obitools/ecopcr
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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/branches/refactoring@57 60f365c0-8329-0410-b2a4-ec073aeeaa1d

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Eric Coissac
2007-06-12 08:38:16 +00:00
parent 51a9cd7399
commit cdc0375356
1 changed files with 13 additions and 13 deletions
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26
src/ecopcr.c
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@ -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] <nucleotidic pattern>\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 <this> 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");