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slackbuilds/academic/wise/patches/10_fix_path_to_data_files.p...

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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orphaned (superseded by exonerate).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
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