added scripts

execute_codopt.py

@@ -0,0 +1,104 @@
+import re
+from functions import get_codon_usage,visualize_codon_usage,optimize_codon_usage
+
+print('\n')
+print('Hi, I will optimize the codon usage of your gene.')
+print('\n')
+print('First, I need some input. Do NOT type any file extensions unless I ask you to. Also, no typos, please.')
+print('\n')
+gene = input('Enter name of gene to be optimized: ')
+gene_OPT = gene + '_opt'
+sequence = re.sub(r"[\n\t\s]*", "", input('Copy and paste the DNA sequence of your gene (only CDS): ').upper())
+
+organism_ORIGIN = input('Enter name of original host organism: ')
+CDS_source_nofile_ORIGIN = input("Enter name of its genbank file ('xxx'.gb) or csv file from Kazusa ('xxx'.csv): ")
+CDS_type_ORIGIN = input("file extension: 'gb' or 'csv?'")
+CDS_source_ORIGIN = CDS_source_nofile_ORIGIN + '.' + CDS_type_ORIGIN
+save_table_ORIGIN = CDS_source_nofile_ORIGIN + '_codon_usage'
+CDSdict_txt_ORIGIN = 'CDS_dict_' + save_table_ORIGIN + '.txt'
+save_table_txt_ORIGIN = save_table_ORIGIN + '.txt'
+save_table_csv_ORIGIN = save_table_ORIGIN + '.csv'
+savefig_ORIGIN = 'codon_usage_' + gene + '_vs_' + organism_ORIGIN + '.pdf'
+
+organism_DEST = input('Enter name of destination organism: ')
+CDS_source_nofile_DEST = input("Enter name of its genbank file ('xxx'.gb) or csv file from Kazusa ('xxx'.csv): ")
+CDS_type_DEST = input("file extension: 'gb' or 'csv?'")
+CDS_source_DEST = CDS_source_nofile_DEST + '.' + CDS_type_DEST
+save_table_DEST = CDS_source_nofile_DEST + '_codon_usage'
+CDSdict_txt_DEST = 'CDS_dict_' + save_table_DEST + '.txt'
+save_table_txt_DEST = save_table_DEST + '.txt'
+save_table_csv_DEST = save_table_DEST + '.csv'
+savefig_DEST = 'codon_usage_' + gene + '_vs_' + organism_DEST + '.pdf'
+
+save_optimized_seq = gene_OPT + '_for_' + organism_DEST + '.txt'
+savefig_OPT = 'codon_usage_' + gene_OPT + '_vs_' + organism_DEST + '.pdf'
+
+print('I create codon usage tables for both organisms.')
+
+get_codon_usage(CDS_source_nofile_ORIGIN,
+ CDS_type_ORIGIN,
+ CDS_source_ORIGIN,
+ CDSdict_txt_ORIGIN,
+ save_table_ORIGIN,
+ save_table_txt_ORIGIN,
+ save_table_csv_ORIGIN)
+get_codon_usage(CDS_source_nofile_DEST,
+ CDS_type_DEST,
+ CDS_source_DEST,
+ CDSdict_txt_DEST,
+ save_table_DEST,
+ save_table_txt_DEST,
+ save_table_csv_DEST)
+
+print("I create bar charts for you.")
+
+visualize_codon_usage(organism_ORIGIN,
+ CDS_type_ORIGIN,
+ save_table_ORIGIN,
+ save_table_txt_ORIGIN,
+ gene,
+ sequence,
+ savefig_ORIGIN)
+visualize_codon_usage(organism_DEST,
+ CDS_type_DEST,
+ save_table_DEST,
+ save_table_txt_DEST,
+ gene,
+ sequence,
+ savefig_DEST)
+print('Now, you can take a look at the figures that I made for you.')
+print("Do you still want to optimize " + gene + " for the usage of " + organism_DEST + "?")
+optimization = input("Type 'Y' or 'N': ")
+
+if optimization == 'Y' or optimization == 'y':
+ print("OK, a '.txt' file containing the optimized sequence will be stored in your folder.")
+
+ optimize_codon_usage(save_table_ORIGIN,
+ save_table_txt_ORIGIN,
+ save_table_DEST,
+ save_table_txt_DEST,
+ gene,
+ sequence,
+ organism_ORIGIN,
+ organism_DEST,
+ save_optimized_seq
+ )
+ with open(save_optimized_seq, 'r') as opt_seq:
+ sequence_OPT = opt_seq.read().replace('\n', '')
+ opt_seq.close
+
+ print('Codon usage optimized.')
+ print('\n')
+ print("Lastly, let's generate bar charts of the codon optimized gene.")
+
+ visualize_codon_usage(organism_DEST,
+ CDS_type_DEST,
+ save_table_DEST,
+ save_table_txt_DEST,
+ gene_OPT,
+ sequence_OPT,
+ savefig_OPT)
+
+ print('Bye.')
+if optimization == 'N' or optimization == 'n':
+ print('Ok, bye.')