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Author: Steffen Moeller <moeller@debian.org>
Last-Update: Sun, 11 Jul 2010 06:27:12 +0200
Description: Add -h argument for help and -v for version info
--- a/w9/efetch.c
+++ b/w9/efetch.c
@@ -126,25 +126,85 @@ void main(int argc, char *argv[])
-s <#> Start at position #\n\
-e <#> Stop at position #\n\
-o More options and info...\n\
+ -h shows this usage text\n\
\n\
by Erik Sonnhammer (esr@sanger.ac.uk)\n\
Version 2.1, ";
- if (!(usage = malloc(strlen(usageText) + 102))) {
- fprintf(stderr, "Malloc error\n");
- exit(1);
- }
+ char *help;
+ static char helpText[] = "\n\
+ EFETCH - retrieve entries from sequence databases.\n\
+\n\
+ Synopsis: efetch -options [database:]<query> \n\
+\n\
+ Databases: SWissprot/SP, PIR, WOrmpep/WP, EMbl, GEnbank/GB, ProDom, ProSite\n\
+\n\
+ Options:\n\
+ -a Search with Accession number\n\
+ -f Fasta format output\n\
+ -q Sequence only output (one line)\n\
+ -s <#> Start at position #\n\
+ -e <#> Stop at position #\n\
+ -o More options and info...\n\
+\n\
+ -D <dir> Specify database directory\n\
+ -H Display index header data\n\
+ -p Display entrynames in search path\n\
+ -r Print sequence in 'raw' format\n\
+ -m Fetch from mixed mini database\n\
+ -M Mini format output\n\
+ -b Do NOT reverse the order of bytes\n\
+ (SunOS, IRIX do reverse, Alpha not)\n\
+ -d <dbfile> Specify database file (avoid this)\n\
+ -i <idxfile> Specify index file (avoid this)\n\
+ -l <divfile> Specify division lookup table (avoid this)\n\
+ -B <database> Specify database (archaic)\n\
+ -A Only return entryname for accession number\n\
+ -n <name> Give the sequence this name\n\
+ -x Don't require query to match entry's name exactly (avoid)\n\
+ -w For Wormpep: also fetch cross-referenced SwissProt entry\n\
+ -h shows this help text\n\
+\n\
+\n\
+ Environment:\n\
+ SWDIR = SwissProt directory - database and EMBL index files\n\
+ PIRDIR = PIR -- \" --\n\
+ WORMDIR = Wormpep -- \" --\n\
+ EMBLDIR = EMBL -- \" --\n\
+ GBDIR = Genbank -- \" --\n\
+ PRODOMDIR = ProDom -- \" --\n\
+ PROSITEDIR = ProSite -- \" --\n\
+ DBDIR = User's own -- \" -- (fasta format)\n\
+\n\
+ SEQDB database file (default SwissProt)\n\
+ SEQDBIDX index file\n\
+ DIVTABL division lookup table\n\
+\n\
+ Ex. setenv DBDIR /pubseq/seqlibs/embl/\n\
+\n\
+ Note that Prodom family consensus seqs can be fetched by PD:_#\n\n\
+ by Erik Sonnhammer (esr@sanger.ac.uk)\n\
+ Version 2.1, ";
- strcpy(usage, usageText);
- strncat(usage, cc_date, 100);
- strcat(usage, "\n");
+ // check if any argument is --help or -help
+ for(i=1; i<argc; i++) {
+ if (0 == strncmp("--help",argv[i],6) || 0 == strncmp("-help",argv[i],5)) {
+ if (!(help = malloc(strlen(helpText) + 102))) {
+ fprintf(stderr, "Malloc error\n");
+ exit(1);
+ }
+ strcpy(help, helpText);
+ strncat(help, cc_date, 100);
+ strcat(help, "\n");
+ fprintf(stderr,"%s\n",helpText);
+ exit(0);
+ }
+ }
/* parse command line */
while ((optc = getopt(argc, argv, optstring)) != -1)
switch (optc) {
- case 'h':
- fprintf(stderr, "\n%s\n", usage); exit(1);
case 'B':
strcpy(dbsource, optarg); break;
case 'a':
@@ -166,43 +226,16 @@ void main(int argc, char *argv[])
strcpy(dbfile, optarg); break;
case 'H':
display_head=1; break;
+ case 'h':
case 'o':
- printf("\n\
- -D <dir> Specify database directory\n\
- -H Display index header data\n\
- -p Display entrynames in search path\n\
- -r Print sequence in 'raw' format\n\
- -m Fetch from mixed mini database\n\
- -M Mini format output\n\
- -b Do NOT reverse the order of bytes\n\
- (SunOS, IRIX do reverse, Alpha not)\n\
- -d <dbfile> Specify database file (avoid this)\n\
- -i <idxfile> Specify index file (avoid this)\n\
- -l <divfile> Specify division lookup table (avoid this)\n\
- -B <database> Specify database (archaic)\n\
- -A Only return entryname for accession number\n\
- -n <name> Give the sequence this name\n\
- -x Don't require query to match entry's name exactly (avoid)\n\
- -w For Wormpep: also fetch cross-referenced SwissProt entry\n\
-\n\
-\n\
- Environment variables:\n\
- SWDIR = SwissProt directory - database and EMBL index files\n\
- PIRDIR = PIR -- \" --\n\
- WORMDIR = Wormpep -- \" --\n\
- EMBLDIR = EMBL -- \" --\n\
- GBDIR = Genbank -- \" --\n\
- PRODOMDIR = ProDom -- \" --\n\
- PROSITEDIR = ProSite -- \" --\n\
- DBDIR = User's own -- \" -- (fasta format)\n\
-\n\
- SEQDB database file (default SwissProt)\n\
- SEQDBIDX index file\n\
- DIVTABL division lookup table\n\
-\n\
- Ex. setenv DBDIR /pubseq/seqlibs/embl/\n\
-\n\
- Note that Prodom family consensus seqs can be fetched by PD:_#\n\n");
+ if (!(help = malloc(strlen(helpText) + 102))) {
+ fprintf(stderr, "Malloc error\n");
+ exit(1);
+ }
+ strcpy(help, helpText);
+ strncat(help, cc_date, 100);
+ strcat(help, "\n");
+ fprintf(stderr,"%s\n",helpText);
exit(0);
case 'p':
search = 1; break;
@@ -229,8 +262,19 @@ void main(int argc, char *argv[])
strcpy(customName, optarg); break;
case 'w':
wormpep2swiss = 1; break;
+ case '-':
+ // omit option indicator
+ break;
default:
+ if (!(usage = malloc(strlen(usageText) + 102))) {
+ fprintf(stderr, "Malloc error\n");
+ exit(1);
+ }
+ strcpy(usage, usageText);
+ strncat(usage, cc_date, 102);
+ strcat(usage, "\n");
fprintf(stderr, "\n%s\n", usage); exit(1);
+ break;
}
if (argc - optind != 1)
|
