[med-svn] [Git][med-team/trnascan-se][upstream] New upstream version 2.0.8+ds
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Tue May 11 20:23:42 BST 2021
Nilesh Patra pushed to branch upstream at Debian Med / trnascan-se
Commits:
cb78e14e by Nilesh Patra at 2021-05-12T00:48:11+05:30
New upstream version 2.0.8+ds
- - - - -
12 changed files:
- src/dbmalloc.h
- src/eufind_const.h
- src/eufind_main.c
- src/gnuregex.c
- src/interleaved.c
- src/pavesi.c
- + src/pavesi.h
- src/scan_main.c
- src/score_main.c
- src/trnascan.c
- tRNAscan-SE.conf.src
- tRNAscan-SE.src
Changes:
=====================================
src/dbmalloc.h
=====================================
@@ -1,7 +1,7 @@
/*
* (c) Copyright 1990, 1991, 1992 Conor P. Cahill (uunet!virtech!cpcahil).
- * You may copy, distribute, and use this software as long as this
- * copyright statement is not removed.
+ *
+ * This code is distributed under GNU GENERAL PUBLIC LICENSE v3.
*/
/*
* $Id: malloc.h.org,v 1.31 1992/06/22 23:40:10 cpcahil Exp $
=====================================
src/eufind_const.h
=====================================
@@ -1,3 +1,5 @@
+#ifndef EUFIND_CONST_
+#define EUFIND_CONST_
/* tRNA scanning cutoffs */
@@ -12,25 +14,25 @@
#define INT_SCORE_THRESH -31.25
#define TOT_SCORE_THRESH -31.8 /* -31.8 */
-#define MAX_AB_BOX_DIST 140 /* not used anymore, instead
+#define MAX_AB_BOX_DIST 140 /* not used anymore, instead */
/* AB_BOX_DIST_RANGE used */
#define MIN_AB_BOX_DIST 24
-#define AB_BOX_DIST_RANGE 116 /* check this far over MIN_AB_BOX
+#define AB_BOX_DIST_RANGE 116 /* check this far over MIN_AB_BOX */
/* distance for A-B box pairs */
#define SEC_AB_BOX_DIST 26
#define SEC_BBOX_DIST_CORR 12
#define MIN_BTERM_DIST 11
-#define MAX_TERM_SEARCH 133 /* Max distance to search for termination
+#define MAX_TERM_SEARCH 133 /* Max distance to search for termination
signal (was 59, changed to 133 (as in
Pavesi paper) on 11/96
since was missing 4 yeast tRNAs */
#define ABOX_LEN 21
#define BBOX_LEN 11
-#define MAX_OVLAP 10 /* max #bp tRNA hits are allowed to
- overlap */
+#define MAX_OVLAP 10 /* max #bp tRNA hits are allowed to
+ overlap */
struct trna_info_s {
char iso_type[5];
@@ -45,7 +47,7 @@ struct trna_info_s {
typedef struct trna_info_s TRNA_TYPE;
-
+#endif /*EUFIND_CONST_*/
=====================================
src/eufind_main.c
=====================================
@@ -22,9 +22,11 @@
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
+#include <getopt.h>
#include "squid.h"
#include "sqfuncs.h"
#include "eufind_const.h"
+#include "pavesi.h"
char eufind_version[] = "1.1";
char eufind_date[] = "Aug 2000";
@@ -62,7 +64,7 @@ main (int argc, char **argv)
not look for poly T terminator
signal */
StrictMode, /* require poly T terminator */
- NoReformat; /* flag to prevent extra work of
+ NoReformat; /* flag to prevent extra work of */
/* changing seqs to DNA & upper case */
/* alphabet */
@@ -165,7 +167,7 @@ main (int argc, char **argv)
Die("Memory failure, couldn't allocate sequence\n");
/* integer-encode sequence */
- if (errno = IntEncodeSeq(iseq,seq,sqinfo.len))
+ if ((errno = IntEncodeSeq(iseq,seq,sqinfo.len)))
Die("Unable to encode sequence %s at base %d\n",
sqinfo.name,errno);
=====================================
src/gnuregex.c
=====================================
@@ -1611,10 +1611,12 @@ regex_compile (pattern, size, syntax, bufp)
if (syntax & RE_NO_BK_PARENS) goto normal_backslash;
if (COMPILE_STACK_EMPTY)
+ {
if (syntax & RE_UNMATCHED_RIGHT_PAREN_ORD)
goto normal_backslash;
else
return REG_ERPAREN;
+ }
handle_close:
if (fixup_alt_jump)
@@ -1631,10 +1633,12 @@ regex_compile (pattern, size, syntax, bufp)
/* See similar code for backslashed left paren above. */
if (COMPILE_STACK_EMPTY)
+ {
if (syntax & RE_UNMATCHED_RIGHT_PAREN_ORD)
goto normal_char;
else
return REG_ERPAREN;
+ }
/* Since we just checked for an empty stack above, this
``can't happen''. */
@@ -2312,7 +2316,7 @@ typedef struct
value. Assumes the variable `fail_stack'. Probably should only
be called from within `PUSH_FAILURE_POINT'. */
#define PUSH_FAILURE_ITEM(item) \
- fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
+ fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) ((unsigned long) item)
/* The complement operation. Assumes `fail_stack' is nonempty. */
#define POP_FAILURE_ITEM() fail_stack.stack[--fail_stack.avail]
@@ -2391,10 +2395,10 @@ typedef struct
} \
\
DEBUG_PRINT2 (" Pushing low active reg: %d\n", lowest_active_reg);\
- PUSH_FAILURE_ITEM ((unsigned long)lowest_active_reg); \
+ PUSH_FAILURE_ITEM (lowest_active_reg); \
\
DEBUG_PRINT2 (" Pushing high active reg: %d\n", highest_active_reg);\
- PUSH_FAILURE_ITEM ((unsigned long)highest_active_reg); \
+ PUSH_FAILURE_ITEM (highest_active_reg); \
\
DEBUG_PRINT2 (" Pushing pattern 0x%x: ", pattern_place); \
DEBUG_PRINT_COMPILED_PATTERN (bufp, pattern_place, pend); \
@@ -2448,7 +2452,7 @@ typedef struct
#define POP_FAILURE_POINT(str, pat, low_reg, high_reg, regstart, regend, reg_info)\
{ \
DEBUG_STATEMENT (fail_stack_elt_t failure_id;) \
- unsigned long this_reg; \
+ int this_reg; \
unsigned char *string_temp; \
\
assert (!FAIL_STACK_EMPTY ()); \
@@ -2480,14 +2484,14 @@ typedef struct
\
/* Restore register info. */ \
high_reg = (unsigned long) POP_FAILURE_ITEM (); \
- DEBUG_PRINT2 (" Popping high active reg: %u\n", high_reg); \
+ DEBUG_PRINT2 (" Popping high active reg: %d\n", high_reg); \
\
low_reg = (unsigned long) POP_FAILURE_ITEM (); \
- DEBUG_PRINT2 (" Popping low active reg: %u\n", low_reg); \
+ DEBUG_PRINT2 (" Popping low active reg: %d\n", low_reg); \
\
for (this_reg = high_reg; this_reg >= low_reg; this_reg--) \
{ \
- DEBUG_PRINT2 (" Popping reg: %u\n", this_reg); \
+ DEBUG_PRINT2 (" Popping reg: %d\n", this_reg); \
\
reg_info[this_reg].word = POP_FAILURE_ITEM (); \
DEBUG_PRINT2 (" info: 0x%x\n", reg_info[this_reg]); \
@@ -2818,7 +2822,7 @@ re_set_registers (bufp, regs, num_regs, starts, ends)
{
bufp->regs_allocated = REGS_UNALLOCATED;
regs->num_regs = 0;
- regs->start = regs->end = (regoff_t) 0;
+ regs->start = regs->end = (regoff_t*) 0;
}
}
=====================================
src/interleaved.c
=====================================
@@ -143,7 +143,7 @@ dataline_clustal(char *buf, char *expected_name)
while (*buf && isspace(*buf)) buf++;
if (*buf == '\0' || strchr(commentsyms, *buf) != NULL)
return 0; /* blank or comment */
- if (expected_name != NULL && strncmp(buf, expected_name, strlen(expected_name) == 0))
+ if (expected_name != NULL && strncmp(buf, expected_name, strlen(expected_name)) == 0)
return 1; /* matches expected seq name */
for (; *buf != '\0'; buf++)
{ /* Clustal has no coord lines to worry about */
@@ -213,7 +213,7 @@ dataline_MSF(char *buf, char *expected_name)
while (*buf && isspace(*buf)) buf++;
if (*buf == '\0' || strchr(commentsyms, *buf) != NULL)
return 0; /* blank or comment */
- if (expected_name != NULL && strncmp(buf, expected_name, strlen(expected_name) == 0))
+ if (expected_name != NULL && strncmp(buf, expected_name, strlen(expected_name)) == 0)
return 1; /* matches expected seq name */
for (; *buf != '\0'; buf++)
{ /* MSF has coordinate lines to worry about */
=====================================
src/pavesi.c
=====================================
@@ -24,6 +24,7 @@
#include <string.h>
#include "squid.h"
#include "eufind_const.h"
+#include "pavesi.h"
/* #define NO_AMBIG -use this option to eliminate conservative
* calling of 'N's as best possible matches
@@ -88,7 +89,7 @@ float BTermDistSc_Mat[BTERM_MAT_SIZE] = {-0.54,-1.40,-2.80,-3.36,
-3.24,-5.44,-5.44,-4.06,-5.44};
-int
+void
Init_tRNA(TRNA_TYPE *tRNA) {
strcpy(tRNA->iso_type,"???");
@@ -135,15 +136,14 @@ GetBbox (float *score, int *seqidx, char *iseq, int seqlen,
*score += Bbox_Mat[(int)(iseq[i+j])][j];
}
if (*score > BBOX_CUTOFF) {
- if (verbose)
- if (strand == 0) {
- printf("Bbox at %i (End=%d), Sc= %.2f\n",i,i+BBOX_LEN+11,
- *score);
- }
- else {
- printf("Bbox at %i (End=%d), Sc= %.2f\n",seqlen-i+1,
- seqlen-(i+BBOX_LEN+11)+1,*score);
- }
+ if (verbose) {
+ if (strand == 0) {
+ printf("Bbox at %i (End=%d), Sc= %.2f\n",i,i+BBOX_LEN+11,*score);
+ }
+ else {
+ printf("Bbox at %i (End=%d), Sc= %.2f\n",seqlen-i+1,seqlen-(i+BBOX_LEN+11)+1,*score);
+ }
+ }
*seqidx = i;
return 1;
}
@@ -221,7 +221,7 @@ GetSecABox(TRNA_TYPE *tRNA, char *seq)
}
-int
+void
GetBestABox (TRNA_TYPE *tRNA, char *seq, char *iseq, int seqlen,
int strand, int verbose, int Max_AB_dist, int prev_Abox_st)
{
@@ -257,7 +257,7 @@ GetBestABox (TRNA_TYPE *tRNA, char *seq, char *iseq, int seqlen,
/* score gap at pos 17 by looking for conserved 'GG' at pos 18 &
19 */
- if ((seq[i+j] == 'G')) { /* && (seq[i+j+1] == 'G')) { */
+ if (seq[i+j] == 'G') { /* && (seq[i+j+1] == 'G')) { */
sc2 = Abox_Mat[GAP_ROW][j];
offset1 = 1;
}
@@ -317,7 +317,7 @@ GetBestABox (TRNA_TYPE *tRNA, char *seq, char *iseq, int seqlen,
tRNA->AboxSc = sc1+sc2+sc3;
best_offset1= offset1;
best_gap = gapct;
- if (verbose)
+ if (verbose) {
if (strand == 0) {
printf("Abox at %d (St=%d) A:%.2f AB(%d):%.2f I:%.2f\n",
i,i-5,tRNA->AboxSc, tRNA->Bbox_st-abox_end-1,tRNA->ABdistSc,
@@ -329,7 +329,7 @@ GetBestABox (TRNA_TYPE *tRNA, char *seq, char *iseq, int seqlen,
tRNA->Bbox_st-abox_end-1,tRNA->ABdistSc,
tRNA->AboxSc+tRNA->BboxSc+tRNA->ABdistSc);
}
-
+ }
}
} /* for gapct, enumerating all possible gaps */
} /* for i, starting pos for A box */
@@ -373,6 +373,7 @@ GetBestTrxTerm (TRNA_TYPE *tRNA, char *seq, int seqlen,
tRNA->TermSc = MAX_PENALTY;
return 0;
}
+ return 0;
}
=====================================
src/pavesi.h
=====================================
@@ -0,0 +1,46 @@
+/* eufindtRNA - Eukaryotic tRNA finder
+ *
+ * pavesi.h - functions for finding transcriptional control regions
+ *
+ * C implementation of algorithm described by Pavesi, Conterio,
+ * Bolchi, Dieci, & Ottonello in NAR 22:1247-56 (94)
+ * "Identification of new eukaryotic tRNA genes in genomic DNA
+ * databases by a multistep weight matix analysis of transcriptional
+ * control regions"
+ *
+ * To be used in tRNAscan-SE package to increase sensitivity by
+ * complementing tRNAscan 1.3 first-pass scan
+ *
+ * by Todd MJ Lowe 4/8/96
+ *
+ * Uses Sean Eddy's function library for biological sequence analysis
+ * (Squid v1.5g)
+ *
+ */
+
+#include "squid.h"
+#include "eufind_const.h"
+
+void Init_tRNA(TRNA_TYPE *tRNA);
+
+int IntEncodeSeq (char *intseq, char *seq, int seqlen);
+
+int GetBbox (float *score, int *seqidx, char *iseq, int seqlen, int strand, int verbose);
+
+float Get_ABdist_weight(int ABdist);
+
+int GetSecABox(TRNA_TYPE *tRNA, char *seq);
+
+void GetBestABox (TRNA_TYPE *tRNA, char *seq, char *iseq, int seqlen, int strand, int verbose, int Max_AB_dist, int prev_Abox_st);
+
+int GetBestTrxTerm (TRNA_TYPE *tRNA, char *seq, int seqlen, float TermPenalty);
+
+void Get_IsoType (TRNA_TYPE *tRNA);
+
+void Get_anticodon (TRNA_TYPE *tRNA, char *seq);
+
+void Get_tRNA_stats (TRNA_TYPE *tRNA, char *seq, int seqlen, int strand);
+
+void Save_tRNA (TRNA_TYPE *tRNA, SQINFO *sqinfo, char *seq, int strand, int ShowScores, long int sqoffset);
+
+int tRNAOverlap (TRNA_TYPE *tRNA1, TRNA_TYPE *tRNA2, int strand);
=====================================
src/scan_main.c
=====================================
@@ -9,10 +9,11 @@
#include <string.h>
#include <time.h>
#include <math.h>
+#include <getopt.h>
-#ifdef NEED_GETOPTH
+/*#ifdef NEED_GETOPTH
#include <getopt.h>
-#endif
+#endif*/
#include "structs.h"
#include "funcs.h"
=====================================
src/score_main.c
=====================================
@@ -11,10 +11,11 @@
#include <string.h>
#include <time.h>
#include <math.h>
+#include <getopt.h>
-#ifdef NEED_GETOPTH
+/*#ifdef NEED_GETOPTH
#include <getopt.h>
-#endif
+#endif*/
#include "structs.h"
#include "funcs.h"
=====================================
src/trnascan.c
=====================================
@@ -69,6 +69,7 @@ where supported options are:\n\
#include <stdio.h>
#include <stdlib.h>
#include <ctype.h>
+#include <getopt.h>
#ifdef MEMDEBUG
#include "dbmalloc.h"
@@ -332,7 +333,7 @@ printresult(FILE *fpo, /* output file pointer */
long int sqoffset /* offset nucleotide numbering by this much (set with -i param) */
);
-main(int argc, char **argv)
+int main(int argc, char **argv)
{
/* pointers to the different files fpi=input file, fpo=output file,
fpcons1= T-Psi-C matrix file, fpcons2= D matrix file */
@@ -1176,8 +1177,8 @@ for (i=0; i<*lsig; i++)
if (table_cons[i][j] == 1.0)
{
k++;
- table_inv[k][1]=i;
- table_inv[k][2]=j;
+ table_inv[k][0]=i;
+ table_inv[k][1]=j;
}
}
}
@@ -1418,7 +1419,7 @@ return seqlen;
/* Calls to this function eliminated for efficiency T. Lowe 11/95 */
-myindex (char *s, char *t)
+int myindex (char *s, char *t)
{
int i, j, k;
for (i=0; s[i] != '\0'; i++) {
@@ -1476,10 +1477,10 @@ int readsignal(char *ptr, /* pointer to the sequence */
/* (original code commented out)
- temp[0]= *(ptr+table_inv[k][1]);
+ temp[0]= *(ptr+table_inv[k][0]);
j = myindex(base,temp); */
- switch (*(ptr+table_inv[k][1])) {
+ switch (*(ptr+table_inv[k][0])) {
case 'a': j=0; break;
case 'c': j=1; break;
case 'g': j=2; break;
@@ -1491,9 +1492,9 @@ int readsignal(char *ptr, /* pointer to the sequence */
#ifdef NO_AMBIG
- if (j == table_inv[k][2])
+ if (j == table_inv[k][1])
#else
- if ((j == table_inv[k][2]) || (j == -1))
+ if ((j == table_inv[k][1]) || (j == -1))
#endif
(*ninv)++;
=====================================
tRNAscan-SE.conf.src
=====================================
@@ -29,6 +29,8 @@ organelle_cm_cutoff: 15
isotype_cm_cutoff.euk: 20
isotype_cm_cutoff.arch: 20
isotype_cm_cutoff.bact: 20
+isotype_cm_cutoff.mito_mammal: 20
+isotype_cm_cutoff.mito_vert: 20
# max size of -w parameter passed to covels when using a pre-scanner (eufind or tRNAscan)
max_tRNA_length: 500
=====================================
tRNAscan-SE.src
=====================================
@@ -4,9 +4,9 @@
# tRNAscan-SE: a program for improved detection of transfer RNA
# genes in genomic sequence
#
-# Version 2.0.7
+# Version 2.0.8
#
-# Copyright (C) 2020 Patricia Chan and Todd Lowe
+# Copyright (C) 2021 Patricia Chan and Todd Lowe
#
# School of Engineering, University of California, Santa Cruz
# trna at soe.ucsc.edu
@@ -39,8 +39,8 @@ use tRNAscanSE::IntResultFile;
use tRNAscanSE::MultiResultFile;
use tRNAscanSE::SS;
-our $version = "2.0.7";
-our $release_date = "Oct 2020";
+our $version = "2.0.8";
+our $release_date = "May 2021";
our $program_id = "tRNAscan-SE-".$version;
# modified by 'make'
@@ -594,7 +594,8 @@ sub prepare_intron_scan
# clean up temp files
sub cleanup
{
- system("rm -f ".$global_constants->get("temp_dir")."/tscan$$".'*');
+ system("rm -f ".$global_constants->get("temp_dir")."/tscan$$"."_*");
+ system("rm -f ".$global_constants->get("temp_dir")."/tscan$$".".*");
system("rm -f ".$opts->fafile().".pid");
}
View it on GitLab: https://salsa.debian.org/med-team/trnascan-se/-/commit/cb78e14e4fcc857762256779d405b2ab83b5c41c
--
View it on GitLab: https://salsa.debian.org/med-team/trnascan-se/-/commit/cb78e14e4fcc857762256779d405b2ab83b5c41c
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