--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CodonSwitchTool/codon_switch.py	Tue May 21 05:24:56 2019 -0400
@@ -0,0 +1,172 @@
+#!/usr/bin/env python
+
+__author__= "Gianmarco Piccinno"
+__version__ = "1.0.0"
+
+from syngenic import *
+from functions import *
+from Bio import *
+import argparse as ap
+
+if __name__ == '__main__':
+
+    parser = ap.ArgumentParser(description="", formatter_class=ap.RawTextHelpFormatter)
+
+    parser.add_argument(
+        '-i', '--input_plasmid', help='Input plasmid', required=True)
+    parser.add_argument(
+        '-l', '--plasmid_format', help='Format of the plasmid: {fasta, genbank}', required=True)
+    parser.add_argument(
+        '-p', '--input_patterns', help='Input patterns separated by new_line', required=True)
+    parser.add_argument(
+        '-g', '--input_genome', help='Input annotated genome', required=True)
+    parser.add_argument(
+        '-q', '--genome_format', help='Format of the annotated genome: {fasta, gbk}', required=True)
+    parser.add_argument(
+        '-c', '--codon_table', help='Codon table to be used {Bacterial}', required=True)
+    parser.add_argument(
+        '-m', '--max_row', help='Max row length when print', required=False)
+    parser.add_argument(
+        '-d', '--demonstration', help='Use demonstration simplication', required=False)
+    parser.add_argument(
+        '-f', '--n_plasmids', help='Use demonstration simplication', required=False)
+    parser.add_argument(
+        '-o', '--output_folder', help='Folder for writing the output file', required=True)
+    args = vars(parser.parse_args())
+
+    """
+
+    python codon_switch_v2.py
+        -i ./pEPSA5_annotated.gb
+        -l genbank
+        -p ./patterns.txt
+        -g S_aureus_JE2.gbf
+        -q gbk -c Bacterial
+        -o ./output
+
+        python codon_switch_v2.py -i ./pEPSA5_annotated.gb -l genbank -p ./patterns.txt -g S_aureus_JE2.gbf -q genbank -c Bacterial -o ./output
+
+    """
+
+
+    pl = SeqIO.read(
+        open(args['input_plasmid'], "r"), args['plasmid_format'])
+
+    if args['demonstration'] == "demonstration":
+        pl = pl[0:3000]
+    pats = read_patterns(args['input_patterns'])
+
+
+    #############################################################
+    #
+    #############################################################
+
+    #pl = fake_from_real(path = "./data/pEPSA5_annotated.gb", id_ = "Trial", name = "Fake_plasmid")
+    print(type(pl))
+    print(pl); print(pl.seq); print(pl.features)
+
+    #for feat in pl.features:
+    #    print(str(feat.extract(pl)))
+    #    print(str(pl[feat.location.start:feat.location.end]))
+    #    print("\n")
+
+
+    n_pl = plasmid(pl)
+    print(n_pl); print(len(n_pl))
+    print(n_pl.features)
+
+
+    patts, n_patts = all_patterns(input_ = pats)
+
+
+    f_patts = n_pl.findpatterns(n_patts, patts)
+    print(f_patts)
+    print(pl.seq)
+    print(len(pl.seq))
+
+
+    n_poss = punctuate_targets(f_patts, n_pl)
+    print(n_poss)
+
+    print_seq(n_pl.seq)
+
+    synonims_tables = synonims_(table_name=args['codon_table'])
+
+    synonims_tables
+
+    plasmids = generalization(n_poss, n_pl, synonims_tables)
+
+    print(len(plasmids))
+
+    #plasmids
+
+    #if len(plasmids) > 5000000:
+        #redo generalization without considering internal bases
+        #in target sites that are not in CDS
+        #this means considering only the outer bases of the target
+    #    plasmids = generalization(n_poss, n_pl, synonims_tables,
+    #                              reduced = True)
+
+    #########################################################
+    # Read plasmid and compute codon usage
+    #########################################################
+
+    genome = annotated_genome(read_annotated_genome(
+            data=args['input_genome'], type_=args['genome_format']))
+
+    out_genome = genome.codon_usage(args['codon_table'])
+    print(out_genome.keys())
+    print(out_genome["Table"])
+
+    print(out_genome["Table"].loc["GCA"]["Proportion"])
+    print(type(out_genome["Table"].loc["GCA"]["Proportion"]))
+
+
+    #########################################################
+    # Evaluate the plasmid
+    #########################################################
+
+    useful_plasmids = evaluate_plasmids(plasmids = plasmids,
+                                        original_plasmid = n_pl,
+                                        codon_usage_table = out_genome["Table"],
+                                        n_patts = n_patts,
+                                        f_patts = patts)
+
+    dat_plasmids = rank_plasmids(original_useful_plasmids = useful_plasmids)
+
+    def_pls = dat_plasmids.index[:int(args['n_plasmids'])]
+
+    for to_save in def_pls:
+        #print(to_save)
+        #print(useful_plasmids[to_save])
+        with open(to_save+".fa", "w") as handle:
+            handle.write(">"+to_save+"\n")
+            handle.write(useful_plasmids[to_save]["sequence"])
+
+
+
+    if args['max_row'] != None:
+        tmp_max_row = int(args['max_row'])
+    else:
+        tmp_max_row = 27
+
+    print_color_seq(original = n_pl,
+                    others = def_pls,
+                    annotation_information = useful_plasmids,
+                    tot = useful_plasmids,
+                    ind_range = None,
+                    patterns = n_poss,
+                    f_patterns = f_patts,
+                    patts = patts,
+                    max_row = tmp_max_row)
+
+
+    print_to_pdf(original = n_pl,
+                 others = def_pls,
+                 annotation_information = useful_plasmids,
+                 tot = useful_plasmids,
+                 ind_range = None,
+                 patterns = n_poss,
+                 f_patterns = f_patts,
+                 patts = patts,
+                 max_row = tmp_max_row)