Version 2.6.0
Added twofeat - Finds neighbouring pairs of features in sequences
Extractfeat - added option (-featinname) to include the name of
the feature as part of the ID name of the sequence that is
written out.
Added sirna - designs siRNA probes in mRNA
Sigcleave sorts results highest score first
Helixturnhelix sorts results highest score first and reports the
score position as an integer
Added pestfind
Moved the following programs into the "domainatrix" embassy
package:
contacts, domainer, fraggle, hetparse, hmmgen, interface,
pdbparse, pdbtosp, profgen, scopalign, scopnr, scopparse,
scoprep, scopreso, scopseqs, seqalign, seqnr, seqsearch,
seqsort, seqwords, siggen, sigplot, sigscan
Palindrome no longer reports palindromes that are only composed
of N's
Msbar can now check that the result doesn't match a set of
input other sequences. For example you could specify that it
doesn't match the input sequence or a set of previously produced
mutation results.
Getorf reporting of circular genome positions tidied up - it now
reports positions starting in the range 1 to the sequence length
and indicates if the ORF goes through the breakpoint. A clear
indication of when ORFs are in the reverse sense has been added.
Pasteseq now behaves correctly when -sask2, -sbegin2 or -send2
are used.
Version 2.5.1
Whichdb new option -showall to see which databases are being
searched for use where searches hang. The order of searching is
undefined - it depends on the order in which databases are
returned from the internal table, which is unrelated to the order
in which they were defined.
Wordmatch alignments save the entire sequence but use part only.
Fixed all alignment formats to work with these by adding a
SubOffset attribute.
Duplicate IDs fix. The database indexing programs skipped
duplicate IDs but did not reset the size of the entryname index
file so some queries could fail to find the later IDs in the
databases. Duplicate IDs are illegal for -nosystemsort (no easy
way to correct because entry numbers are stored internally). For
the default case duplicate IDs are merged even if they are
different. REFSEQ is the main problem area.
Writing data files used EMBOSS_DATA, or by default the install
directory. Earlier versions, if not installed, could write to the
source tree emboss/data directory. Fixed to continue if there is
no install data directory, and to check EMBOSS_DATA (if defined) is
a real directory.
sigcleave options pval and nval hardcoded. They depend on the
weight matrix size - which is hardcoded as 15 in the ACD file and
is not checked in the program. They were introduced in EGCG in
1988 but never used because no other weight matrix length was
tried.
Version 2.5.0
"fasta" format now uses the "ncbi" parser, so both formats report
"fasta" as the format. "pearson" is the old "fasta" format for a few
cases (empty IDs for example) there ncbi parsing fails completely.
SPLITTER changed to match documentation. Old behaviour is
now selectable by using the -addoverlap command line
option.
Configuration modifications. --without-x works. Removed odd
but harmless -I definitions. PNG detection improved.
Corrected EMBLCD index searching for queries that start with a
wildcard. For example, tembl-key:?* should search for all entries
that have a keyword (key:* is regarded as 'all entries'). Entries
with no keyword (in PIR's pir4.ref file for example) will be
ignored.
Updated source code docs for EFUNC and EDATA. Corrected all bad
headers. efunc.out has no errors. efunc.check only reports
'missing headers' for duplicated function names (#ifdef code)
which is a known 'feature'.
Updated source code to fix most lines over 80 bytes.
Calculated ACD attributes now QA tested. Feature attributes will
be correctly set, although none are used in the ACD files at present.
purify.pl has a new option -block=n where n is a number from 1
upwards. 1 runs the first 10 tests, 2 runs the next 10
(blocksize=10 is hardcoded for now).
Cleaned up string position code. Inspections showed ajStrPos and
related functions gave results from 0 to length of a string. This
caused confusion in many other functions and applications. These
functions are now static strPos functions because only ajstr.c had
calls to them (though the ajStrPos versions are still available).
All calls were checked for positions out of range. As a result,
many calls to ajStrAssSub and AjStrCut were fixed. ajStrInsertC
requires a value from 0 to length (start position to insert can be
before or after the string, or any position in bwteen). Fixed by
passing length+1 to strPosII.
Added a functions ajUtilCatch for use in debugging with gdb. When
a nasty special case occurs, call ajUtilCatch and make it a
breakpoint in gdb. The resulting backtrace will give the call stack
and all variable values.
Cleaned up code for chunk HTML input. Added a new variable
EMBOSS_HTTPVERSION which defaults to 1.0 (so HTTP is not chunked)
and a DB attribute httpversion. This must be a floating point
number, and is included in the HTTP header to specify the HTTP
protocol version to be used. There is no check in the code to
change behaviour for different versions. This is used in the
SRSWWW and URL access methods.
Added check to qatest.pl to report any EMBOSS (rather than
EMBASSY) applications for which there is no defined test. The
EMBASSY test uses wossname results, checked against the names of
ACD files in the source tree, as qatest always runs in the test/qa
directory.
Allowed sequences as values for EMBL rpt_unit feature qualifiers
because so many entries have them. They are illegal according to
the Version 4.0 (current) feature table document.
Allow ? before from and to feature locations in SwissProt. For
now, these are ignored, though we could add something to hold them
for accurate output.
Added modified Harrison solubility probability to PEPSTATS
ACD attributes now have descriptions in the ajacd.c code which are
reported by 'entrails'. All ACD attributes have been checked by
inspection of the code to note those which are used/unused by ACD.
The ACD "type" attribute for files is renamed "standardtype" to
reflect its intended use to note standard file types for linking
applications. Sequences and alignments still have a "type"
attribute for protein or dna sequence types.
aaindexextract (new) reads the AAINDEX database and writes each
entry to data/AAINDEX directory. New function ajFileDataDirNew to
read data files from a named directory. New ACD datafile attribute
'directory' passed to ajFileDataDirNew. AAINDEX directory defined
for pepwindow and pepwindowall.
palindrome can now read in multiple sequences
palindrome now does not print a '|' in an alignment where there
is a mismatched pair of bases.
Added filelist datatype to ACD
mwcontam program added. Displays molecular weights that are common
across a set of files.
showfeat - added '-sort join' to display joined features on one line.
diffseq - don't give summary of SNPs if the sequences are proteins.
Inclusion of stat64 and readdir64 for offsetbits=64 (ajfile.c
and ajsys.c)
Workaround for broken Solaris readdir64_r (jembossctl)
infoseq can now optionally display GI and Sequence Version numbers.
notseq can now read in a file of sequence names.
Added '-alternative' qualifier to transeq to allow reverse frame
translations to be done using the codons counted from the start
of the reversed sequence, rather than, by default, using the
codons of the corresponding forward frame.
Added the qualifier '-join' to the program extractfeat.
If '-join' is set then joined features, such as 'CDS' and 'mRNA'
are output as a single concatenated sequence.
Changed the default output filename from 'stdout' to a file for
the following:
infoalign
megamerger
merger
showalign
showfeat
showseq
textsearch
Lindna/cirdna can now draw filled boxes and the user can change the
text size on the command-line. They can also read and display
complete genomic sequences.
Major new revision of protein structure applications - w/o full
documentation.
New applications have been added:
pdbparse.c / acd
scopseqs.c / acd
scopnr.c / acd
seqsearch.c / acd
seqwords.c / acd
seqalign.c / acd
hetparse.c / acd
scopreso.c / acd
scoprep.c / acd
profgen.c / acd
funky.c / acd
hmmgen.c / acd
fraggle.c / acd
Some applications have been deleted:
scope.c / acd
nrscope.c / acd
psiblasts.c / acd
swissparse.c / acd
alignwrap.c / acd
dichet.c / acd
The deleted applications have been replaced as follows:
coordenew --> pdbparse (coordnew was deleted a while back)
scope --> scopparse
nrscope --> scopnr
psiblasts --> seqsearch
swissparse --> seqwords
alignwrap --> seqalign
New versions of code have been committed:
pdbparse.c / acd
domainer.c / acd
contacts.c / acd
interface.c / acd
pdbtosp.c / acd
scopparse.c / acd
scopreso.c / acd
scopseqs.c / acd
scopnr.c / acd
scoprep.c / acd
scopalign.c / acd
seqsearch.c / acd
seqwords.c / acd
seqsort.c / acd
seqnr.c / acd
seqalign.c / acd
siggen.c / acd
sigscan.c / acd
sigplot.c / acd
hetparse.c / acd
profgen.c / acd
funky.c / acd
hmmgen.c / acd
Plus
ajxyz.c / ajxyz.h
Short summaries of the applications are as follows:
pdbparse - Parses pdb files and writes cleaned-up protein
coordinate files.
domainer - Reads protein coordinate files and writes
domains coordinate files.
contacts - Reads coordinate files and writes files of
intra-chain residue-residue contact data.
interface- Reads coordinate files and writes files of
inter-chain residue-residue contact data.
pdbtosp - Convert raw swissprot:pdb equivalence file to
embl-like format.
scopparse- Converts raw scop classification files to a
file in embl-like format.
scopreso - Removes low resolution domains from a scop
classification file.
scopseqs - Adds pdb and swissprot sequence records to a
scop classification file.
scopnr - Removes redundant domains from a scop
classification file.
scoprep - Reorder scop classificaiton file so that the
representative structure of each family is
given first.
scopalign- Generate alignments for families in a scop
classification file by using STAMP.
seqsearch- Generate files of hits for families in a scop
classification file by using PSI-BLAST with
seed alignments.
seqwords - Generate files of hits for scop families by
searching swissprot with keywords.
seqsort - Reads multiple files of hits and writes a
non-ambiguous file of hits (scop families file)
plus a validation file.
seqnr - Removes redundant hits from a scop families file.
seqalign - Generate extended alignments for families in
a scop families file by using CLUSTALW with seed
alignments.
siggen - Generates a sparse protein signature from an
alignment and residue contact data.
sigscan - Scans a signature against swissprot and writes
a signature hits files.
sigplot - Reads a signature hits file and validation file
and generates gnuplot data files of signature
performance.
profgen - Generates various profiles for each alignment
in a directory.
hmmgen - Generates a hidden Markov model for each alignment
in a directory.
hetparse - Converts raw dictionary of heterogen groups to
a file in embl-like format.
funky - Reads clean coordinate files and writes file
of protein-heterogen contact data.
Updated "make check" program entrails. Corrected sequence format
reports, added report and alignment formats and database access
methods.
Added scripts/logreport1.pl to report EMBOSS usage from the
logfile. Takes the logfile name on the command line. Reports
total use, most active user, and total user count.
extractseq now only reads one sequence as input.
Version 2.4.1
Fixed error reading multiple databases
Fixed MacOSX reading of incomplete sequence files
Fixed indexing of REFSEQ
Version 2.4.0
New Jemboss authorising server code. This uses a new set-uid
program (jembossctl) to perform tasks as the user.
New alignment output format "match" for wordmatch, reports the
length, sequence names, and range in each sequence.
emboss.default.template has been changed to include the new SRSWWW
access method and the fields definitions for the test databases.
In dbiblast, renamed the -filename option -filenames to match the
other dbi indexing programs, and because wildcard filenames are
supported.
Removed the -staden option for the dbi indexing programs. This had
no efect (it was originally included to rename files as
division.lookup for use by internal utilities at the Sanger
Centre).
In qatest.pl test script, added test for missing expected file.
Only seen for obsolete secondary output files, no tests were passing
that should have failed.
Script (scripts/dbilist.pl) to report the contents of EMBLCD
database indices created by dbiflat, dbigcg, dbifasta or dbiblast.
Proxy HTTP access for remote servers. Define EMBOSS_PROXY as an
environment variable, or in emboss.defaults. Can also be set for
any database as proxy: "hostname:port" or overridden with
proxy: ":" to use a local server for a database. This is used by
both the URL and SRSWWW access methods.
New ajListUnique function to remove duplicate nodes in a list.
New embxyz.c / .h embXyzSeqsetNRRange functions added
Report format "table" is the default for several applications. In
this format, the sequence USA has been removed because it already
appears in the sequenec header part of the report. A new format
"-rformat nametable" will produce the previous report output for
users who are relying on parsing it.
Output files defined with the "nullok" attribute in ACD are not
created unless requested. The file name and extension are ignored.
It is possible to add a new associated qualifier to control this
behaviour, but its use may be confusing with more than one output
file.
Precision attribute for report score (default is 3). Other
floating point report values are written as strings by the
original application so their precision is defined in the
code. The score is a float, as part of the internal (GFF) feature
structure. A zero value produces an integer score (strictly, it
uses %.0f as the format). Set precision for etandem, fuzznuc,
fuzzpro, fuzztran, patmatdb, patmatmotifs (integer scores) and
restrict (no score)
Report output for equicktandem and etandem, with -origfile to
write the original output format for sites (Sanger for example)
who still require it. By default, the origfile output file is
not created.
Report output for patmatdb and patmatmotifs. For patmatmotifs the
prosite documentation appears in the report footer, with the
addition of the motif name and the number of matches in the
sequence.
Report headers and footers automatically trim last newline.
Reports in -rformat SeqTable right-align numbers.
Report output for marscan (-rformat GFF by default)
Report output for fuzztran (-rformat table with the translation
included as a report field). Using -rformat seqtable with fuzztran
now also shows the original DNA sequence.
Report output for fuzznuc and fuzzpro (-rformat SeqTable by default)
New report qualifiers -raccshow to include accession in header
and -rdesshow to include description in header
Two access methods "file" and "offset" were defined as valid in
database definitions, but are really reserved for simple file reading.
They are removed from the database access methods list.
Two access methods "cmd" and "nbrf" are obsolete (cmd was never
implemented, nbrf is replaced by gcg which includes a query
mechanism). Both are removed from the database access methods list,
and the source code is commented out.
SRS, SRSFASTA and SRSWWW database access can read all entries This
is not recommended for SRSWWW access because it will read
everything into memory - all of EMBL for example - then strip out
HTML tags before reading. For SRS it is not recommended because
"methodall: direct" is faster. For SRSFASTA it is necessary
because using SRSFASTA implies EMBOSS does not read the original
data format. However, not iomplementing an "all" search left a gap
in the SRS access methods which would generate a bad SRS command
line or URL.
NBRF sequence reading trims last character only if it is '*'
to catch cases where SRS reports the sequence as 'plain'
GCG database text has the spaces in ". ." strings removed.
Database entry text and sequence saved for binary formats (GCG, BLAST)
for use by entret and other applications
dbiblast indices with split databases (formatdb -v) fixed for reading
all entries (was only reading the first file)
dbiblast and dbigcg indices support exclude and file definitions
to create database subsets
Database include and file definitions can use the simple filename.
In some cases the full path was used. Database files are checked
both with and without the directory path for back-compatibility.
srswww access method created to query a remote web server.
Preferred to using URL access as SRS queries can be built
Sequence objects include the SeqVersion, Keyword list and Taxonomy
list.
The GI number is read as an alternative SeqVersion where it is
available (GenBank and some NCBI formats). The GI number is
reported in GenBank format if available, but the GenBank VERSION
line may have only the SeqVersion if, for example, the sequence
was reead from an EMBL entry. "sv" queries check both the
SeqVersion and GI number.
Accession numbers have a strict definition, which covers the old
and new EMBL/GenBank format, SwissProt, PIR, and REFSEQ
(NM_nnnnnn). Earlier versions would accept any "accession number"
in some sequence formats, especially NCBI format.
SeqVersion (EMBL SV line, GenBank VERSION line) is used in preference
to accession number where available. Can also be read in FASTA
and NCBI formats. Where only the SeqVersion is available, the
accession number is generated.
USA queries implement searches by SV, DES, ORG and KEY. These work
with SRS access methods (SRS, SRSFASTA, SRSWWW) by building SRS
queries, and with direct access (simple file reading) by
testing the sequence object.
Key and Org queries are for full keywords (including spaces) and
for each level of the taxonomy.
Des queries, if the access method does not provide a mechanism,
(if the access method does not have its own index) are applied to
words within the description. Words start with a letter or number,
and end with a letter or number. SRS typically does the same, but
allows a single quote at the end. This catches words such as 3'
and 5' but is a problem with some quoted text.
Queries for ID ACC SV DES ORG and KEY are valid for all file
access methods, including URL, external, cmd, app, file and by
default any new method added. If the internal query data is not
flagged by the access method (to show the database has been
queried) the sequence object is automatically tested.
Missing description, keyword, organism, or seqversion fields cause
queries to fail if they are used on inappropriate data.
dbiflat, dbigcg dbifasta and dbiblast can index the new
fields. All fields are available in dbiflat and dbigcg. The sv and
des fields are available in dbifasta and dbiblast. If any specific
formats make it possible to parse the org (or key) field they can
be added as new formats.
The new EMBLCD index files are named as follows: des for the
descriptions (no obvious standard name), seqvn for the seqversion
(no obvious standard name), keyword for keywords (EMBLCD
distribution name) and taxon to organism (EMBCD distribution
name). The EMBLCD distribution also included a freetext index
which is similar to the SRS alltext search so we did not use the
name for the desctription index.
We are working through the EMBLCD format documentation to make
EMBOSS indices more compatible. For example, all tokens in the TRG
index files should have trailing spaces. We use a NULL to mark the
end of the string.
EMBLCD index files now expand to fit the longest token, including
the entryname index which was limited to 12 characters (only one
site reported a problem with this in dbifasta with long ID names).
A new qualifier -maxindex sets an upper limit (25 is recommended)
to limit the size of all index files. Currently this applies to
all indices. We can add separate maxima for each field if
needed. We expect very few sites to use the extra index fields
as SRS is a simpler alternative.
New database definition token 'fields' with a list of indexed fields
can be set to 'sv des org key' for SRS databases.
USAs check the query field against the database 'fields'
definition. ID and ACC are always allowed. dbname:name still
searches ID and ACC (no change from previous version)
USAs with a filename can include the new query fields. The syntax is
filename:field:query for example empro.dat:id:eclaci (the extended
syntax is because empro.dat-id:eclaci looks like a filename ending
in -id)
Application 'tranalign' added.
This aligns nucleic coding regions based on a set of aligned proteins.
Version 2.3.1
est2genome fixed for large alignments (over 40Mbase for
est * genomic sequence length)
sequence reading for ABI files fixed (and selex files tested)
genbank feature input working
pepinfo PNG output larger to make the text readable (only affects
PNG output)
empty sequence file input fails gracefully
empty sequence input fails gracefully (and only needs one
^D from stdin)
Version 2.3.0
Seqretall, seqretallfeat and seqretset moved to 'make check'.
Seqret has all the functionality of the above.
Fix for NBRF accession number reading (ajseqread.c)
Whichdb program added.
Fix for dbifasta and wormpep
Fix for problem reading plain format sequences by primer3.
Primer3 renamed eprimer3 to avoid conflicts with the Whitehead's
primer3 version 3.0.6.
transeq's '-frame' can have a list of values, as: '-frame=1,2,3'
Non-existent files in lists are again ignored
Various wildcard database search fixes
ESIM4 added as an embassy package
