Create codon_optimize_cds_by_proteins_gui.py

synbio/codon_optimize_cds_by_proteins_gui.py

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+# python3
+from gooey import *
+from Bio import SeqIO
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+from dnachisel import *
+# imput parameters
+@Gooey(required_cols=3, program_name='codon optimize cds by proteins', header_bg_color= '#DCDCDC', terminal_font_color= '#DCDCDC', terminal_panel_color= '#DCDCDC')
+def main():
+    ap = GooeyParser()
+    ap.add_argument("-fa", "--fasta", required=True, widget='FileChooser', help="input single fasta file with coding sequence")
+    ap.add_argument("-prot", "--proteins", required=True, widget='FileChooser', help="input multi fasta file with protein sequences")
+    ap.add_argument("-org","--organism", required=True, help="organism to input(use either the names of the genomes avaliable on dnachisel or use the taxid of the organisms that exist in http://www.kazusa.or.jp/codon/)")
+    ap.add_argument("-opt","--optimized", required=True, widget='FileSaver', help="optimized fasta file")
+    args = vars(ap.parse_args())
+# main
+    cds = SeqIO.read(args["fasta"], "fasta")
+    optimized_seqs = [] # setup an empty list
+    for record in SeqIO.parse(args['proteins'], "fasta"):
+        problem = DnaOptimizationProblem(sequence=str(cds.seq),
+        constraints=[EnforceTranslation(translation=str(record.seq))],
+        objectives=[CodonOptimize(species= args['organism'])])
+        problem.optimize()
+        # add this record to the list
+        optimized_seqs.append(SeqRecord(Seq(problem.sequence),id=record.id,description=""))
+# export to fasta
+    SeqIO.write(optimized_seqs, args['optimized'], "fasta")
+
+if __name__ == '__main__':
+    main()