Package: wise / 2.4.1-21

10_fix_path_to_data_files.patch Patch series | download
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Author: Andreas Tille <tille@debian.org>
Last-Update: Mon, 04 Aug 2014 19:25:58 +0200
Description: Brute force patch to fix the PATH to the data files to make the
 tools finding the needed data for the test suite
 .
 In principle the PATH should be configurable and the test suite script even
 contains a parameter (-cf) for this - but this seems to be ignored.
 .
 The correct way to deal with this would be a configuration option but I had
 no intend to spend to much time into some software that was declared to be
 orphaned (superseded by exonerate).  So this primitive patch works to run
 the test suite successfully (which is not the case without the patch).

--- a/src/models/estwise.c
+++ b/src/models/estwise.c
@@ -484,8 +484,8 @@ boolean build_objects(void)
 
 void build_defaults(void)
 {
-  codon_file = "codon.table";
-  matrix_file = "BLOSUM62.bla";
+  codon_file = "/usr/share/wise/codon.table";
+  matrix_file = "/usr/share/wise/BLOSUM62.bla";
   
 
 
--- a/src/models/estwisedb.c
+++ b/src/models/estwisedb.c
@@ -78,7 +78,7 @@ char * qend_str      = NULL;
 int qend             = -1;
 
 
-char * matrix_file      = "BLOSUM62.bla";
+char * matrix_file      = "/usr/share/wise/BLOSUM62.bla";
 CompMat * mat           = NULL;
 
 char * gap_str          = "12";
@@ -849,8 +849,8 @@ void show_version(FILE * ofp)
 
 void build_defaults(void)
 {
-  codon_file = "codon.table";
-  matrix_file = "BLOSUM62.bla";
+  codon_file = "/usr/share/wise/codon.table";
+  matrix_file = "/usr/share/wise/BLOSUM62.bla";
   
 
 }
--- a/src/models/pswdb.c
+++ b/src/models/pswdb.c
@@ -40,7 +40,7 @@ int max_desc = 500;
 
 char * querydb             = NULL;
 char * targetdb            = NULL;
-char * matrix_file      = "BLOSUM62.bla";
+char * matrix_file      = "/usr/share/wise/BLOSUM62.bla";
 char * output_file 	= "-";
 
 char * cutoff_str    = NULL;
@@ -65,7 +65,7 @@ void show_help(FILE * ofp)
    fprintf(ofp,"\npswdb <options> <query_db> <target_db>\nSeqs in fasta format\n"
           "\t-g gap penalty (default 12)\n"
           "\t-e ext penatly (default 2)\n"
-          "\t-m comp matrix (default BLOSUM62.bla)\n"
+          "\t-m comp matrix (default /usr/share/wise/BLOSUM62.bla)\n"
           "\t-abc use the abc model\n"
           "\t-a   a penalty for above (default 120)\n"
           "\t-b   b penalty for above (default 10)\n"
@@ -397,7 +397,7 @@ int main(int argc,char *argv[])
 
    matrix_file = strip_out_assigned_argument(&argc,argv,"m");
    if( matrix_file == NULL)
-      matrix_file = "BLOSUM62.bla";
+      matrix_file = "/usr/share/wise/BLOSUM62.bla";
 
    /* database implementation stuff */
    dbsi = new_DBSearchImpl_from_argv(&argc,argv);
--- a/src/models/genewisedb.c
+++ b/src/models/genewisedb.c
@@ -77,7 +77,7 @@ int qend             = -1;
 char * gene_file        = NULL;
 GeneFrequency21 * gf    = NULL;
 
-char * matrix_file      = "BLOSUM62.bla";
+char * matrix_file      = "/usr/share/wise/BLOSUM62.bla";
 CompMat * mat           = NULL;
 
 char * gap_str          = "12";
@@ -1015,9 +1015,9 @@ void show_version(FILE * ofp)
 
 void build_defaults(void)
 {
-  gene_file = "human.gf";
-  codon_file = "codon.table";
-  matrix_file = "BLOSUM62.bla";
+  gene_file = "/usr/share/wise/human.gf";
+  codon_file = "/usr/share/wise/codon.table";
+  matrix_file = "/usr/share/wise/BLOSUM62.bla";
   
 
 }
--- a/src/models/genewise.c
+++ b/src/models/genewise.c
@@ -749,10 +749,10 @@ boolean build_objects(void)
 
 void build_defaults(void)
 {
-  gene_file = "human.gf";
-  new_gene_file = "gene.stat";
-  codon_file = "codon.table";
-  matrix_file = "BLOSUM62.bla";
+  gene_file = "/usr/share/wise/human.gf";
+  new_gene_file = "/usr/share/wise/gene.stat";
+  codon_file = "/usr/share/wise/codon.table";
+  matrix_file = "/usr/share/wise/BLOSUM62.bla";
   
 
 }
--- a/src/models/scanwisep.c
+++ b/src/models/scanwisep.c
@@ -157,7 +157,7 @@ ScanWiseHSPImpl * new_ScanWiseHSPImpl_fr
   out->use_multiscan = FALSE;
   out->ior_file = NULL;
   out->direct_sequence = NULL;
-  out->matrix_file = "BLOSUM62.bla";
+  out->matrix_file = "/usr/share/wise/BLOSUM62.bla";
   out->step = 32;
   out->host = "localhost";
   out->port = 4050;
@@ -546,7 +546,7 @@ int main(int argc,char ** argv)
 
   /* ugly, but we don't want to bounce matrices around the network... */
 
-  mat = read_Blast_file_CompMat("BLOSUM62.bla");
+  mat = read_Blast_file_CompMat("/usr/share/wise/BLOSUM62.bla");
   
   erroroff(REPORT);
 
--- a/src/models/psw.c
+++ b/src/models/psw.c
@@ -24,7 +24,7 @@ void show_help(FILE * ofp)
 	  "\tOPTIONS\n"
 	  "\t-g gap penalty (default 12)\n"
 	  "\t-e ext penatly (default 2)\n"
-	  "\t-m comp matrix (default BLOSUM62.bla)\n"
+	  "\t-m comp matrix (default /usr/share/wise/BLOSUM62.bla)\n"
 	  "\t-abc use the abc model\n"
 	  "\t-a   a penalty for above (default 120)\n"
 	  "\t-b   b penalty for above (default 10)\n"
@@ -126,7 +126,7 @@ int main(int argc,char ** argv)
   
   comp_file = strip_out_assigned_argument(&argc,argv,"m");
   if( comp_file == NULL)
-    comp_file = "BLOSUM62.bla";
+    comp_file = "/usr/share/wise/BLOSUM62.bla";
 
   if( (temp = strip_out_assigned_argument(&argc,argv,"dpenv")) != NULL ) {
     dpenv = read_DPEnvelope_file(temp);
--- a/src/test/basic_cdna.out
+++ b/src/test/basic_cdna.out
@@ -3,13 +3,13 @@ This program is freely distributed under
 Copyright (c) GRL limited: portions of the code are from separate copyrights
 
 Query protein:    roa1_drome
-Comp Matrix:      BLOSUM62.bla
+Comp Matrix:      /usr/share/wise/BLOSUM62.bla
 Gap open:         12
 Gap extension:    2
 Start/End         default
 Target Sequence   HSHNCPA1
 Strand:           both
-Codon Table:      codon.table
+Codon Table:      /usr/share/wise/codon.table
 Subs error:       1e-05
 Indel error:      1e-05
 Algorithm         333
--- a/src/test/basic_genomic.out
+++ b/src/test/basic_genomic.out
@@ -3,17 +3,17 @@ This program is freely distributed under
 Copyright (c) GRL limited: portions of the code are from separate copyright
 
 Query protein:       roa1_drome
-Comp Matrix:         BLOSUM62.bla
+Comp Matrix:         /usr/share/wise/BLOSUM62.bla
 Gap open:            12
 Gap extension:       2
 Start/End            default
 Target Sequence      HSHNCPA1
 Strand:              forward
 Start/End (protein)  default
-Gene Parameter file: gene.stat
+Gene Parameter file: /usr/share/wise/gene.stat
 Splice site model:   GT/AG only
 GT/AG bits penalty   -9.96
-Codon Table:         codon.table
+Codon Table:         /usr/share/wise/codon.table
 Subs error:          1e-06
 Indel error:         1e-06
 Null model           syn
--- a/src/test/pswdb.out
+++ b/src/test/pswdb.out
@@ -12,7 +12,7 @@ Gap open:       12
 Gap extension:  2
 Query info from:     road.pep
 Database info from:  pep.fa
-Comp Matrix:         BLOSUM62.bla
+Comp Matrix:         /usr/share/wise/BLOSUM62.bla
 [Warning: Can't fit histogram to a db smaller than 1,000]
 
 
--- a/src/models/genestats.c
+++ b/src/models/genestats.c
@@ -22,7 +22,7 @@ void show_help_GeneModelParam(FILE * ofp
   fprintf(ofp,"  -splice_score_offset    [%.1f]  score offset for splice sites\n",DEFAULT_SPLICE_OFFSET_SCORE);
   fprintf(ofp,"  -[no]splice_gtag        make just gtag splice sites (default is gtag, ie no model)\n");  
   fprintf(ofp,"  -splice_gtag_prob       [0.001] probability for gt/ag \n");
-  fprintf(ofp,"  -genestats              [gene.stat]\n");
+  fprintf(ofp,"  -genestats              [/usr/share/wise/gene.stat]\n");
 
 }
 
@@ -270,7 +270,7 @@ GeneModelParam * std_GeneModelParam(void
   out->min_collar   = -5.0;
   out->max_collar   = +5.0;
   out->score_offset = DEFAULT_SPLICE_OFFSET_SCORE;
-  out->gene_stats_file = stringalloc("gene.stat");
+  out->gene_stats_file = stringalloc("/usr/share/wise/gene.stat");
   out->use_gtag_splice = TRUE;
 
   out->prob_for_gtag = 0.001;
--- a/src/models/genestats.dy
+++ b/src/models/genestats.dy
@@ -103,7 +103,7 @@ void show_help_GeneModelParam(FILE * ofp
   fprintf(ofp,"  -splice_score_offset    [%.1f]  score offset for splice sites\n",DEFAULT_SPLICE_OFFSET_SCORE);
   fprintf(ofp,"  -[no]splice_gtag        make just gtag splice sites (default is gtag, ie no model)\n");  
   fprintf(ofp,"  -splice_gtag_prob       [0.001] probability for gt/ag \n");
-  fprintf(ofp,"  -genestats              [gene.stat]\n");
+  fprintf(ofp,"  -genestats              [/usr/share/wise/gene.stat]\n");
 
 }
 
@@ -290,7 +290,7 @@ GeneModelParam * std_GeneModelParam(void
   out->min_collar   = -5.0;
   out->max_collar   = +5.0;
   out->score_offset = DEFAULT_SPLICE_OFFSET_SCORE;
-  out->gene_stats_file = stringalloc("gene.stat");
+  out->gene_stats_file = stringalloc("/usr/share/wise/gene.stat");
   out->use_gtag_splice = TRUE;
 
   out->prob_for_gtag = 0.001;
--- a/src/models/testgenestat.c
+++ b/src/models/testgenestat.c
@@ -23,7 +23,7 @@ int main(int argc,char ** argv)
 
   seq = read_fasta_file_Sequence("../../test_data/human.genomic");
   
-  ifp = openfile("gene.stat","r");
+  ifp = openfile("/usr/share/wise/gene.stat","r");
   
   st = read_GeneStats(ifp); 
   
--- a/src/test/hmm_genomic.out
+++ b/src/test/hmm_genomic.out
@@ -7,10 +7,10 @@ Start/End            local
 Target Sequence      HSHNCPA1
 Strand:              forward
 Start/End (protein)  local
-Gene Parameter file: gene.stat
+Gene Parameter file: /usr/share/wise/gene.stat
 Splice site model:   GT/AG only
 GT/AG bits penalty   -9.96
-Codon Table:         codon.table
+Codon Table:         /usr/share/wise/codon.table
 Subs error:          1e-06
 Indel error:         1e-06
 Null model           syn
--- a/src/test/hmm_cdna.out
+++ b/src/test/hmm_cdna.out
@@ -6,7 +6,7 @@ Query model:      unnamed
 Start/End         default
 Target Sequence   HSHNCPA1
 Strand:           both
-Codon Table:      codon.table
+Codon Table:      /usr/share/wise/codon.table
 Subs error:       1e-05
 Indel error:      1e-05
 Algorithm         333L
--- a/src/test/genewise-db.out
+++ b/src/test/genewise-db.out
@@ -12,8 +12,8 @@ Search mode:           Single protein vs
 Protein info from:     rrm.HMM
 Dna info from:         dna.db
 Start/End (protein)    global
-Gene Paras:            human.gf
-Codon Table:           codon.table
+Gene Paras:            /usr/share/wise/human.gf
+Codon Table:           /usr/share/wise/codon.table
 Subs error:            1e-05
 Indel error:           1e-05
 Model splice?          model
--- a/src/test/genewise-db-lite.out
+++ b/src/test/genewise-db-lite.out
@@ -12,8 +12,8 @@ Search mode:           Single protein vs
 Protein info from:     rrm.HMM
 Dna info from:         dna.db
 Start/End (protein)    global
-Gene Paras:            human.gf
-Codon Table:           codon.table
+Gene Paras:            /usr/share/wise/human.gf
+Codon Table:           /usr/share/wise/codon.table
 Subs error:            1e-05
 Indel error:           1e-05
 Model splice?          model
--- a/src/test/estwise-db.out
+++ b/src/test/estwise-db.out
@@ -13,7 +13,7 @@ Search mode:           Single protein vs
 Protein info from:     rrm.HMM
 Dna info from:         dna.db
 Start/End              local
-Codon Table:           codon.table
+Codon Table:           /usr/share/wise/codon.table
 Subs error:            0.01
 Indel error:           0.01
 Null model:            synchronous
--- a/src/test/genewisedb-pfam.out
+++ b/src/test/genewisedb-pfam.out
@@ -12,8 +12,8 @@ Search mode:           Single genomic vs
 Protein info from:     rrm.HMM
 Dna info from:         short.dna
 Start/End (protein)    default
-Gene Paras:            human.gf
-Codon Table:           codon.table
+Gene Paras:            /usr/share/wise/human.gf
+Codon Table:           /usr/share/wise/codon.table
 Subs error:            1e-05
 Indel error:           1e-05
 Model splice?          model