From 1c421f5903fc353a587359b528d85794542ee80b Mon Sep 17 00:00:00 2001 From: Eric Coissac Date: Thu, 21 Jun 2007 13:57:53 +0000 Subject: [PATCH] git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/branches/refactoring@77 60f365c0-8329-0410-b2a4-ec073aeeaa1d --- src/ecopcr.c | 33 +++++++++++++++------------------ 1 file changed, 15 insertions(+), 18 deletions(-) diff --git a/src/ecopcr.c b/src/ecopcr.c index 794fbd9..9d8a948 100644 --- a/src/ecopcr.c +++ b/src/ecopcr.c @@ -18,33 +18,29 @@ 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] \n"); + PP "usage: ecoPCR [options] \n"); PP "------------------------------------------\n"); PP "options:\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 " ecoPCRFormat.py creates three file types :\n"); 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 " 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 "-h : [H]elp - print help\n\n"); PP "-i : [I]gnore the given taxonomy id.\n"); - PP " taxonomy id are available using the ecofind program.\n"); - PP " see its help typing ecofind -h for more information.\n"); - PP "-k : [K]ingdom mode\n"); - PP " set the kingdom mode\n"); + PP " Taxonomy id are available using the ecofind program.\n"); + PP " see its help typing ecofind -h for more information.\n\n"); + PP "-k : [K]ingdom mode : set the kingdom mode\n"); PP " super kingdom mode by default.\n\n"); - PP "-l : minimum [L]ength\n"); - PP " define the minimum amplication length. \n\n"); - PP "-L : maximum [L]ength\n"); - PP " define the maximum amplicationlength. \n\n"); - PP "-r : [R]estricts the search to the given taxonomy id.\n"); - PP " taxonomy id are available using the ecofind program.\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 "-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 "\n"); PP "------------------------------------------\n"); @@ -63,16 +59,17 @@ static void PrintHelp() PP "column 9 : family taxonomic id\n"); PP "column 10 : family name\n"); PP "column 11 : super kingdom taxonomic id\n"); - PP "column 11 : super kingdom name\n"); + PP "column 12 : super kingdom name\n"); PP "column 13 : strand (direct or reverse)\n"); PP "column 14 : first oligonucleotide\n"); PP "column 15 : number of errors for the first strand\n"); PP "column 16 : second oligonucleotide\n"); PP "column 17 : number of errors for the second strand\n"); PP "column 18 : amplification length\n"); - PP "column 19 : sequence description\n"); + PP "column 19 : sequence\n"); + PP "column 20 : definition\n"); PP "------------------------------------------\n"); - PP " https://www.grenoble.prabi.fr/trac/ecoPCR/wiki\n"); + PP " http://www.grenoble.prabi.fr/trac/ecoPCR/\n"); PP "------------------------------------------\n\n"); PP "\n");