Create ligate_by_pair_gui.py

synbio/ligate_by_pair_gui.py

@@ -0,0 +1,44 @@
+# python3
+from gooey import *
+import itertools
+from Bio import SeqIO
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+from Bio.Alphabet import generic_dna
+# imput parameters
+@Gooey(required_cols=3, program_name='digital ligation', header_bg_color= '#DCDCDC', terminal_font_color= '#DCDCDC', terminal_panel_color= '#DCDCDC')
+def main():
+    ap = GooeyParser(description="ligate linear vector with DNA insert by pair from each input multi-fasta file")
+    ap.add_argument("-vr", "--vector", required=True, widget='FileChooser', help="linear vectors (multi-fasta file the order is inportant as the 1st vector matches the 1st insert in the file etc)")
+    ap.add_argument("-in", "--insert", required=True, widget='FileChooser', help="sequences to insert in the vectors (multi-fasta file the order is inportant as the 1st insert matches the 1st vector in the file etc)")
+    ap.add_argument("-out", "--output", required=True, widget='FileSaver', help="output genbank file with circular sequences")
+    args = vars(ap.parse_args())
+# main 
+# linear vector
+    output_handle = open(args['output'], "w")
+# setup  empty lists
+    plasmid_seqs = []
+    plasmid_ids = []
+# select all plasmid sequences and ids to seperate lists
+    for plasmid in SeqIO.parse(args['vector'], "fasta"):
+        plasmid_seqs.append(plasmid.seq)
+        plasmid_ids.append(plasmid.id)
+# DNA insert
+    insert_ids = []
+    insert_seqs = []
+    for record in SeqIO.parse(args['insert'], "fasta"):
+        insert_seqs.append(record.seq)
+        insert_ids.append(record.id)
+# iter all element of the lists by groups of 4 variables
+    records = []
+    for (a, b, c, d) in itertools.zip_longest(plasmid_ids, plasmid_seqs, insert_ids, insert_seqs):
+        # merge
+        seqad = str(d) + str(b)
+            # add this record to the list
+        records.append(SeqRecord(Seq(seqad,generic_dna),id='_'.join([str(c),str(a)]),description="",annotations={"topology":"circular"}))
+# export to fasta
+    SeqIO.write(records,output_handle, "genbank")
+    output_handle.close()
+
+if __name__ == '__main__':
+    main()