diff cherry_pick_fasta.py @ 3:c282a8a47dd9 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"

--- a/cherry_pick_fasta.py	Tue Mar 16 23:25:57 2021 +0000
+++ b/cherry_pick_fasta.py	Fri May 21 09:34:14 2021 +0000
@@ -1,51 +1,63 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
-"""
-Chery pick of fasta sequences satisfying a query string in their header/name
-"""
+# Chery pick of fasta sequences satisfying a query string in their header/name
+import argparse
 
-import argparse
+from Bio import SeqIO
 
 
 def Parser():
     the_parser = argparse.ArgumentParser(
-        description="Cherry pick fasta sequences")
-    the_parser.add_argument('--input', action="store", type=str,
-                            help="input fasta file")
-    the_parser.add_argument('--searchfor', action="store", type=str,
-                            help="with, without, or withlist, withoutlist")
-    the_parser.add_argument('--query-string', dest="query_string",
-                            action="store", type=str,
-                            help="headers containing the string will be \
+        description='Cherry pick fasta sequences')
+    the_parser.add_argument('--input', action='store', type=str,
+                            help='input fasta file')
+    the_parser.add_argument('--searchfor', action='store', type=str,
+                            help='with, without, or withlist, withoutlist')
+    the_parser.add_argument('--mode', action='store', type=str,
+                            default='includes', help='exact or includes')
+    the_parser.add_argument('--query-string', dest='query_string',
+                            action='store', type=str,
+                            help='headers containing the string will be \
                                   extracted or excluded as well as the \
-                                  corresponding sequence")
-    the_parser.add_argument('--query-file', dest="query_file",
-                            action="store", type=str,
-                            help="headers containing any of the strings provided in the \
-                                  text file (1 string per line) will be \
-                                  extracted or excluded as well as the \
-                                  corresponding sequence")
-
-    the_parser.add_argument(
-        '--output', action="store", type=str, help="output fasta file")
+                                  corresponding sequence')
+    the_parser.add_argument('--query-file', dest='query_file',
+                            action='store', type=str,
+                            help='headers containing any of the strings \
+                                  provided in the text file (1 string per \
+                                  line) will be extracted or excluded as well \
+                                   as the corresponding sequence')
+    the_parser.add_argument('--output', action='store', type=str,
+                            help='output fasta file')
     args = the_parser.parse_args()
     return args
 
 
-def parse_fasta_with(query, FastaListe):
+def parse_fasta_dict(query, fasta_dict, mode):
     if not isinstance(query, list):
         query = [query]
     accumulator = []
-    for sequence in FastaListe:
-        for string in query:
-            if string in sequence:
-                accumulator.append(sequence)
-                continue
-    return accumulator
+    if mode == 'includes':
+        for seq_id in fasta_dict:
+            for string in query:
+                if string in seq_id:
+                    accumulator.append(seq_id)
+                    continue
+    elif mode == 'exact':
+        for seq_id in fasta_dict:
+            for string in query:
+                if string == seq_id:
+                    accumulator.append(seq_id)
+                    continue
+    res_dict = {k: fasta_dict[k] for k in fasta_dict if k in accumulator}
+    return res_dict
 
 
-def complement_fasta(fullfasta, subfasta):
-    return sorted(list(set(fullfasta) - set(subfasta)))
+def complement_fasta_dict(fasta_dict, subfasta_dict):
+    fasta_ids = list(fasta_dict.keys())
+    subfasta_ids = list(subfasta_dict.keys())
+    complement_ids = list(set(fasta_ids) - set(subfasta_ids))
+    sub_dict = {k: fasta_dict[k] for k in fasta_dict if k in complement_ids}
+    return sub_dict
 
 
 def getquerylist(file):
@@ -55,37 +67,37 @@
     return querylist
 
 
-def __main__():
-    """ main function """
-    args = Parser()
-    searchterm = args.query_string
-    CrudeFasta = open(args.input, "r").read()
-    Output = open(args.output, "w")
-    FastaListe = CrudeFasta.split(">")[1:]
-    if args.query_string:
-        if args.searchfor == 'with':
-            contList = parse_fasta_with(searchterm, FastaListe)
-            contFasta = ">%s" % ">".join(contList)
-            Output.write(contFasta)
-        elif args.searchfor == 'without':
-            notcontList = complement_fasta(FastaListe,
-                                           parse_fasta_with(searchterm,
-                                                            FastaListe))
-            notcontFasta = ">%s" % ">".join(notcontList)
-            Output.write(notcontFasta)
-    if args.query_file:
-        searchlist = getquerylist(args.query_file)
-        if args.searchfor == 'with':
-            contList = parse_fasta_with(searchlist, FastaListe)
-            contFasta = ">%s" % ">".join(contList)
-            Output.write(contFasta)
-        elif args.searchfor == 'without':
-            notcontList = complement_fasta(FastaListe, parse_fasta_with(
-                                           searchlist, FastaListe))
-            notcontFasta = ">%s" % ">".join(notcontList)
-            Output.write(notcontFasta)
-    Output.close()
+def buid_fasta_dict(fasta):
+    seq_dict = {rec.id: rec.seq for rec in SeqIO.parse(fasta, "fasta")}
+    return seq_dict
+
+
+def write_fasta_result(fasta_dict, file):
+    line_length = 60
+    with open(file, 'w') as f:
+        for header in sorted(fasta_dict):
+            f.write('>%s\n' % header)
+            for i in range(line_length, len(fasta_dict[header]), line_length):
+                f.write('%s\n' % fasta_dict[header][i-line_length:i])
+            f.write('%s\n' % fasta_dict[header][i:])
 
 
-if __name__ == "__main__":
+def __main__():
+    ''' main function '''
+    args = Parser()
+    fasta_dict = buid_fasta_dict(args.input)
+    if args.query_string:
+        query = args.query_string
+    elif args.query_file:
+        query = getquerylist(args.query_file)
+    if args.searchfor == 'with':
+        fasta_result_dict = parse_fasta_dict(query, fasta_dict, args.mode)
+    elif args.searchfor == 'without':
+        fasta_result_dict = complement_fasta_dict(fasta_dict, parse_fasta_dict(
+                                                  query, fasta_dict,
+                                                  args.mode))
+    write_fasta_result(fasta_result_dict, args.output)
+
+
+if __name__ == '__main__':
     __main__()