diff --git a/src/ecoprimer.c b/src/ecoprimer.c index c6bc79c..4d5ab34 100644 --- a/src/ecoprimer.c +++ b/src/ecoprimer.c @@ -25,9 +25,59 @@ static void PrintHelp() { - PP "------------------------------------------\n"); - PP " ecoPrimer Version %s\n", VERSION); - PP "------------------------------------------\n"); + PP "------------------------------------------\n"); + PP " ecoPrimer Version %s\n", VERSION); + PP "------------------------------------------\n"); + PP "synopsis : finding primers and measureing the quality of primers and barcode region\n"); + PP "usage: ./ecoPrimer [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 ecoPCR/tools directory.\n"); + 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 " ecoPrimer needs all the file type. As a result, you have to write the\n"); + PP " database radical without any extension. For example /ecoPrimerDB/fstvert\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\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\n"); + PP "-c : Consider that the database sequences are [c]ircular\n\n"); + PP "-3 : Three prime strict match\n\n"); + PP "-q : Strict matching [q]uorum, percentage of the sequences in which strict primers are found. By default it is 70\n\n"); + PP "-s : [S]ensitivity quorum\n\n"); + PP "-t : required [t]axon level for results, by default the results are computed at species level\n\n"); + PP "-x : false positive quorum\n\n"); + PP "-D : set in [d]ouble strand mode\n\n"); + PP "-S : Set in [s]ingle strand mode\n\n"); + PP "-U : No multi match\n\n"); + PP "\n"); + PP "------------------------------------------\n"); + PP "Table result description : \n"); + PP "column 1 : serial number\n"); + PP "column 2 : primer1\n"); + PP "column 3 : primer2\n"); + PP "column 4 : good/bad\n"); + PP "column 5 : in sequence count\n"); + PP "column 6 : out sequence count\n"); + PP "column 7 : yule\n"); + PP "column 8 : in taxa count\n"); + PP "column 9 : out taxa count\n"); + PP "column 10 : coverage\n"); + PP "column 11 : specificity\n"); + PP "column 12 : minimum amplified length\n"); + PP "column 13 : maximum amplified length\n"); + PP "column 14 : average amplified length\n"); + PP "------------------------------------------\n"); + PP " http://www.grenoble.prabi.fr/trac/ecoPrimer/\n"); + PP "------------------------------------------\n\n"); + PP "\n"); + } static void ExitUsage(int stat) @@ -180,6 +230,8 @@ void printpairs (ppairtree_t pairs, poptions_t options) size_t i,j; int32_t count; + //printf("Index\tPrimer1\tPrimer2\tGB\tInexampleCount\tOutexampleCount\tYule\tIntaxaCount\tOuttaxaCount\tCoverage\tSpecificity\tMinAmplifiedLength\tMaxAmplifiedLength\tAvgAmplifiedLength\n"); + fprintf(stderr,"Total pair count : %d\n",pairs->count); sortedpairs = ECOMALLOC(pairs->count*sizeof(ppair_t),"Cannot Allocate ordered pairs"); @@ -374,9 +426,9 @@ int main(int argc, char **argv) /* -------------------- */ case 'h': /* help */ /* -------------------- */ - PrintHelp(); - exit(0); - break; + PrintHelp(); + exit(0); + break; /* ------------------------- */ case 'l': /* min amplification lenght */