--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fibronectin/args.py	Wed Nov 10 15:15:50 2021 +0000
@@ -0,0 +1,100 @@
+# -*- coding: utf-8 -*-
+import sys, getopt, os
+
+
+class Args:
+
+    def __init__(self):
+        """
+        Instanciate Files object
+        """
+        self.input = None
+        self.output_dir = None
+        self.pattern = None
+        self.site_res_5 = None
+        self.site_res_3 = None
+        self.getargs()
+
+    def usage(self, info):
+        text = None
+        text = "Fibronectin script.\n\n"
+        if (info): text += info
+        temp = "Option\t\t\t\tfile\t\t\tDescription\n"
+        text += temp
+        text += '-' * (len(temp) + 60)
+        text += '\n'
+        text += "-i, --input\t\t\tfile.fasta\t\tFasta file that contains the DNA sequences\n"
+        text += "-o, --output_dir\t\t/path/for/output\tDirectory where output files will be written\n"
+        text += "-p, --pattern\t\t\tstring\t\t\tPattern of the sequence bank\n"
+        text += "-5, --restriction-site-5\tstring\t\t\tSequence of the restriction site in 5'\n"
+        text += "-3, --restriction-site-3\tstring\t\t\tSequence of the restriction site in 3'\n"
+        return text
+
+    def case(self):
+        # Test des fichiers et repertoires
+        if not self.input:
+            sys.exit(self.usage("input (-i,--input) : \"%s\" must be indicated\n" % (self.input)))
+        if not self.output_dir:
+            sys.exit(self.usage("output directory (-o,--output_dir) : \"%s\" must be indicated\n" % (self.output_dir)))
+        if not self.pattern:
+            sys.exit(
+                self.usage("Pattern of the sequence bank (-p,--pattern) : \"%s\" must be indicated\n" % (self.pattern)))
+        if not self.site_res_5:
+            sys.exit(self.usage(
+                "Sequence of the restriction site in 5' (-5,--restriction-site-5) : \"%s\" must be indicated\n" % (
+                    self.site_res_5)))
+        if not self.site_res_3:
+            sys.exit(self.usage(
+                "Sequence of the restriction site in 3' (-3,--restriction-site-3) : \"%s\" must be indicated\n" % (
+                    self.site_res_3)))
+
+    def data_format(self):
+        """
+        Check if information are correct
+        """
+        # Run without arguments
+        if len(sys.argv) == 1:
+            sys.exit(self.usage(None))
+            # Test input file argument
+        if self.input:
+            if not os.path.isfile(self.input):
+                print(self.input)
+                print(os.path.isfile(self.input))
+                #sys.exit(self.usage("Error with \"%s\" : -i required an input file\n" % self.multilist))
+
+                # Determine les fichiers fournis en arguments
+
+    def getargs(self):
+        """
+        Determine the files provided as arguments
+        @return: Choosen options
+        """
+        # Sans argument
+        if len(sys.argv) <= 1: sys.exit("Do './fibronectin.py -h' for a usage summary")
+        # test des option
+        try:
+            (opts, args) = getopt.getopt(sys.argv[1:], "i:o:p:5:3:h",
+                                         ["input=", "output_dir=", "pattern=", "site_res_5=", "site_res_3="])
+        except getopt.GetoptError as err:
+            # print help information and exit:
+            print(str(err))  # will print something like "option -a not recognized"
+            sys.exit(self.usage(None))
+        # Identification of options
+        for (o, a) in opts:
+            if o in ("-i", "--input"):
+                self.input = a
+            elif o in ("-o", "--output_dir"):
+                self.output_dir = a
+            elif o in ("-p", "--pattern"):
+                self.pattern = a
+            elif o in ("-5", "--restriction-site-5"):
+                self.site_res_5 = a
+            elif o in ("-3", "--restriction-site-3"):
+                self.site_res_3 = a
+            elif o in ("-h", "--help"):
+                sys.exit(self.usage(None))
+            else:
+                assert False, "unhandled option"
+            # Verification of cases
+        self.case()
+        self.data_format()