[med-svn] [Git][med-team/phast][upstream] New upstream version 1.5+dfsg
Andreas Tille
gitlab at salsa.debian.org
Fri Oct 19 08:15:21 BST 2018
Andreas Tille pushed to branch upstream at Debian Med / phast
Commits:
01c9ee8d by Andreas Tille at 2018-10-19T06:26:27Z
New upstream version 1.5+dfsg
- - - - -
12 changed files:
- .gitignore
- include/external_libs.h
- include/misc.h
- src/lib/base/matrix.c
- src/lib/msa/maf.c
- src/lib/msa/maf_block.c
- src/lib/msa/sufficient_stats.c
- src/make-include.mk
- src/util/clean_genes.c
- src/util/msa_view.c
- test/test_phast.sh
- version
Changes:
=====================================
.gitignore
=====================================
@@ -0,0 +1,7 @@
+*.a
+*.o
+*.help
+
+bin/
+doc/man/
+
=====================================
include/external_libs.h
=====================================
@@ -33,7 +33,7 @@
#else
#ifdef VECLIB
-#include <vecLib/clapack.h>
+#include <Accelerate/Accelerate.h>
#define LAPACK_INT __CLPK_integer
#define LAPACK_DOUBLE __CLPK_doublereal
#else
=====================================
include/misc.h
=====================================
@@ -87,6 +87,17 @@ int int_pow(int x, int y) {
return retval;
}
+/** Take x,y & max as int and cast x & y as double
+ * * raise x to the power y. return min(x^y,max) as int*/
+
+static PHAST_INLINE
+int pow_bounded(int x, int y, int max) {
+ double z = pow((double) x, (double) y);
+ return ( z > (double) max ? max : (int)z);
+}
+
+
+
/** \name Log based calculation functions
\{ */
=====================================
src/lib/base/matrix.c
=====================================
@@ -293,7 +293,8 @@ int mat_invert(Matrix *M_inv, Matrix *M) {
same dimension, and C is diagonal. C is described by a vector
representing its diagonal elements. */
void mat_mult_diag(Matrix *A, Matrix *B, Vector *C, Matrix *D) {
- int i, j, k;
+
+/* int i, j, k;
for (i = 0; i < C->size; i++) {
for (j = 0; j < C->size; j++) {
A->data[i][j] = 0;
@@ -302,7 +303,27 @@ void mat_mult_diag(Matrix *A, Matrix *B, Vector *C, Matrix *D) {
}
}
}
+*/
+
+A->data[0][0] = B->data[0][0] * C->data[0] * D->data[0][0] + B->data[0][1] * C->data[1] * D->data[1][0] + B->data[0][2] * C->data[2] * D->data[2][0] + B->data[0][3] * C->data[3] * D->data[3][0];
+A->data[0][1] = B->data[0][0] * C->data[0] * D->data[0][1] + B->data[0][1] * C->data[1] * D->data[1][1] + B->data[0][2] * C->data[2] * D->data[2][1] + B->data[0][3] * C->data[3] * D->data[3][1];
+A->data[0][2] = B->data[0][0] * C->data[0] * D->data[0][2] + B->data[0][1] * C->data[1] * D->data[1][2] + B->data[0][2] * C->data[2] * D->data[2][2] + B->data[0][3] * C->data[3] * D->data[3][2];
+A->data[0][3] = B->data[0][0] * C->data[0] * D->data[0][3] + B->data[0][1] * C->data[1] * D->data[1][3] + B->data[0][2] * C->data[2] * D->data[2][3] + B->data[0][3] * C->data[3] * D->data[3][3];
+A->data[1][0] = B->data[1][0] * C->data[0] * D->data[0][0] + B->data[1][1] * C->data[1] * D->data[1][0] + B->data[1][2] * C->data[2] * D->data[2][0] + B->data[1][3] * C->data[3] * D->data[3][0];
+A->data[1][1] = B->data[1][0] * C->data[0] * D->data[0][1] + B->data[1][1] * C->data[1] * D->data[1][1] + B->data[1][2] * C->data[2] * D->data[2][1] + B->data[1][3] * C->data[3] * D->data[3][1];
+A->data[1][2] = B->data[1][0] * C->data[0] * D->data[0][2] + B->data[1][1] * C->data[1] * D->data[1][2] + B->data[1][2] * C->data[2] * D->data[2][2] + B->data[1][3] * C->data[3] * D->data[3][2];
+A->data[1][3] = B->data[1][0] * C->data[0] * D->data[0][3] + B->data[1][1] * C->data[1] * D->data[1][3] + B->data[1][2] * C->data[2] * D->data[2][3] + B->data[1][3] * C->data[3] * D->data[3][3];
+A->data[2][0] = B->data[2][0] * C->data[0] * D->data[0][0] + B->data[2][1] * C->data[1] * D->data[1][0] + B->data[2][2] * C->data[2] * D->data[2][0] + B->data[2][3] * C->data[3] * D->data[3][0];
+A->data[2][1] = B->data[2][0] * C->data[0] * D->data[0][1] + B->data[2][1] * C->data[1] * D->data[1][1] + B->data[2][2] * C->data[2] * D->data[2][1] + B->data[2][3] * C->data[3] * D->data[3][1];
+A->data[2][2] = B->data[2][0] * C->data[0] * D->data[0][2] + B->data[2][1] * C->data[1] * D->data[1][2] + B->data[2][2] * C->data[2] * D->data[2][2] + B->data[2][3] * C->data[3] * D->data[3][2];
+A->data[2][3] = B->data[2][0] * C->data[0] * D->data[0][3] + B->data[2][1] * C->data[1] * D->data[1][3] + B->data[2][2] * C->data[2] * D->data[2][3] + B->data[2][3] * C->data[3] * D->data[3][3];
+A->data[3][0] = B->data[3][0] * C->data[0] * D->data[0][0] + B->data[3][1] * C->data[1] * D->data[1][0] + B->data[3][2] * C->data[2] * D->data[2][0] + B->data[3][3] * C->data[3] * D->data[3][0];
+A->data[3][1] = B->data[3][0] * C->data[0] * D->data[0][1] + B->data[3][1] * C->data[1] * D->data[1][1] + B->data[3][2] * C->data[2] * D->data[2][1] + B->data[3][3] * C->data[3] * D->data[3][1];
+A->data[3][2] = B->data[3][0] * C->data[0] * D->data[0][2] + B->data[3][1] * C->data[1] * D->data[1][2] + B->data[3][2] * C->data[2] * D->data[2][2] + B->data[3][3] * C->data[3] * D->data[3][2];
+A->data[3][3] = B->data[3][0] * C->data[0] * D->data[0][3] + B->data[3][1] * C->data[1] * D->data[1][3] + B->data[3][2] * C->data[2] * D->data[2][3] + B->data[3][3] * C->data[3] * D->data[3][3];
+
+}
int mat_equal(Matrix *A, Matrix *B) {
int i, j;
if (A->nrows != B->nrows || A->ncols != B->ncols) return 0;
=====================================
src/lib/msa/maf.c
=====================================
@@ -139,12 +139,10 @@ MSA *maf_read_cats_subset(FILE *F, FILE *REFSEQF, int tuple_size,
msa->alloc_len = msa->length = refseqlen; //this may still not be big enough because of gaps in refseq
else
msa->alloc_len = 50000;
- max_tuples = max(1000000, (int)pow(strlen(msa->alphabet)+strlen(msa->missing)+1,
- 2 * msa->nseqs * tuple_size));
+ max_tuples = pow_bounded(strlen(msa->alphabet)+strlen(msa->missing)+1, 2 * msa->nseqs * tuple_size, 1000000);
}
else
- max_tuples = min(1000000,
- (int)pow(strlen(msa->alphabet)+strlen(msa->missing)+1, 2 * msa->nseqs * tuple_size));
+ max_tuples = pow_bounded(strlen(msa->alphabet)+strlen(msa->missing)+1, 2 * msa->nseqs * tuple_size, 1000000);
if (max_tuples > 10000000 || max_tuples < 0) max_tuples = 10000000;
if (max_tuples < 1000000) max_tuples = 1000000;
@@ -596,15 +594,13 @@ MSA *maf_read_unsorted(FILE *F, FILE *REFSEQF, int tuple_size, char *alphabet,
if (store_order) {
msa->length = map != NULL ? map->msa_len : refseqlen;
- max_tuples = min(msa->length,
- (int)pow(strlen(msa->alphabet)+strlen(msa->missing)+1, msa->nseqs * tuple_size));
+ max_tuples = pow_bounded(strlen(msa->alphabet)+strlen(msa->missing)+1, msa->nseqs * tuple_size, msa->length);
if (max_tuples < 0) max_tuples = msa->length;
if (max_tuples > 1000000) max_tuples = 1000000;
}
else {
msa->length = 0;
- max_tuples = min(50000,
- (int)pow(strlen(msa->alphabet)+strlen(msa->missing)+1, msa->nseqs * tuple_size));
+ max_tuples = pow_bounded(strlen(msa->alphabet)+strlen(msa->missing)+1, msa->nseqs * tuple_size, 50000);
if (max_tuples < 0) max_tuples = 50000;
}
=====================================
src/lib/msa/maf_block.c
=====================================
@@ -13,7 +13,7 @@
#include <maf_block.h>
#include <hashtable.h>
#include <ctype.h>
-
+#include <assert.h>
MafBlock *mafBlock_new() {
MafBlock *block = smalloc(sizeof(MafBlock));
@@ -201,7 +201,10 @@ void mafBlock_add_iLine(String *line, MafSubBlock *sub) {
for (i=0; i<6; i++) str_free((String*)lst_get_ptr(l, i));
lst_free(l);
+ if (sub->numLine >= 4) die("Error: bad MAF file");
sub->lineType[sub->numLine++] = 'i';
+
+
}
@@ -247,7 +250,9 @@ void mafBlock_add_qLine(String *line, MafSubBlock *sub) {
for (i=0; i<2; i++) str_free((String*)lst_get_ptr(l, i));
lst_free(l);
+ if (sub->numLine >= 4) die("Error: bad MAF file");
sub->lineType[sub->numLine++] = 'q';
+
}
@@ -710,7 +715,8 @@ void mafSubBlock_strip_iLine(MafSubBlock *sub) {
for (i=0; i<sub->numLine; i++)
if (sub->lineType[i]=='i') break;
if (i < sub->numLine) {
- for (j=i+1; j<sub->numLine; j++) {
+ assert(i < 4);
+ for (j=i+1; j<sub->numLine && j<4; j++) {
sub->lineType[j-1] = sub->lineType[j];
if (sub->lineType[j] == 'i')
die("ERROR mafSubBlock_strip_iLine: sub->lineType[%i]=%c\n",
=====================================
src/lib/msa/sufficient_stats.c
=====================================
@@ -117,8 +117,8 @@ void ss_from_msas(MSA *msa, int tuple_size, int store_order,
upper_bound = source_msa->ss->ntuples;
else if (source_msa != NULL) upper_bound = source_msa->length;
else upper_bound = min(msa->length, MAX_NTUPLE_ALLOC);
- max_tuples = min((int)pow(strlen(msa->alphabet)+ (int)strlen(msa->missing) + 1,
- msa->nseqs * tuple_size),
+ max_tuples = pow_bounded(strlen(msa->alphabet)+ (int)strlen(msa->missing) + 1,
+ msa->nseqs * tuple_size,
upper_bound);
if (max_tuples < 0) max_tuples = upper_bound; //protect against overflow
ss_new(msa, tuple_size, max_tuples, do_cats, store_order);
@@ -139,8 +139,8 @@ void ss_from_msas(MSA *msa, int tuple_size, int store_order,
upper_bound = msa->ss->ntuples + source_msa->ss->ntuples;
else
upper_bound = msa->ss->ntuples + source_msa->length;
- max_tuples = min((int)pow(strlen(msa->alphabet) + (int)strlen(msa->missing) + 1,
- msa->nseqs * tuple_size),
+ max_tuples = pow_bounded(strlen(msa->alphabet) + (int)strlen(msa->missing) + 1,
+ msa->nseqs * tuple_size,
upper_bound);
if (max_tuples < 0) max_tuples = upper_bound;
ss_realloc(msa, tuple_size, max_tuples, do_cats, store_order);
=====================================
src/make-include.mk
=====================================
@@ -133,7 +133,7 @@ endif
# vecLib
ifdef VECLIB
CFLAGS += -DVECLIB
-LIBS = -lphast -framework vecLib -lc -lm
+LIBS = -lphast -framework Accelerate -lc -lm
# CLAPACK
else
=====================================
src/util/clean_genes.c
=====================================
@@ -34,16 +34,16 @@
typedef enum {OKAY, BAD_REF, BAD_REF_START, BAD_REF_STOP, BAD_REF_5_SPLICE,
BAD_REF_3_SPLICE, BAD_REF_ORF, BAD_REF_INDEL_STRICT_FAIL,
NO_ALN, BAD_START, BAD_STOP, BAD_5_SPLICE, BAD_3_SPLICE,
- BAD_5_SPLICE_UTR, BAD_3_SPLICE_UTR, NONSENSE, FSHIFT,
- BAD_INTRON, TOO_MANY_Ns, WARN_FSHIFT, WARN_Ns, NTYPES}
+ BAD_5_SPLICE_UTR, BAD_3_SPLICE_UTR, NONSENSE, FRAMESHIFT,
+ BAD_INTRON, TOO_MANY_Ns, WARN_FRAMESHIFT, WARN_Ns, NTYPES}
status_type; /* NTYPES marks the total number */
-/* possible gap types for cds exon -- frame-shift gaps (FSHIFT_BAD),
- no apparent frame shift (FSHIFT_OK), all gaps multiple of 3 in len
+/* possible gap types for cds exon -- frame-shift gaps (FRAMESHIFT_BAD),
+ no apparent frame shift (FRAMESHIFT_OK), all gaps multiple of 3 in len
(CLN_GAPS), gaps mult. of 3 and nonoverlapping (NOVRLP_CLN_GAPS),
and no gaps present (NGAPS). Defined in order of least to most
stringent criterion (ordering gets used) */
-typedef enum {FSHIFT_BAD, FSHIFT_OK, CLN_GAPS,
+typedef enum {FRAMESHIFT_BAD, FRAMESHIFT_OK, CLN_GAPS,
NOVRLP_CLN_GAPS, NGAPS, NGAP_TYPES}
cds_gap_type; /* NGAP_TYPES marks the total number */
@@ -102,7 +102,7 @@ typedef struct Problem {
status_type status;
int start;
int end;
- cds_gap_type cds_gap; /* if status if FSHIFT */
+ cds_gap_type cds_gap; /* if status if FRAMESHIFT */
} Problem;
/* create a new problem. feat can be null for whole gene.
@@ -311,7 +311,7 @@ int gap_compare(const void *ptr1, const void* ptr2) {
return g1->start - g2->start;
}
/* scans a cds for gaps. Returns CLN_GAPS, NOVRLP_CLN_GAPS, NO_GAPS,
- or FSHIFT_BAD; doesn't try to check for compensatory indels, which
+ or FRAMESHIFT_BAD; doesn't try to check for compensatory indels, which
is more complicated (this is left for the special-purpose function
below) */
int scan_for_gaps(GFF_Feature *feat, MSA *msa, Problem **problem) {
@@ -322,7 +322,7 @@ int scan_for_gaps(GFF_Feature *feat, MSA *msa, Problem **problem) {
cds_gap_type retval = NGAPS;
List *gaps = lst_new_ptr(10);
- for (j = 0; retval != FSHIFT_BAD && j < msa->nseqs; j++) {
+ for (j = 0; retval != FRAMESHIFT_BAD && j < msa->nseqs; j++) {
for (i = msa_start; i <= msa_end; i++) {
if (ss_get_char_pos(msa, i, j, 0) == GAP_CHAR) {
int gap_start, gap_end;
@@ -336,9 +336,9 @@ int scan_for_gaps(GFF_Feature *feat, MSA *msa, Problem **problem) {
gap_end--; /* inclusive */
if ((gap_end - gap_start + 1) % 3 != 0) {
- retval = FSHIFT_BAD;
- *problem = problem_new(feat, FSHIFT, gap_start, gap_end);
- (*problem)->cds_gap = FSHIFT_BAD;
+ retval = FRAMESHIFT_BAD;
+ *problem = problem_new(feat, FRAMESHIFT, gap_start, gap_end);
+ (*problem)->cds_gap = FRAMESHIFT_BAD;
break;
}
@@ -449,18 +449,18 @@ int is_fshift_okay(GFF_Feature *feat, MSA *msa) {
"clean" gaps (all multiples of 3 in length; CLEAN_GAPS)
non-overlapping clean gaps (NOVRLP_CLN_GAPS), "okay" gaps (only
temporary frame shifts, corrected by compensatory indels;
- FSHIFT_OK), or real frame-shift gaps (FSHIFT_BAD) */
+ FRAMESHIFT_OK), or real frame-shift gaps (FRAMESHIFT_BAD) */
cds_gap_type get_cds_gap_type(GFF_Feature *feat, MSA *msa, List *problems) {
Problem *problem = NULL;
cds_gap_type retval = scan_for_gaps(feat, msa, &problem);
- if (retval == FSHIFT_BAD && is_fshift_okay(feat, msa)) {
- retval = FSHIFT_OK;
+ if (retval == FRAMESHIFT_BAD && is_fshift_okay(feat, msa)) {
+ retval = FRAMESHIFT_OK;
/* most of the time the call to
is_fshift_okay won't be
necessary */
- problem->status = WARN_FSHIFT;
- problem->cds_gap = FSHIFT_OK;
+ problem->status = WARN_FRAMESHIFT;
+ problem->cds_gap = FRAMESHIFT_OK;
}
if (problem != NULL) {
lst_push_ptr(problems, problem);
@@ -669,9 +669,9 @@ void write_log(FILE *logf, GFF_FeatureGroup *group, status_type status,
case NONSENSE:
reason = "Nonsense mutation";
break;
- case FSHIFT:
+ case FRAMESHIFT:
{
- if (problem->cds_gap == FSHIFT_OK)
+ if (problem->cds_gap == FRAMESHIFT_OK)
reason = "Frame-shift gap [gaps not clean]";
else if (problem->cds_gap == CLN_GAPS)
reason = "Frame-shift gap [gaps clean but overlapping/near boundary]";
@@ -689,7 +689,7 @@ void write_log(FILE *logf, GFF_FeatureGroup *group, status_type status,
reason = "Too many Ns";
print_alignment = FALSE;
break;
- case WARN_FSHIFT:
+ case WARN_FRAMESHIFT:
reason = "Frame shift gap (with compensatory gap)";
break;
case WARN_Ns:
@@ -741,13 +741,13 @@ char *status_type_str(status_type status) {
return "bad_3_splice_utr";
case NONSENSE:
return "nonsense";
- case FSHIFT:
+ case FRAMESHIFT:
return "frameshift";
case BAD_INTRON:
return "bad_intron";
case TOO_MANY_Ns:
return "too_many_Ns";
- case WARN_FSHIFT:
+ case WARN_FRAMESHIFT:
return "warning_fshift";
case WARN_Ns:
return "warning_Ns";
@@ -980,7 +980,7 @@ int main(int argc, char *argv[]) {
*discards=NULL, *intron_splice = lst_new_ptr(10);
char *rseq_fname = NULL;
FILE *logf = NULL, *mlogf = NULL, *statsf = NULL, *discardf = NULL;
- cds_gap_type fshift_mode = FSHIFT_BAD;
+ cds_gap_type fshift_mode = FRAMESHIFT_BAD;
char *groupby = "transcript_id";
msa_coord_map *map;
int *countNs, *countCDSs;
@@ -1029,11 +1029,11 @@ int main(int argc, char *argv[]) {
break;
case 'f':
check_alignment = 1;
- fshift_mode = FSHIFT_OK;
+ fshift_mode = FRAMESHIFT_OK;
break;
case 'c':
check_alignment = check_start = check_stop = check_splice = check_nonsense = 1;
- if (fshift_mode < FSHIFT_OK) fshift_mode = FSHIFT_OK;
+ if (fshift_mode < FRAMESHIFT_OK) fshift_mode = FRAMESHIFT_OK;
break;
case 'N':
Nfrac = get_arg_dbl_bounds(optarg, 0, 1);
@@ -1166,7 +1166,7 @@ int main(int argc, char *argv[]) {
List *gfeatures = group->features;
GFF_Feature *feat;
status_type status = OKAY;
- cds_gap_type gt = FSHIFT_BAD;
+ cds_gap_type gt = FRAMESHIFT_BAD;
problems_clear(problems);
/* make sure have frame info for CDSs */
@@ -1295,9 +1295,9 @@ int main(int argc, char *argv[]) {
else if (str_equals_charstr(feat->feature, GFF_CDS_TYPE)) {
- if (fshift_mode > FSHIFT_BAD
+ if (fshift_mode > FRAMESHIFT_BAD
&& (gt = get_cds_gap_type(feat, msa, problems)) < fshift_mode) {
- if (status == OKAY || status == NONSENSE) status = FSHIFT;
+ if (status == OKAY || status == NONSENSE) status = FRAMESHIFT;
}
if (check_nonsense && !is_nonsense_clean(feat, msa, problems)) {
@@ -1336,8 +1336,8 @@ int main(int argc, char *argv[]) {
for (j = 0; j < lst_size(problems); j++) {
struct Problem *problem = lst_get_ptr(problems, j);
status_type ftype = problem->status;
- if ((ftype == FSHIFT || ftype == NONSENSE) &&
- status != FSHIFT && status != NONSENSE)
+ if ((ftype == FRAMESHIFT || ftype == NONSENSE) &&
+ status != FRAMESHIFT && status != NONSENSE)
continue; /* don't count secondary frame shifts
and nonsense mutations */
@@ -1350,7 +1350,7 @@ int main(int argc, char *argv[]) {
/* also keep track of the total number of "conserved exons", and
the number having each kind of gap */
- if ((status == OKAY || (status == FSHIFT && gt >= FSHIFT_OK))) {
+ if ((status == OKAY || (status == FRAMESHIFT && gt >= FRAMESHIFT_OK))) {
nconserved_exons++;
nce_gap_type[gt]++; /* number of conserved exons having
given type of gaps */
@@ -1429,10 +1429,10 @@ int main(int argc, char *argv[]) {
nconsid[BAD_5_SPLICE], nfail[BAD_3_SPLICE], nconsid[BAD_3_SPLICE],
nfail[BAD_5_SPLICE_UTR], nconsid[BAD_5_SPLICE_UTR],
nfail[BAD_3_SPLICE_UTR], nconsid[BAD_3_SPLICE_UTR],
- nfail[BAD_INTRON], nfail[NONSENSE], nfail[FSHIFT],
+ nfail[BAD_INTRON], nfail[NONSENSE], nfail[FRAMESHIFT],
nfail[TOO_MANY_Ns], nconserved_exons, nce_gap_type[NGAPS],
nce_gap_type[NOVRLP_CLN_GAPS], nce_gap_type[CLN_GAPS],
- nce_gap_type[FSHIFT_OK]);
+ nce_gap_type[FRAMESHIFT_OK]);
fprintf(statsf, "%s", STATS_DESCRIPTION);
}
=====================================
src/util/msa_view.c
=====================================
@@ -627,7 +627,7 @@ int main(int argc, char* argv[]) {
if (f->frame == GFF_NULL_FRAME) f->frame = 0;
if (fourD_refseq == NULL) fourD_refseq = str_new_charstr(f->seqname->chars);
else if (!str_equals(fourD_refseq, f->seqname))
- die("--4d requires all features have same source column");
+ die("--4d requires all features are on the same chromosome");
if (str_equals_charstr(f->feature, "CDS") && f->strand != '-')
str_cpy_charstr(f->feature, "CDSplus");
else if (str_equals_charstr(f->feature, "CDS") && f->strand == '-')
=====================================
test/test_phast.sh
=====================================
@@ -37,39 +37,39 @@ tree_doctor --scale 3.0 hpmr.mod > hpmr_fast.mod
******************** phyloP ********************
phyloFit hmrc.ss --tree "(human, (mouse,rat), cow)" --quiet
- at phyloP --null 10 phyloFit.mod
+ at phyloP --seed 123 --null 10 phyloFit.mod
msa_view -o SS --end 100 hmrc.ss > hmrc_short.ss
- at phyloP phyloFit.mod hmrc_short.ss
- at phyloP --method LRT --base-by-base phyloFit.mod hmrc.ss
- at phyloP --method LRT --mode CONACC --wig-scores phyloFit.mod hmrc.ss
- at phyloP -d 12345 --method SCORE --mode NNEUT --base-by-base phyloFit.mod hmrc.ss
- at phyloP --method GERP --mode ACC --wig-scores phyloFit.mod hmrc.ss
- at phyloP --method GERP --base-by-base phyloFit.mod hmrc.ss
- at phyloP -d 12345 --method SCORE --wig-scores phyloFit.mod hmrc.ss
- at phyloP --method LRT --wig-scores phyloFit.mod hmrc.ss
- at phyloP --method LRT --base-by-base phyloFit.mod hmrc.ss
- at phyloP -d 12345 --method SCORE --wig-scores --refidx 2 phyloFit.mod hmrc.ss
+ at phyloP --seed 123 phyloFit.mod hmrc_short.ss
+ at phyloP --seed 123 --method LRT --base-by-base phyloFit.mod hmrc.ss
+ at phyloP --seed 123 --method LRT --mode CONACC --wig-scores phyloFit.mod hmrc.ss
+ at phyloP --seed 123 -d 12345 --method SCORE --mode NNEUT --base-by-base phyloFit.mod hmrc.ss
+ at phyloP --seed 123 --method GERP --mode ACC --wig-scores phyloFit.mod hmrc.ss
+ at phyloP --seed 123 --method GERP --base-by-base phyloFit.mod hmrc.ss
+ at phyloP --seed 123 -d 12345 --method SCORE --wig-scores phyloFit.mod hmrc.ss
+ at phyloP --seed 123 --method LRT --wig-scores phyloFit.mod hmrc.ss
+ at phyloP --seed 123 --method LRT --base-by-base phyloFit.mod hmrc.ss
+ at phyloP --seed 123 -d 12345 --method SCORE --wig-scores --refidx 2 phyloFit.mod hmrc.ss
echo -e "chr1\t0\t10\nchr1\t50\t100\nchr1\t200\t300" > temp.bed
- at phyloP --method LRT --mode CONACC --features temp.bed phyloFit.mod hmrc.ss
- at phyloP --method SCORE --features temp.bed -g phyloFit.mod hmrc.ss
+ at phyloP --seed 123 --method LRT --mode CONACC --features temp.bed phyloFit.mod hmrc.ss
+ at phyloP --seed 123 --method SCORE --features temp.bed -g phyloFit.mod hmrc.ss
tree_doctor --name-ancestors phyloFit.mod > phyloFit-named.mod
- at phyloP --method LRT --mode CONACC --subtree mouse-rat --base-by-base phyloFit-named.mod hmrc.ss
- at phyloP --method LRT --mode ACC --branch mouse-rat -w phyloFit-named.mod hmrc.ss
- at phyloP --posterior phyloFit.mod hmrc_short.ss
- at phyloP --fit-model -w --subtree mouse-rat phyloFit-named.mod hmrc_short.ss
- at phyloP --epsilon 0.0001 phyloFit-named.mod hmrc_short.ss
- at phyloP --confidence-interval 0.05 phyloFit-named.mod hmrc_short.ss
- at phyloP --quantiles --null 100 phyloFit-named.mod
+ at phyloP --seed 123 --method LRT --mode CONACC --subtree mouse-rat --base-by-base phyloFit-named.mod hmrc.ss
+ at phyloP --seed 123 --method LRT --mode ACC --branch mouse-rat -w phyloFit-named.mod hmrc.ss
+ at phyloP --seed 123 --posterior phyloFit.mod hmrc_short.ss
+ at phyloP --seed 123 --fit-model -w --subtree mouse-rat phyloFit-named.mod hmrc_short.ss
+ at phyloP --seed 123 --epsilon 0.0001 phyloFit-named.mod hmrc_short.ss
+ at phyloP --seed 123 --confidence-interval 0.05 phyloFit-named.mod hmrc_short.ss
+ at phyloP --seed 123 --quantiles --null 100 phyloFit-named.mod
# want to try subtree with LRT, SCORE, SPH, with both --base-by-base and --features
# note that bugs in SCORE method mean tests will fail against revisions < 6563
- at phyloP --method LRT --subtree mouse-rat --mode CONACC --base-by-base phyloFit-named.mod hmrc.ss
- at phyloP --method LRT --subtree mouse-rat --mode CONACC --features temp.bed phyloFit-named.mod hmrc.ss
- at phyloP --method SCORE --subtree mouse-rat --mode CONACC --base-by-base phyloFit-named.mod hmrc.ss
- at phyloP --method SCORE --subtree mouse-rat --mode CONACC --features temp.bed phyloFit-named.mod hmrc.ss
- at phyloP --method SPH --subtree mouse-rat --mode CONACC --base-by-base phyloFit-named.mod hmrc.ss
- at phyloP --method SPH --subtree mouse-rat --mode CONACC --features temp.bed phyloFit-named.mod hmrc.ss
+ at phyloP --seed 123 --method LRT --subtree mouse-rat --mode CONACC --base-by-base phyloFit-named.mod hmrc.ss
+ at phyloP --seed 123 --method LRT --subtree mouse-rat --mode CONACC --features temp.bed phyloFit-named.mod hmrc.ss
+ at phyloP --seed 123 --method SCORE --subtree mouse-rat --mode CONACC --base-by-base phyloFit-named.mod hmrc.ss
+ at phyloP --seed 123 --method SCORE --subtree mouse-rat --mode CONACC --features temp.bed phyloFit-named.mod hmrc.ss
+ at phyloP --seed 123 --method SPH --subtree mouse-rat --mode CONACC --base-by-base phyloFit-named.mod hmrc.ss
+ at phyloP --seed 123 --method SPH --subtree mouse-rat --mode CONACC --features temp.bed phyloFit-named.mod hmrc.ss
rm -f hmrc_short.ss phyloFit.mod phyloFit-named.mod temp.bed
=====================================
version
=====================================
@@ -1 +1 @@
-v1.3
+v1.4
View it on GitLab: https://salsa.debian.org/med-team/phast/commit/01c9ee8d01efbf8b89e9b016104a7f0ba07d0741
--
View it on GitLab: https://salsa.debian.org/med-team/phast/commit/01c9ee8d01efbf8b89e9b016104a7f0ba07d0741
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20181019/0acf3596/attachment-0001.html>
More information about the debian-med-commit
mailing list