Commit 194ec811 by Celine Mercier

Fixes #2 by adding the missing -D option in the help

parent 126bf806
...@@ -23,6 +23,8 @@ static void PrintHelp() ...@@ -23,6 +23,8 @@ static void PrintHelp()
PP "usage: ecoPCR [options] <nucleotidic patterns>\n"); PP "usage: ecoPCR [options] <nucleotidic patterns>\n");
PP "------------------------------------------\n"); PP "------------------------------------------\n");
PP "options:\n"); PP "options:\n");
PP "-a : Salt concentration in M for Tm computation (default 0.05 M)\n\n");
PP "-c : Consider that the database sequences are [c]ircular\n\n");
PP "-d : [D]atabase : to match the expected format, the database\n"); PP "-d : [D]atabase : to match the expected format, the database\n");
PP " has to be formated first by the ecoPCRFormat.py program located.\n"); PP " has to be formated first by the ecoPCRFormat.py program located.\n");
PP " in the tools directory.\n"); PP " in the tools directory.\n");
...@@ -31,8 +33,11 @@ static void PrintHelp() ...@@ -31,8 +33,11 @@ static void PrintHelp()
PP " .tdx : contains information concerning the taxonomy\n"); PP " .tdx : contains information concerning the taxonomy\n");
PP " .rdx : contains the taxonomy rank\n\n"); PP " .rdx : contains the taxonomy rank\n\n");
PP " ecoPCR needs all the file type. As a result, you have to write the\n"); PP " ecoPCR needs all the file type. As a result, you have to write the\n");
PP " database radical without any extension. For example /ecoPCRDB/gbmam\n\n"); PP " database radical without any extension. For example /ecoPCRDB/gbmam\n\n");
PP "-e : [E]rror : max error allowed by oligonucleotide (0 by default)\n\n"); PP "-D : Keeps the specified number of nucleotides on each side of the in silico \n");
PP " amplified sequences (including the amplified DNA fragment plus the two target \n");
PP " sequences of the primers).\n\n");
PP "-e : [E]rror : max errors allowed by oligonucleotide (0 by default)\n\n");
PP "-h : [H]elp - print <this> help\n\n"); PP "-h : [H]elp - print <this> help\n\n");
PP "-i : [I]gnore the given taxonomy id.\n"); PP "-i : [I]gnore the given taxonomy id.\n");
PP " Taxonomy id are available using the ecofind program.\n"); PP " Taxonomy id are available using the ecofind program.\n");
...@@ -41,13 +46,11 @@ static void PrintHelp() ...@@ -41,13 +46,11 @@ static void PrintHelp()
PP " super kingdom mode by default.\n\n"); PP " super kingdom mode by default.\n\n");
PP "-l : minimum [L]ength : define the minimum amplication length. \n\n"); PP "-l : minimum [L]ength : define the minimum amplication length. \n\n");
PP "-L : maximum [L]ength : define the maximum amplicationlength. \n\n"); PP "-L : maximum [L]ength : define the maximum amplicationlength. \n\n");
PP "-r : [R]estricts the search to the given taxonomic id.\n");
PP " Taxonomy id are available using the ecofind program.\n");
PP " see its help typing ecofind -h for more information.\n");
PP "-c : Consider that the database sequences are [c]ircular\n");
PP "-m : Salt correction method for Tm computation (SANTALUCIA : 1\n"); PP "-m : Salt correction method for Tm computation (SANTALUCIA : 1\n");
PP " or OWCZARZY:2, default=1)\n\n"); PP " or OWCZARZY:2, default=1)\n\n");
PP "-a : Salt contentration in M for Tm computation (default 0.05 M)\n\n"); PP "-r : [R]estricts the search to the given taxonomic id.\n");
PP " Taxonomy id are available using the ecofind program.\n");
PP " see its help typing ecofind -h for more information.\n\n");
PP "\n"); PP "\n");
PP "------------------------------------------\n"); PP "------------------------------------------\n");
PP "first argument : oligonucleotide for direct strand\n\n"); PP "first argument : oligonucleotide for direct strand\n\n");
......
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