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.gitignore 0 → 100644
View file @ 92c90e8c
*.o
afetch
alistat
compalign
compstruct
libsquid.a
revcomp
seqsplit
seqstat
sfetch
shuffle
sindex
sreformat
translate
weight
hmmalign
hmmbuild
hmmcalibrate
hmmconvert
hmmemit
hmmfetch
hmmindex
hmmpfam
hmmsearch
libhmmer.a
alignalign_test
evd_test
masks_test
parsingviterbi_test
tophits_test
trace_test
viterbi_exercise
weeviterbi_test
sreaa*
*.OPT.HMM.ssi
hmmalign2
hmmbuild2
hmmcalibrate2
hmmconvert2
hmmemit2
hmmfetch2
hmmindex2
hmmpfam2
hmmsearch2
libhmmer2.so
hmmalign
hmmbuild
hmmcalibrate
hmmconvert
hmmemit
hmmfetch
hmmindex
hmmpfam
hmmsearch
libhmmer.so
Bugs/BUGTRAX 0 → 100644
View file @ 92c90e8c
ID 1
STATUS closed
DESCRIPTION BPA1_HUMAN crashes Pfam server
NOTED_DATE 1/16/98
NOTED_XREF
REPORTED_BY David Kerk
REPRODUCE_WITH
REPRODUCE_ON ANY
CLOSED_DATE 1/16/98
CLOSED_XREF
CLOSED_ACTION
//
ID 2
STATUS closed
DESCRIPTION null2 consistency problem between per-seq and per-domain
NOTED_DATE 1/7/99
NOTED_XREF notebook STL1 p.117
REPORTED_BY David Kerk
REPRODUCE_WITH bug2.pl
REPRODUCE_ON ANY
CLOSED_DATE SRE, Tue Dec 19 17:45:46 2000
CLOSED_XREF STL3 notebook, p.127
CLOSED_ACTION created postprocess_hit() in hmmpfam.c
//
ID 3
STATUS closed
DESCRIPTION hmmbuild segfaults on alignments labeled with #=ID
NOTED_DATE 1/15/99
NOTED_XREF
REPORTED_BY SRE
REPRODUCE_WITH
REPRODUCE_ON Solaris
CLOSED_DATE 1/19/99
CLOSED_XREF
CLOSED_ACTION
//
ID 4
STATUS closed
DESCRIPTION sreformat core dumps when reformatting single seq to SELEX
NOTED_DATE 1/18/99
NOTED_XREF
REPORTED_BY sre
REPRODUCE_WITH
REPRODUCE_ON any
CLOSED_DATE 1/19/99
CLOSED_XREF
CLOSED_ACTION
//
ID 5
STATUS closed
DESCRIPTION hmmbuild core dumps when building model from single
seqs FASTA file
NOTED_DATE 1/18/99
NOTED_XREF
REPORTED_BY agb
REPRODUCE_WITH
REPRODUCE_ON
CLOSED_DATE 1/19/99
CLOSED_XREF
CLOSED_ACTION
//
ID 6
STATUS closed
DESCRIPTION getseq clashes with GCG program of same name
NOTED_DATE 1/18/99
NOTED_XREF
REPORTED_BY sre
REPRODUCE_WITH
REPRODUCE_ON n/a
CLOSED_DATE 1/19/99
CLOSED_XREF
CLOSED_ACTION renamed getseq to sfetch
//
ID 7
STATUS closed
DESCRIPTION Digital 4.0d binaries do not run on 4.0b;
pthread_setconcurrency() missing
NOTED_DATE 1/18/99
NOTED_XREF
REPORTED_BY Bill Pearson
REPRODUCE_WITH
REPRODUCE_ON Digital UNIX
CLOSED_DATE 1/19/99
CLOSED_XREF
CLOSED_ACTION
//
ID 8
STATUS closed
DESCRIPTION hmmpfam segfaults on GCG-reformatted Swissprot file
NOTED_DATE 1/19/99
NOTED_XREF
REPORTED_BY James Holzwarth
REPRODUCE_WITH
REPRODUCE_ON
CLOSED_DATE 1/19/99
CLOSED_XREF
CLOSED_ACTION
//
ID 9
STATUS OPEN
DESCRIPTION C->T transition doesn't seem to be parsed from save files
NOTED_DATE 6/29/99
NOTED_XREF
REPORTED_BY Bob Farrington
REPRODUCE_WITH
REPRODUCE_ON
CLOSED_DATE
CLOSED_XREF
CLOSED_ACTION
//
ID 10
STATUS closed
DESCRIPTION Floating point exception in ExtremeValueP() on Digital 4.0b:
range error.
NOTED_DATE 7/2/99
NOTED_XREF
REPORTED_BY ju@harvard
REPRODUCE_WITH
REPRODUCE_ON Digital UNIX 4.0b
CLOSED_DATE 9/17/99
CLOSED_XREF
CLOSED_ACTION
//
ID 11
STATUS OPEN
DESCRIPTION hmmbuild, illegal B->E in traceback
NOTED_DATE 11/15/99
NOTED_XREF
REPORTED_BY marcel@cs.berkeley.edu
REPRODUCE_WITH
REPRODUCE_ON
CLOSED_DATE
CLOSED_XREF
CLOSED_ACTION
//
ID 12
STATUS closed
DESCRIPTION --domE, --domT don't work correctly in hmmpfam; E-value
is assumed to be monotonic w/ score.
NOTED_DATE 11/29/00
NOTED_XREF STL3 p.127
REPORTED_BY vanschlun@gcg.com
REPRODUCE_WITH bug12.pl
REPRODUCE_ON any
CLOSED_DATE SRE, Tue Dec 19 17:47:01 2000
CLOSED_XREF STL3 p.127
CLOSED_ACTION removed the break statements when looping over domain list.
//
ID 13
STATUS closed
DESCRIPTION hmmconvert happily converts a bogus HMM database w/
both DNA and protein
NOTED_DATE 12/24/00
NOTED_XREF STL3 p.133
REPORTED_BY vanschlun@gcg.com, email 12/14/00
REPRODUCE_WITH bug13.pl
REPRODUCE_ON any
CLOSED_DATE SRE, Sun Dec 24 11:58:28 2000
CLOSED_XREF STL3 p.133
CLOSED_ACTION hmmio.c now checks for changes in Alphabet_type while reading HMMs.
//
ID 14
STATUS closed
DESCRIPTION hmmconvert doesn't complain about appending binary to
ASCII HMMs, or vice versa
NOTED_DATE 12/24/00
NOTED_XREF STL3 p.133
REPORTED_BY vanschlun@gcg.com, email 12/14/00
REPRODUCE_WITH bug13.pl
REPRODUCE_ON any
CLOSED_DATE SRE, Sun Dec 24 15:33:11 2000
CLOSED_XREF STL3 p. 133
CLOSED_ACTION hmmconvert.c now tests for this case
//
ID 15
STATUS untested
DESCRIPTION hmmpfam slave process leak when nhmm < nslaves
NOTED_DATE 10/25/01
NOTED_XREF STL5 p. 66
REPORTED_BY John Blanchard (johnb@incyte.com), email 10/17/01
REPRODUCE_WITH
REPRODUCE_ON any PVM
CLOSED_DATE
CLOSED_XREF STL5 p.66
CLOSED_ACTION hmmpfam.c modified: kill slaves off in a separate loop
//
ID 16
STATUS untested
DESCRIPTION PVMConfirmSlaves() assumes nslaves=nhosts
NOTED_DATE 10/25/01
NOTED_XREF STL5 p. 66
REPORTED_BY John Blanchard (johnb@incyte.com), email 10/17/01
REPRODUCE_WITH
REPRODUCE_ON any PVM; only when DEBUGLEVEL>0
CLOSED_DATE
CLOSED_XREF STL5 p.66
CLOSED_ACTION pvm.c:PVMConfirmSlaves()... replace pvm_config() w/ pvm_tasks().
//
ID 17
STATUS closed
DESCRIPTION threaded, unthreaded hmmsearch don't give same histogram
NOTED_DATE 2/27/02
NOTED_XREF STL6 p.1
REPORTED_BY Yang Yang
REPRODUCE_WITH bug17.sh
REPRODUCE_ON any
CLOSED_DATE 2/27/02
CLOSED_XREF STL6 p.1
CLOSED_ACTION modifications to hmmsearch.c; see notes.
//
ID 18
STATUS closed
DESCRIPTION HMMs differ when built from mul vs. Stockholm format
NOTED_DATE 3/16/02
NOTED_XREF STL6 p.12
REPORTED_BY Sam Griffiths (sjg@sanger.ac.uk)
REPRODUCE_WITH bug18.sh - was deleted from CVS.
REPRODUCE_ON Alpha (waterbug)
CLOSED_DATE 3/29/02
CLOSED_XREF STL6 p.12
CLOSED_ACTION Not a bug.
//
ID h19
TITLE floating point exception on Alpha/Linux
STATUS CLOSED
XREF none
REPORTED_BY "Yungok S. Ihm" <youngok@iastate.edu>
CLOSED_DATE SRE, Fri May 9 15:31:23 2003
DESCRIPTION
hmmpfam crashes on extremely low scoring hits (<-1000),
on Alpha/Linux. Appears in both 2.2g and 2.3dev.
mathsupport.c:PValue() doesn't check for underflow before
calling sreEXP2() on the score; the Alpha crashes on this.
No test case built for bugs.sqc.
//
ID h20
TITLE hmmpfam E-values dependent on # of threads.
STATUS CLOSED
XREF STL7 p.70
REPORTED_BY Robert A. Wilson <robwilso@us.ibm.com>
CLOSED_DATE SRE, Fri Jun 6 18:56:43 2003
DESCRIPTION
Original report cited difference in E-values between
IBM 2.2g binaries and 2.3 binaries. Investigation shows
problem is really in both: # of threads is added to
nhmms, and counted as Z, so E-values end up depending
on thread #. (IBM 2.2g binaries weren't compiled w/ threads,
hence the difference seen by IBM.) In hmmpfam.c:worker_thread(),
we were bumping nhmm++ before successfully reading the HMM,
so on normal exit, each thread bumps nhmm one extra time after
the HMM file is emptied.
To reproduce: hmmpfam --cpu 0 <any hmm> <any seq> vs.
hmmpfam --cpu <n> <any hmm> <any seq>
should give identical E-values.
Fixed; verified on Intel/Linux.
No test case built for bugs.sqc.
//
ID h21
TITLE "make install" doesn't create target directories
STATUS CLOSED
XREF STL7 p.70
REPORTED_BY Gisle Slensminde <gisle@ii.uib.no> [10 Jun 2003]
CLOSED_DATE SRE, Thu Jun 12 12:37:54 2003
DESCRIPTION
"make install" doesn't create target directories if they
don't exist, and fails w/ poor error message. Added and documented
mkdir -p steps in Makefile.in
//
ID h22
TITLE hmmpfam crash related to resizing DP matrix
STATUS CLOSED
XREF STL7 p.70
REPORTED_BY James Cuff <james@sanger.ac.uk> 12 June 2003
CLOSED_DATE SRE, Fri Jun 13 14:56:42 2003
DESCRIPTION
hmmpfam crashes on Pfam_ls.
Problem is with reallocation in ResizePlan7Matrix(), when it
is called with N < maxN - it didn't reinitialize ptrs up to
maxN, it only did it up to N.
//
ID h23
TITLE Does not compile w/ --enable-pvm
STATUS CLOSED
XREF STL7 p.71
REPORTED_BY Goran Ceric <goran@genetics.wustl.edu> 12 June 2003
CLOSED_DATE SRE, Fri Jun 13 14:57:58 2003
DESCRIPTION
Didn't compile w/ PVM support, because of #define name changes
in 2.3.
//
ID h24
TITLE Does not use CPPFLAGS, LDFLAGS in environment
STATUS CLOSED
XREF STL7 p.71
REPORTED_BY Ajay Khanna <askhanna@genetics.wustl.edu> 13 June 2003
CLOSED_DATE SRE, Fri Jun 13 14:59:13 2003
DESCRIPTION
./configure claims to use CPPFLAGS, LDFLAGS from environment,
but doesn't.
//
ID h25
TITLE Memory-related hmmsearch crash on Swissprot.
STATUS CLOSED
XREF STL7 p.121
REPORTED_BY Niklaus Fankhauser <niklaus.fankhauser@izb.unibe.ch> 26 Sept 2003;
Kaivalya Dixit <dixit@austin.ibm.com>, 24 Sept 2003.
OPENED_DATE SRE, Tue Sep 30 14:53:19 2003
CLOSED_DATE SRE, Wed Oct 1 08:07:18 2003
DESCRIPTION
hmmsearch crashes unpredictably on Swissprot searches (EMBL
format).
AMD contributes an Insure++ report showing three problems:
1. Alphabet[] is not a string but is being passed to strchr();
2. readEMBL is looking for a \0 in a growing seq, but a growing
seq has no \0 until ReadSeq() polishes it off;
3. xmx[] is shown as a dangling/wild ptr in core_algorithms.c
and fast_algorithms.c.
AMD and/or Intel also indicate, via Kaivalya, that the problem
is in sqio.c: they explicitly nul-terminate after every reallocation
of the seq, and the problem disappears.
Fixed problems 1 and 2. Can't find the problem that Insure++ is
bitching about for 3; worrying. Bug goes away: it was clearly the result
of problem 2. Bugs in #1 should only appear for databases with
nonstandard residues.
//
ID h26
TITLE Memory crash in hmmpfam.
STATUS CLOSED
XREF STL7 p.122.
REPORTED_BY Gary Montry <montry@spsoft.com>, 15 Aug 2003.
OPENED_DATE SRE, Wed Oct 1 12:29:25 2003
CLOSED_DATE SRE, Thu Oct 2 11:20:00 2003
DESCRIPTION
hmmpfam search with 125,000aa sequence eventually crashes
because of lack of RAM, instead of successfully using small
memory routines.
Problem is that the code assumed that M,N can't both grow in
allocating a matrix, but that's not true in hmmpfam; after P7SmallViterbi(),
we may hand various sized bits of sequence off for subalignment,
with different sized models.
Wrote P7ViterbiSpaceOK(); used it instead of P7ViterbiSize() to switch
between normal and small variants; allow creation routine to grow in M
and N (padM and padN can both be positive); make initial allocs for
hmmpfam matrices to be 300x300, to avoid pathologically asymmetric
matrices.
//
ID h27
TITLE Negative element in dsq; char vs. unsigned char.
STATUS CLOSED
XREF STL7 p.123
REPORTED_BY Kaivalya Dixit <dixit@austin.ibm.com>, Sept 2003.
OPENED_DATE SRE, Thu Oct 2 2003
CLOSED_DATE SRE, Thu Oct 2 11:25:57 2003
DESCRIPTION
Turned up in SPEC certification process. Alan L. MacKay
<amackay@us.ibm.com>, of IBM AIX Compilers/Performance group, sends
an Insure++ report that shows a case where dsq[] was a negative
number. Kaivalya reports that they "fixed" this by forcing compilers
to use unsigned chars by default. A confusing discussion ensues;
MacKay thinks the problem is the use of char dsq[] as an array index,
whereas I think the code "guarantees" nonnegative dsq[] and that
there isn't a problem here; I think the crash IBM saw was coming
from memory corruption due to bug #h25.
Nonetheless, he has a point: if I'm going to use dsq[] as an array
index, it would be better coding practice to declare it as
unsigned char.
Changed dsq from char to unsigned char throughout (and some
instances of sym, symidx). Removed (int) casts whereever dsq[],
symidx were being used as array indices.
//
ID h28
TITLE P7Forward typo: bsc[M-1] should be bsc[M]
STATUS CLOSED
XREF STL7 p.123
REPORTED_BY Robel Kahsay <kahsay@mail.capsl.udel.edu>
CLOSED_DATE SRE, Fri Oct 3 12:48:50 2003
DESCRIPTION
Calculation of mmx[M] should touch bsc[M], not bsc[M-1].
//
ID h29
TITLE hmmsearch does not scale on SMP Xeons with hyperthreads
STATUS CLOSED
XREF notebook/0115-hmmer-bug-h29
REPORTED_BY Gordon Gremme <gremme@zbh.uni-hamburg.de>
OPENED_DATE SRE, Thu Jan 15 13:30:00 2004
CLOSED_DATE SRE, Thu Jan 15 15:43:25 2004
DESCRIPTION
See the notes [xref] for details.
This appears to be a Linux 2.4 SMP scheduler problem.
No action taken.
//
ID h30
TITLE get_wee_midpt crashes out if given seq of L=1
STATUS CLOSED
XREF 2004:1119-hmmer-bug-h30
REPORTED_BY James Stroud <jstroud@mbi.ucla.edu>
OPENED_DATE SRE, Fri Nov 19 13:28:55 2004
CLOSED_DATE SRE, Fri Nov 19 13:58:08 2004
DESCRIPTION
hmmpfam crashes on Pfam_fs w/ "FATAL: you can't init get_wee_midpt
with a T", on a long HMM Arena_RNA_pol.
The problem is that P7WeeViterbi() is called w/ subseq of L=1. The
init of P7WeeViterbi sets begin,end points initially to STS, STT;
but when 1==L, assignment of tassign[L] to STT clobbers tassign[1].
Fixing this properly will require rethinking get_wee_midpt carefully.
Instead, hack around it. P7WeeViterbi() is only called once, from
within P7SmallViterbi(). Insert an extra test; if sqlen==1, do not
call P7WeeViterbi(), instead allocate a tiny L=1 matrix and use
P7Viterbi().
Document P7WeeViterbi(): it can't take L=1.
//
Bugs/bug11.msf 0 → 100644
View file @ 92c90e8c
This diff is collapsed.
Bugs/bug12-ELAV_DROME 0 → 100644
View file @ 92c90e8c
>ELAV_DROME ELAV PROTEIN (EMBRYONIC LETHAL ABNORMAL VISUAL PROTEIN).
MDFIMANTGAGGGVDTQAQLMQSAAAAAAVAATNAAAAPVQNAAAVAAAA
QLQQQQVQQAILQVQQQQTQQAVAAAAAAVTQQLQQQQQAVVAQQAVVQQ
QQQQAAAVVQQAAVQQAVVPQPQQAQPNTNGNAGSGSQNGSNGSTETRTN
LIVNYLPQTMTEDEIRSLFSSVGEIESVKLIRDKSQVYIDPLNPQAPSKG
QSLGYGFVNYVRPQDAEQAVNVLNGLRLQNKTIKVSFARPSSDAIKGANL
YVSGLPKTMTQQELEAIFAPFGAIITSRILQNAGNDTQTKGVGFIRFDKR
EEATRAIIALNGTTPSSCTDPIVVKFSNTPGSTSKIIQPQLPAFLNPQLV
RRIGGAMHTPVNKGLARFSPMAGDMLDVMLPNGLGAAAAAATTLASGPGG
AYPIFIYNLAPETEEAALWQLFGPFGAVQSVKIVKDPTTNQCKGYGFVSM
TNYDEAAMAIRALNGYTMGNRVLQVSFKTNKAK
Bugs/bug12-minipfam 0 → 100644
View file @ 92c90e8c
This diff is collapsed.
Bugs/bug12.pl 0 → 100644
View file @ 92c90e8c
#! /usr/local/bin/perl
# Setting a --domE or --domT threshold that removes the second
# domain from:
# rrm 1/3 151 235 .. 1 72 [] 82.9 6.6e-21
# rrm 2/3 250 322 .. 1 72 [] 77.0 3.9e-19
# rrm 3/3 404 475 .. 1 72 [] 106.3 6e-28
# should not remove domain 3 too.
# SRE, Fri Dec 15 10:04:41 2000
#
$usage = "Usage: ./bug12.pl [BINARYPATH]\n";
$binpath = "";
if ($#ARGV > 0) { print $usage; exit 1; }
elsif ($#ARGV == 0) { $binpath = shift; }
$hmmpfam = "$binpath/hmmpfam";
print "Bug 12 ...\t";
$output = `$hmmpfam bug12-minipfam bug12-ELAV_DROME`;
if (! &hmmpfam_output_has_domain($output, "rrm", 151, 235)) { print("OOPS. er, something else is wrong (1).\n"); exit 1;}
if (! &hmmpfam_output_has_domain($output, "rrm", 250, 322)) { print("OOPS. er, something else is wrong (2).\n"); exit 1;}
if (! &hmmpfam_output_has_domain($output, "rrm", 404, 475)) { print("OOPS. er, something else is wrong (3).\n"); exit 1;}
$output = `$hmmpfam --domE 9e-24 bug12-minipfam bug12-ELAV_DROME`;
if (! &hmmpfam_output_has_domain($output, "rrm", 151, 235)) { print("OOPS. er, something else is wrong (4).\n"); exit 1;}
if (! &hmmpfam_output_has_domain($output, "rrm", 404, 475)) { print("DETECTED! (1)\n"); exit 1;}
$output = `$hmmpfam --domT 80 bug12-minipfam bug12-ELAV_DROME`;
if (! &hmmpfam_output_has_domain($output, "rrm", 151, 235)) { print("OOPS. er, something else is wrong. (5)\n"); exit 1;}
if (! &hmmpfam_output_has_domain($output, "rrm", 404, 475)) { print("DETECTED! (2)\n"); exit 1;}
print "not detected.\n";
exit 0;
sub
hmmpfam_output_has_domain {
my $output = shift;
my $domain_name = shift;
my $domain_start = shift;
my $domain_end = shift;
foreach $line (split(/^/, $output)) {
if ($line =~ /^Parsed for domains/) { $in_domains = 1; }
if ($in_domains &&
$line =~ /^${domain_name}\s+\S+\s+${domain_start}\s+${domain_end}\s/)
{ return 1; }
if ($line =~ /^Alignments of top-scoring/) { break; }
}
return 0;
}
Bugs/bug13-mixed1.hmm 0 → 100644
View file @ 92c90e8c
HMMER2.0 [2.1.4]
NAME dna
LENG 16
ALPH Nucleic
RF no
CS no
MAP yes
COM ../binaries/hmmbuild -F dna.hmm dna.slx
NSEQ 5
DATE Sun Dec 24 11:21:23 2000
CKSUM 9400
XT -9967 -1 -1000 -1000 -9967 -1 -9967 -1
NULT -1 -9967
NULE 0 0 0 0
HMM A C G T
m->m m->i m->d i->m i->i d->m d->d b->m m->e
-222 * -2807
1 1415 -1170 -1170 -1170 1
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 -222 *
2 -1170 1415 -1170 -1170 2
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
3 -1170 -1170 1415 -1170 3
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
4 -1170 -1170 -1170 1415 4
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
5 1415 -1170 -1170 -1170 5
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
6 -1170 1415 -1170 -1170 6
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
7 -1170 -1170 1415 -1170 7
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
8 -1170 -1170 -1170 1415 8
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
9 1415 -1170 -1170 -1170 9
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
10 -1170 1415 -1170 -1170 10
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
11 -1170 -1170 1415 -1170 11
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
12 -1170 -1170 -1170 1415 12
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
13 1415 -1170 -1170 -1170 13
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
14 -1170 1415 -1170 -1170 14
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
15 -1170 -1170 1415 -1170 15
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
16 -1170 -1170 -1170 1415 16
- * * * *
- * * * * * * * * 0
//
HMMER2.0 [2.1.4]
NAME protein
LENG 20
ALPH Amino
RF no
CS no
MAP yes
COM ../binaries/hmmbuild -F protein.hmm protein.slx
NSEQ 5
DATE Sun Dec 24 11:21:58 2000
CKSUM 4510
XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4
NULT -4 -8455
NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644
HMM A C D E F G H I K L M N P Q R S T V W Y
m->m m->i m->d i->m i->i d->m d->d b->m m->e
-585 * -1585
1 2806 -444 -1270 -1265 -1732 -744 -1182 -1034 -1212 -1545 -1010 -869 -1380 -1102 -1325 -156 -259 -640 -2039 -1721 1
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 -585 *
2 -608 5196 -2368 -2362 -1635 -1253 -1702 -987 -2034 -1540 -1191 -1745 -1831 -1953 -1922 -934 -927 -770 -1855 -1692 2
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
3 -1130 -2063 3441 243 -2502 -1157 -662 -2514 -843 -2578 -2029 -96 -1658 -421 -1434 -970 -1239 -2138 -2388 -1915 3
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
4 -988 -1921 379 3052 -2309 -1196 -495 -2108 -350 -2194 -1612 -103 -1621 -210 -770 -862 -1042 -1799 -2207 -1742 4
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
5 -1601 -1340 -2512 -2455 3740 -2315 -379 -478 -2225 -175 -190 -1874 -2503 -1781 -2079 -1892 -1647 -683 210 1257 5
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
6 -759 -1104 -1314 -1488 -2461 3330 -1563 -2503 -1721 -2645 -2082 -1325 -1776 -1591 -1791 -959 -1094 -1922 -2199 -2280 6
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
7 -1192 -1547 -812 -781 -520 -1557 4586 -1881 -457 -1789 -1357 -866 -1913 -669 -600 -1231 -1258 -1678 -918 -90 7
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
8 -1016 -805 -2637 -2367 -591 -2470 -1853 3039 -2040 329 346 -2180 -2589 -1943 -2070 -1879 -1051 1184 -1698 -1261 8
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
9 -1028 -1686 -800 -442 -2171 -1521 -263 -1873 3103 -1859 -1251 -547 -1750 74 599 -1004 -972 -1620 -1812 -1528 9
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
10 -1369 -1199 -2542 -2295 -129 -2453 -1603 488 -1867 2607 742 -2168 -2539 -1724 -1835 -1992 -1384 130 -1284 -897 10
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
11 -965 -982 -2125 -1844 -276 -2022 -1302 373 -1390 610 4141 -1701 -2229 -1356 -1425 -1444 -1028 126 -1279 -880 11
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
12 -637 -1349 -5 -148 -1773 -1078 -624 -1965 -499 -2112 -1514 3456 -1574 -435 -810 -661 -818 -1560 -1900 -1327 12
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
13 -934 -1220 -1352 -1451 -2187 -1314 -1456 -2160 -1488 -2268 -1827 -1359 3760 -1471 -1571 -1129 -1216 -1780 -2050 -2023 13
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
14 -862 -1548 -321 -247 -1672 -1336 -419 -1721 130 -1660 -1161 -427 -1678 3540 -59 -855 -904 -1495 -1728 -1237 14
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
15 -1181 -1614 -1431 -903 -2066 -1632 -446 -1944 559 -1867 -1326 -899 -1873 -156 3432 -1225 -1148 -1717 -1746 -1529 15
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
16 116 -498 -840 -867 -1751 -671 -949 -1625 -916 -1896 -1218 -622 -1304 -824 -1097 2786 -220 -1038 -1992 -1530 16
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
17 -52 -555 -1173 -1112 -1571 -872 -1041 -862 -950 -1353 -866 -843 -1455 -937 -1084 -285 3069 -557 -1898 -1539 17
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
18 -700 -665 -2337 -2135 -873 -1965 -1727 1107 -1863 -105 22 -1851 -2286 -1794 -1920 -1368 -823 2927 -1816 -1362 18
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
19 -1926 -1577 -2416 -2370 192 -2070 -795 -1602 -1882 -1347 -1210 -2018 -2383 -1854 -1777 -2150 -1992 -1643 5696 560 19
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
20 -1667 -1473 -2001 -1964 1181 -2210 -25 -1224 -1658 -1018 -871 -1505 -2415 -1423 -1618 -1747 -1692 -1248 501 4149 20
- * * * * * * * * * * * * * * * * * * * *
- * * * * * * * * 0
//
Bugs/bug13-mixed2.hmm 0 → 100644
View file @ 92c90e8c
HMMER2.0 [2.1.4]
NAME protein
LENG 20
ALPH Amino
RF no
CS no
MAP yes
COM ../binaries/hmmbuild -F protein.hmm protein.slx
NSEQ 5
DATE Sun Dec 24 11:21:58 2000
CKSUM 4510
XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4
NULT -4 -8455
NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644
HMM A C D E F G H I K L M N P Q R S T V W Y
m->m m->i m->d i->m i->i d->m d->d b->m m->e
-585 * -1585
1 2806 -444 -1270 -1265 -1732 -744 -1182 -1034 -1212 -1545 -1010 -869 -1380 -1102 -1325 -156 -259 -640 -2039 -1721 1
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 -585 *
2 -608 5196 -2368 -2362 -1635 -1253 -1702 -987 -2034 -1540 -1191 -1745 -1831 -1953 -1922 -934 -927 -770 -1855 -1692 2
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
3 -1130 -2063 3441 243 -2502 -1157 -662 -2514 -843 -2578 -2029 -96 -1658 -421 -1434 -970 -1239 -2138 -2388 -1915 3
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
4 -988 -1921 379 3052 -2309 -1196 -495 -2108 -350 -2194 -1612 -103 -1621 -210 -770 -862 -1042 -1799 -2207 -1742 4
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
5 -1601 -1340 -2512 -2455 3740 -2315 -379 -478 -2225 -175 -190 -1874 -2503 -1781 -2079 -1892 -1647 -683 210 1257 5
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
6 -759 -1104 -1314 -1488 -2461 3330 -1563 -2503 -1721 -2645 -2082 -1325 -1776 -1591 -1791 -959 -1094 -1922 -2199 -2280 6
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
7 -1192 -1547 -812 -781 -520 -1557 4586 -1881 -457 -1789 -1357 -866 -1913 -669 -600 -1231 -1258 -1678 -918 -90 7
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
8 -1016 -805 -2637 -2367 -591 -2470 -1853 3039 -2040 329 346 -2180 -2589 -1943 -2070 -1879 -1051 1184 -1698 -1261 8
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
9 -1028 -1686 -800 -442 -2171 -1521 -263 -1873 3103 -1859 -1251 -547 -1750 74 599 -1004 -972 -1620 -1812 -1528 9
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
10 -1369 -1199 -2542 -2295 -129 -2453 -1603 488 -1867 2607 742 -2168 -2539 -1724 -1835 -1992 -1384 130 -1284 -897 10
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
11 -965 -982 -2125 -1844 -276 -2022 -1302 373 -1390 610 4141 -1701 -2229 -1356 -1425 -1444 -1028 126 -1279 -880 11
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
12 -637 -1349 -5 -148 -1773 -1078 -624 -1965 -499 -2112 -1514 3456 -1574 -435 -810 -661 -818 -1560 -1900 -1327 12
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
13 -934 -1220 -1352 -1451 -2187 -1314 -1456 -2160 -1488 -2268 -1827 -1359 3760 -1471 -1571 -1129 -1216 -1780 -2050 -2023 13
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
14 -862 -1548 -321 -247 -1672 -1336 -419 -1721 130 -1660 -1161 -427 -1678 3540 -59 -855 -904 -1495 -1728 -1237 14
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
15 -1181 -1614 -1431 -903 -2066 -1632 -446 -1944 559 -1867 -1326 -899 -1873 -156 3432 -1225 -1148 -1717 -1746 -1529 15
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
16 116 -498 -840 -867 -1751 -671 -949 -1625 -916 -1896 -1218 -622 -1304 -824 -1097 2786 -220 -1038 -1992 -1530 16
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
17 -52 -555 -1173 -1112 -1571 -872 -1041 -862 -950 -1353 -866 -843 -1455 -937 -1084 -285 3069 -557 -1898 -1539 17
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
18 -700 -665 -2337 -2135 -873 -1965 -1727 1107 -1863 -105 22 -1851 -2286 -1794 -1920 -1368 -823 2927 -1816 -1362 18
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
19 -1926 -1577 -2416 -2370 192 -2070 -795 -1602 -1882 -1347 -1210 -2018 -2383 -1854 -1777 -2150 -1992 -1643 5696 560 19
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -33 -6045 -7087 -894 -1115 -701 -1378 * *
20 -1667 -1473 -2001 -1964 1181 -2210 -25 -1224 -1658 -1018 -871 -1505 -2415 -1423 -1618 -1747 -1692 -1248 501 4149 20
- * * * * * * * * * * * * * * * * * * * *
- * * * * * * * * 0
//
HMMER2.0 [2.1.4]
NAME dna
LENG 16
ALPH Nucleic
RF no
CS no
MAP yes
COM ../binaries/hmmbuild -F dna.hmm dna.slx
NSEQ 5
DATE Sun Dec 24 11:21:23 2000
CKSUM 9400
XT -9967 -1 -1000 -1000 -9967 -1 -9967 -1
NULT -1 -9967
NULE 0 0 0 0
HMM A C G T
m->m m->i m->d i->m i->i d->m d->d b->m m->e
-222 * -2807
1 1415 -1170 -1170 -1170 1
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 -222 *
2 -1170 1415 -1170 -1170 2
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
3 -1170 -1170 1415 -1170 3
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
4 -1170 -1170 -1170 1415 4
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
5 1415 -1170 -1170 -1170 5
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
6 -1170 1415 -1170 -1170 6
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
7 -1170 -1170 1415 -1170 7
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
8 -1170 -1170 -1170 1415 8
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
9 1415 -1170 -1170 -1170 9
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
10 -1170 1415 -1170 -1170 10
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
11 -1170 -1170 1415 -1170 11
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
12 -1170 -1170 -1170 1415 12
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
13 1415 -1170 -1170 -1170 13
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
14 -1170 1415 -1170 -1170 14
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
15 -1170 -1170 1415 -1170 15
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
16 -1170 -1170 -1170 1415 16
- * * * *
- * * * * * * * * 0
//
Bugs/bug13.pl 0 → 100644
View file @ 92c90e8c
#! /usr/local/bin/perl
# Any program that reads multiple HMMs should refuse to
# deal with "mixed" databases of DNA and protein HMMs,
# because behavior will be undefined.
#
# First detected as an hmmconvert problem (by GCG's Christiane
# VanSchlun), and it's easiest to test there too. The other
# executables are not tested because they share the
# same mechanism (mixed HMMs are detected in hmmio.c).
#
$usage = "Usage: ./bug13.pl [BINARYPATH]\n";
$binpath = "";
if ($#ARGV > 0) { print $usage; exit 1; }
elsif ($#ARGV == 0) { $binpath = shift; }
$hmmconvert = "$binpath/hmmconvert";
print "Bug 13 ...\t";
# These two commands should fail with non-zero exit status.
#
$output = `$hmmconvert -F bug13-mixed1.hmm bug13.tmp 2>/dev/null`;
if ($? == 0) { print "DETECTED! (1)\n"; unlink "bug13.tmp"; exit 1; }
$output = `$hmmconvert -F bug13-mixed2.hmm bug13.tmp 2>/dev/null`;
if ($? == 0) { print "DETECTED! (2)\n"; unlink "bug13.tmp"; exit 1; }
print "not detected.\n";
unlink "bug13.tmp";
exit 0;
Bugs/bug14-ascii.hmm 0 → 100644
View file @ 92c90e8c
HMMER2.0 [2.1.4]
NAME dna
LENG 12
ALPH Nucleic
RF no
CS no
MAP yes
COM ../binaries/hmmbuild dna.hmm dna.slx
NSEQ 5
DATE Sun Dec 24 15:24:31 2000
CKSUM 8440
XT -9967 -1 -1000 -1000 -9967 -1 -9967 -1
NULT -1 -9967
NULE 0 0 0 0
HMM A C G T
m->m m->i m->d i->m i->i d->m d->d b->m m->e
-222 * -2807
1 1415 -1170 -1170 -1170 1
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 -222 *
2 -1170 1415 -1170 -1170 2
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
3 -1170 -1170 1415 -1170 3
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
4 -1170 -1170 -1170 1415 4
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
5 1415 -1170 -1170 -1170 5
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
6 -1170 1415 -1170 -1170 6
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
7 -1170 -1170 1415 -1170 7
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
8 -1170 -1170 -1170 1415 8
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
9 1415 -1170 -1170 -1170 9
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
10 -1170 1415 -1170 -1170 10
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
11 -1170 -1170 1415 -1170 11
- 0 0 0 0
- -10 -7714 -8756 -894 -1115 -701 -1378 * *
12 -1170 -1170 -1170 1415 12
- * * * *
- * * * * * * * * 0
//
Bugs/bug14.pl 0 → 100644
View file @ 92c90e8c
#! /usr/local/bin/perl
# hmmconvert should refuse to append ASCII HMMs to binary files,
# and vice versa.
# bug14-ascii.hmm - a small ascii HMM
# bug14-binary.hmm - a small binary HMM
$usage = "Usage: ./bug14.pl [BINARYPATH]\n";
$binpath = "";
if ($#ARGV > 0) { print $usage; exit 1; }
elsif ($#ARGV == 0) { $binpath = shift; }
$hmmconvert = "$binpath/hmmconvert";
print "Bug 14 ...\t";
# These two commands should fail with non-zero exit status.
#
# 1. An attempt to append binary to an existing ascii file.
system("cp bug14-ascii.hmm bug14.tmp");
$output = `$hmmconvert -Ab bug14-ascii.hmm bug14.tmp 2>/dev/null`;
if ($? == 0) { print "DETECTED! (1)\n"; unlink "bug14.tmp"; exit 1; }
# 2. An attempt to append ASCII (converted) to an existing binary file.
system("cp bug14-binary.hmm bug14.tmp");
$output = `$hmmconvert -A bug14-binary.hmm bug14.tmp 2>/dev/null`;
if ($? == 0) { print "DETECTED! (2)\n"; unlink "bug14.tmp"; exit 1; }
# These two commands should succeed with zero exit status.
#
# 3. An attempt to append ASCII (converted) to an existing ascii file
system("cp bug14-ascii.hmm bug14.tmp");
$output = `$hmmconvert -A bug14-binary.hmm bug14.tmp 2>/dev/null`;
if ($? != 0) { print "DETECTED! (3)\n"; unlink "bug14.tmp"; exit 1; }
# 4. An attempt to append binary (converted) to an existing binary file
system("cp bug14-binary.hmm bug14.tmp");
$output = `$hmmconvert -Ab bug14-ascii.hmm bug14.tmp 2>/dev/null`;
if ($? != 0) { print "DETECTED! (4)\n"; unlink "bug14.tmp"; exit 1; }
print "not detected.\n";
unlink "bug14.tmp";
exit 0;
Bugs/bug17.sh 0 → 100644
View file @ 92c90e8c
#! /bin/sh
# Exercises and tests bug #17.
# CVS $Id$
../binaries/shuffle -i -n 100 -t 200 --amino > bug17.fa
../binaries/hmmsearch ../testsuite/fn3.hmm bug17.fa > bug17.out1
../binaries/hmmsearch --cpu 0 ../testsuite/fn3.hmm bug17.fa > bug17.out2
diff bug17.out1 bug17.out2
if (test $? != 0) then
echo "FAILED: threaded/nonthreaded hmmsearch identity test (bug 17)"
fi
rm bug17.fa bug17.out1 bug17.out2
\ No newline at end of file
Bugs/bug2-S30431.fa 0 → 100644
View file @ 92c90e8c
>S30431 MSP-300 protein - fruit fly (Drosophila melanogaster)
EFPEGELRTTSLPVLEEQLAHYKKLLSDAENKGGLINDVSEQGKSILPTL
SNADKLKLNDDIKNMKDRYGRIKNTIDDRVNALGDHIKKYKDAKSRLAEC
SQFLGNIQQKLRELNRPIGSRIEDVQDLLGAYEGILKELKDSKSKMGDMQ
MDDLPELQSILAQQDDMIKLIEDQLAHLRQLLLLREQFIALINEIIAFIM
KYTDVIIDIENSPDSLEDKINKYDDVIVKIQECEGVLASANDKGQKIASE
GNAADKNSITEQLQSLKNQLQNLRKAVESQRQKHQLQLESHKKMAAELSE
ILDWLHSHEGAAKSRPLLDRDPESVERDVQKHQSLSQDIESYLNKFNKIN
DGVKTEIGMPSSLLEMLSEGRSLVASLPHELEEREKYLKNNRDSRLEYMQ
LVAKFNDWVHEAELRLQNSQHGIDYEHLVQDLDEHKIFFGNEAPIRNLVH
KQIQEAADKIWSSLNNYEQSELSAELAQFQTKLTNTLANAKTQQSELEKE
AERGGNTNSQSIASRPPSNVPSSLMSPSKIWLDSTSISRSCRTPLASVQS
QNSDLTLVNQQAQSLIRQADARNRQLIEQDNAGLNRSWQDLVRTLEQRRD
NLQQLAEHWDGFENSLHAWEKALGRLEDKFRNVDPTVRSRRHLEDTKNAI
QELREESNQLKSSHKEIEALSKSILTFLGEVHKPSAEAIQAKVDKLVEQQ
AKLNDTLRDKEQQVSKDLEEIEQVFRRISQLQDKLNALHEQLQSVHVYDE
HIAQTEQLLITLNSQVQQAAEESKLLVAQTTAHYQAKQNQLPSDIAQEFT
ALELLAERVQVTMETKEKDFKRAKTVRTEYVDGVDEVQRWLLQAEVQVQE
RSLTPTQMKELLQRINHEITAIYERFTLVKTNGQLIIENCRNSEEKTLVQ
TTIDQLAASLAQVRGWLDEKKQAVGDSLDASTRFMNLYQIVMSWASEKRN
FTDQTIELRTLPEARNKLNDYVTSVKSIKPIVKHLSEMDKELEHIGQVTT
VGDLKDKLQEAEDAKISVEAVLLERNSLLQEACEEWDQCERKIKDIRSWH
EKTKQGLDSSQQQKKPLRDQLGFCEKTLADINVQKTKLRLSIEKLEVHFR
NGMGGDPRLSENVDDLVRVLDGLGELVKAKSQSLEQTLAQIDVYQQQMQS
LRQRIIQEEQHVRLVMAPTYLPHDASAH
Bugs/bug2-spectrin.hmm 0 → 100644
View file @ 92c90e8c
This diff is collapsed.
Bugs/bug2.pl 0 → 100644
View file @ 92c90e8c
#! /usr/local/bin/perl
# The sum of domain hits should equal the total sequence score.
# Else, it's possible to have a sequence that actually scores
# *less* than some of its individual domains... such as
# the example in the bug 2 report, Pfam's spectrin HMM vs.
# S30431.
#
# xref STL3 notebook p. 127.
# SRE, Tue Dec 19 14:47:30 2000
use hmmer;
$usage = "Usage: ./bug2.pl [BINARYPATH]\n";
$binpath = "";
if ($#ARGV > 0) { print $usage; exit 1; }
elsif ($#ARGV == 0) { $binpath = shift; }
$hmmpfam = "$binpath/hmmpfam";
$hmmsearch = "$binpath/hmmsearch";
print "Bug 2 ...\t";
$output = `$hmmpfam -E100 bug2-spectrin.hmm bug2-S30431.fa`;
&hmmer::ParseHMMER($output);
$seqsc = $hmmer::seqscore{"spectrin"};
$sum_of_domains = 0.;
foreach $sc (@hmmer::domscore) { $sum_of_domains += $sc; }
if (abs($sum_of_domains-$seqsc) >=0.1) { print "DETECTED! (1)\n"; exit 1;}
$output = `$hmmsearch -E100 bug2-spectrin.hmm bug2-S30431.fa`;
&hmmer::ParseHMMER($output);
$seqsc = $hmmer::seqscore{"S30431"};
$sum_of_domains = 0.;
foreach $sc (@hmmer::domscore) { $sum_of_domains += $sc; }
if (abs($sum_of_domains-$seqsc) >= 0.1) { print "DETECTED! (2)\n"; exit 1;}
print "not detected.\n";
exit 0;
Bugs/bug22.hmm 0 → 100644
View file @ 92c90e8c
This diff is collapsed.
Bugs/bugs.sqc 0 → 100644
View file @ 92c90e8c
# HMMER bug reproduction exercises, in sqc command format
#
# ../ssdk/sqc 2 bugs.sqc . ../src ../squid
#
# SRE, Thu Jun 12 14:19:11 2003
# CVS $Id$
# bug #h22: hmmpfam crash, reallocation problem.
#
1 prep h22-seq @shuffle@ -i -n 1 -t 2000 --amino -o %H22.seq%
1 exercise h22 @hmmpfam@ bug22.hmm %H22.seq%
\ No newline at end of file
Bugs/hmmer.pm 0 → 100644
View file @ 92c90e8c
# @LICENSE@
# hmmer.pm
# Perl routines for parsing HMMER output
#
# SRE, Wed Oct 28 11:27:17 1998
# CVS $Id$
package hmmer;
#------------ ParseHMMER ------------
#
# Parse hmmsearch or hmmpfam output into
# arrays that we can use in perl scripts.
#
# Nothing fancy, we just put the info into
# module-specific variables, expecting that we'll just
# be writing small scripts with this module.
#
# Illustrative example:
# use hmmer;
# $output = `hmmsearch foo.hmm swissprot36`;
# &hmmer::ParseHMMER($output);
# printf "The top scoring sequence is %s\n", $hmmer:targname[0];
# printf "The total number of domains hit is %d\n", $hmmer::ndom;
#
# Data made available:
# $query - name of query HMM or sequence, e.g. "rrm"
# $querydesc - description of query, e.g. "RNA recognition motif"
#
# $ntarget - total number of targets hit in per-seq output
# @targname - array of target names (e.g. RU1A_HUMAN)
# %targdesc - target descriptions (indexed by target name)
# %seqscore - per-seq score (indexed by target name)
# %seqeval - per-seq E-value (indexed by target name)
# %seqndom - number of domains hit (indexed by target name)
#
# $ndom - total number of hits in domain output
# @domname - target names hit e.g. $domname[0] = "RU1A_HUMAN"
# @domnum - e.g. "1/2"
# @domsqfrom - sequence from coords (start positions)
# @domsqto - sequence to coords (end positions)
# @domsqbounds - e.g. "[]" or ".." for seq
# @domhmmfrom - array of hmm-from coords
# @domhmmto - array of hmm-to coords
# @domhmmbounds - e.g. "[]" or ".." for HMM
# @domscore - domain scores
# @domevalue - domain E-values
#
# $aligndata - the raw alignment text (currently not parsed further)
#
sub ParseHMMER {
my($output) = @_;
my($indom, $inseq, $inali);
my(@lines, $line);
$query = "";
$querydesc = "";
$ntarget = 0;
@targname = ();
%targdesc = ();
%seqscore = ();
%seqeval = ();
%seqndom = ();
$ndom = 0;
@domname = ();
@domnum = ();
@domsqfrom = ();
@domsqto = ();
@domsqbounds = ();
@domhmmfrom = ();
@domhmmto = ();
@domhmmbounds= ();
@domscore = ();
@domevalue = ();
$aligndata = "";
@lines = split(/^/, $output);
$ndom=0;
$ntarget=0;
foreach $line (@lines)
{
if ($line =~ /^Query:\s+(\S+)\s+(.+)$/) {$query = $1; $querydesc = $2;}
if ($line =~ /^Scores for/) {$indom = 0; $inseq = 1;}
if ($line =~ /^Parsed for domains/) {$indom = 1; $inseq = 0;}
if ($line =~ /^Histogram of all scores/) {$indom = 0; $inseq = 0; $inali = 0; }
if ($line =~ /^Alignments of top-scoring/) {$inali = 1; $indom = 0; $inseq = 0; }
if ($inseq && $line =~ /^\s*(\S+)\s+(.+?)\s+(\S+)\s+(\S+)\s+(\d+)\s*$/)
{
$targname[$ntarget]= $1;
$targdesc{$1} = $2;
$seqscore{$1} = $3;
$seqeval{$1} = $4;
$seqndom{$1} = $5;
$ntarget++;
}
if ($indom && $line =~ /^\s*\S+\s+\d+\/\d+/)
{
($domname[$ndom],
$domnum[$ndom],
$domsqfrom[$ndom],
$domsqto[$ndom],
$domsqbounds[$ndom],
$domhmmfrom[$ndom],
$domhmmto[$ndom],
$domhmmbounds[$ndom],
$domscore[$ndom],
$domevalue[$ndom]) = split ' ', $line;
$ndom++;
}
if ($inali) { $aligndata .= $line; }
}
1;
}
1;
COPYRIGHT
View file @ 92c90e8c
HMMER - Biological sequence analysis with profile hidden Markov models
Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
Copyright (C) 1992-2006 HHMI Janelia Farm
This suite of programs is free software. You can redistribute it
and/or modify it under the terms of the GNU General Public License as
......@@ -20,8 +20,8 @@ license, or the Netscape Public License), please contact me
Incorporation into commercial software under non-GPL terms is possible
by obtaining a specially licensed version from Washington University
School of Medicine. Contact Jack Pincus (jhpincus@cris.com) to arrange
licensing terms.
School of Medicine. Contact Tom Hagerty (HagertyT@otm.wustl.edu) at
our Office for Technology Management to arrange licensing terms.
This software is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
......