+ if toprint==1:
+ for i in temp_entry:
+ xmlo.write(i)
+ if isFasta==0:
+ db=define_db(database)
+ seq_fasta=wrap(seq,80)
+ fastao.write(">"+db+"|"+a+"|"+name+" "+fullname+'\n'+seq_fasta+"\n")
+ toprint=0
+
+ else:
+ if flag_entry==0:
+ xmlo.write(line)
+ else:
+ temp_entry.append(line)
+
+
+xmlo.close()
+if isFasta==0:
+ fastao.close()
+
+
+
--
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