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Gentoo's Bugzilla – Attachment 93119 Details for
Bug 142269
sci-biology/clover new ebuild
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[patch]
this is the patch to have motif file in env variable
clover-args.patch (text/plain), 2.91 KB, created by
dawe
on 2006-07-31 05:15:15 UTC
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Description:
this is the patch to have motif file in env variable
Filename:
MIME Type:
Creator:
dawe
Created:
2006-07-31 05:15:15 UTC
Size:
2.91 KB
patch
obsolete
>--- args.cpp.new 2006-06-15 15:09:53.000000000 +0200 >+++ args.cpp 2006-06-15 15:10:11.000000000 +0200 >@@ -5,7 +5,6 @@ > > #include <ostream> > #include <unistd.h> // getopt >-#include <stdlib.h> // getenv > #include "MCFgen.hpp" // die, tostring > #include "MCFbio.hpp" // count_residues > #include "args.hpp" >@@ -58,7 +57,7 @@ > of sequence motifs in a FASTA-like format described below. Any non-alphabetic\n\ > characters in the sequences are ignored, and any alphabetic characters except A,\n\ > C, G, T (uppercase or lowercase) are converted to 'n' and excluded from matching\n\ >-motifs. The motif file, specified either in the CLOVER_MOTIF_FILE variable or as clover option, should look like this:\n\ >+motifs. The motif file should look like this:\n\ > \n\ > >TATA\n\ > 0 0 0 10\n\ >@@ -130,7 +129,6 @@ > In addition to the two required inputs, there several options for modifying\n\ > Clover's behavior:\n\ > -h Help: print documentation. You already know this one.\n\ >- -f alternative motif file (overrides CLOVER_MOTIF_FILE variable)\n\ > -r Number of randomized/control raw scores to calculate for comparison with\n\ > each target raw score.\n\ > -t P-value threshold: only print results for motifs whose P-values don't\n\ >@@ -162,12 +160,9 @@ > "; > > const string usage = >- "Usage summary: clover [options] myseqs.fa [BGfiles]\n" >- "\nYou should set the CLOVER_MOTIF_FILE environmental variable\n" >- "or specify the path to a motif file as clover option\n\n" >+ "Usage summary: clover [options] mymotifs myseqs.fa [BGfiles]\n" > "Options:\n" > "-h help: print documentation\n" >- "-f alternative motif file (overrides CLOVER_MOTIF_FILE variable)\n" > "-r number of randomizations (" + tostring(shuffles) + ")\n" > "-t P-value threshold (" + tostring(pthresh) + ")\n" > "-u motif score threshold (" + tostring(hit_thresh) + ")\n" >@@ -180,20 +175,13 @@ > "-s seed for random number generator (" + tostring(random_seed) + ")\n" > ; > >- char *cptr; >- if ((cptr = getenv( "CLOVER_MOTIF_FILE" )) != NULL ) { >- mat_file = cptr; >- } > int c; > >- while ((c = getopt(argc, argv, "hf:r:t:u:ndmlvp:s:")) != -1) >+ while ((c = getopt(argc, argv, "hr:t:u:ndmlvp:s:")) != -1) > switch (c) { > case 'h': > cout << doc << endl; > exit(0); >- case 'f': >- mat_file = optarg; >- break; > case 'r': > shuffles = atoi(optarg); > break; >@@ -228,12 +216,10 @@ > mcf::die("\n" + usage); // "invalid option" message is printed by getopt > } > >- if (mat_file.empty()) >- mcf::die("*** Error: Motif file not specified\n\n" + usage); >- >- if (optind + 1 > argc) // there should be 2 more non-option arguments >- mcf::die("*** Error: sequence file required\n\n" + usage); >+ if (optind + 2 > argc) // there should be 2 more non-option arguments >+ mcf::die("Error: motif and sequence files required\n\n" + usage); > >+ mat_file = argv[optind++]; > seq_file = argv[optind++]; > > while (optind < argc)
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Attachments on
bug 142269
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93118
| 93119 |
113365
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174464
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241027