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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/branches/refactoring@77 60f365c0-8329-0410-b2a4-ec073aeeaa1d

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Eric Coissac
2007-06-21 13:57:53 +00:00
parent c77c360782
commit 1c421f5903
1 changed files with 15 additions and 18 deletions
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src/ecopcr.c
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@ -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] <nucleotidic pattern>\n");
PP "usage: ecoPCR [options] <nucleotidic patterns>\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 <this> 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");