diff --git a/src/ecopcr.c b/src/ecopcr.c index f203dd6..f2790db 100644 --- a/src/ecopcr.c +++ b/src/ecopcr.c @@ -18,11 +18,18 @@ static void PrintHelp() PP " ecoPCR Version %s\n", VERSION); PP "------------------------------------------\n"); PP "synopsis : searching for sequence and taxonomy hybriding with given primers\n"); - PP "usage: ecoPCR [options] datafile\n"); + PP "usage: ecoPCR [options] \n"); PP "------------------------------------------\n"); PP "options:\n"); - PP "-1 : [FIRST] oligonucleotide for direct strand\n\n"); - PP "-2 : [SECOND] oligonucleotide for reverse strand\n\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 " in the tools directory.\n"); + PP " ecoPCRFormat.py creates three file types :"); + PP " .sdx : contains the sequences\n"); + PP " .tdx : contains information concerning the taxonomy\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 " database radical without any extension. For example /ecoPCRDB/gbmam\n"); PP "-e : [E]rror \n"); PP " : max error allowed by oligonucleotide\n\n"); PP "-h : [H]elp - print help\n\n"); @@ -41,15 +48,8 @@ static void PrintHelp() PP " see its help typing ecofind -h for more information.\n"); PP "\n"); PP "------------------------------------------\n"); - PP "datafile : to match the expected format, the database\n"); - PP "has to be formated first by the ecoPCRFormat.py program located.\n"); - PP "in the tools directory.\n"); - PP "ecoPCRFormat.py creates three file types :"); - PP " .sdx : contains the sequences\n"); - PP " .tdx : contains information concerning the taxonomy\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 "datafile radical without any extension. For example /database/gbmam\n"); + PP "first argument : oligonucleotide for direct strand\n\n"); + PP "second argument : oligonucleotide for reverse strand\n\n"); PP "------------------------------------------\n"); PP "Table result description : \n"); PP "column 1 : accession number\n"); @@ -72,7 +72,7 @@ static void PrintHelp() PP "column 18 : amplification length\n"); PP "column 19 : sequence description\n"); PP "------------------------------------------\n"); - PP " https://www.grenoble.prabi.fr/trac/ecoPCR/wiki"); + PP " https://www.grenoble.prabi.fr/trac/ecoPCR/wiki\n"); PP "------------------------------------------\n\n"); PP "\n");