[EMBOSS] EMBOSS 6.0.0 released

[ajb at ebi.ac.uk]

EMBOSS 6.0.0 is now available from:

  ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.0.0.tar.gz

The associated EMBASSY packages are in the same directory. Note that,
as usual, these are specific to the main package so versions downloaded
for a previous release will not work with 6.0.0.

Changes in 6.0.0 include new applications, improvement of existing
applications, library API consistency changes, bugfixes etc. Most are
described in the relevant section of the ChangeLog which is reproduced
below.


mEMBOSS-6.0.0 is available from:

  ftp://emboss.open-bio.org/pub/EMBOSS/windows/mEMBOSS-6.0.0-setup.exe

mEMBOSS contains all the EMBOSS changes plus improvements and bugfixes
for the GUI (Jemboss). Also, this release of mEMBOSS contains the C runtime
library files; these had to be installed separately in previous
versions.

Alan





Version 6.0.0
	New application aligncopy reads a set of aligned sequences and
	prints a report in one of the standard alignment formats that can
	accept the same number of sequences. Pairwise alignment formats
	can only be used if the input has exactly two sequences.

	New application aligncopypair reads a set of aigned sequences and
	prints a report or each pair of aligned sequences in one of the
	standard alignment formats.

	New application featreport reads a sequence and a feature table,
	and writes a report in and of the standard report formats.

	New application featcopy reads and writes a feature table to
	convert feature formats.

	New applications maskambignuc and maskambigprot replace ambiguity
	characters in nucleotide sequences with 'N' and in protein
	sequences with 'X'.

	New application consambig reports an alignment consensus sequence
	using ambiguity characters. The intended use cases are sequencing
	reads and SNP reporting.

	New application sizeseq sorts sequences in ascending or descending
	order of length. This is a port of the application seqsort from
	the domsearch EMBASSY package.

	New application skipredundant uses pairwise sequence matches to
	exclude sequences that are similar from an input set. This is a
	modified version of the application seqnr from the domsearch
	EMBASSY package.

	New applications provide utility functions for former GCG users:
	nohtml removes HTML tags, notab replaces tabs with spaces,
	nospace removes all whitespace from a file, skipspace removes
	extra whitespace from a file.

	Older EMBOSS applications can now generate a warning message
	stating that they are marked as 'obsolete' with an explanation and
	an indication of alternative programs in EMBOSS or in an EMBASSY
	package. This warning can be turned off by defining environment
	variable EMBOSS_WARNOBSOLETE with a value of "N" or by defining
	the same variable in the emboss.defaults or ~/.embossrc files. We
	will begin to mark applications as 'obsolete' in future releases.

	A new EMBASSY package "myembossdemo" contains the demonstration
	applications demoalign, demofeatures, demolist, demoreport,
	demosequence, demostring, demostringnew and demotable that
	illustrate how to use EMBOSS data types in your own
	applications. The myembossdemo package allows novice developers to
	try simple EMBOSS programming. The myemboss package is available
	for adding your own applications. The demo applications are no
	longer distributed with the main EMBOSS package. They were not
	installed and were only built with the "make check" option.

	Application short descriptions have been revised. The minimum
	length of application one line descriptions is increased from 60
	to 70 characters. The descriptions are easier to write. Output
	from wossname can now be 90 characters wide. Interfaces that use
	the description in menus may need to allow some extra space.

	Function names in ajfile.c have been standardised. Old names are
	still accepted but are marked as "deprecated" and will generate
	warnings with the gcc compiler (see ajstr below). Other compilers
	will see no difference. New source files ajfiledata.c and
	ajfileio.c have been added. The buffered file data structures are
	renamed internally to be more consistent (AjPFileBuff to AjPFilebuff).

	notseq was unable to search for IDs containing '|' characters
	but uses string matching (not regular expressions) and these
	characters are valid in NCBI-style FASTA files if read with the
	"pearson" format which accepts the whole ID string without parsing.

	The sequence alignment code has been updated. Sequence alignments
	with low gap penalties failed to allow two gaps (one in each
	sequence) without a match in between. The embAlign functions are
	now simplified. Scores are returned by the PathCalc functions. The
	Walk functions that walk through the path and return the aligned
	sequences are faster and need fewer parameters. Profile alignments
	occasionally duplicated residues in the sequence around gap
	positions. Fast alignments around a limited width include
	additional residues at each end and require an offset rather than
	separate start positions. The offset if the difference between the
	two start positions used in 5.0.0 and earlier releases.

	Eprimer3 citations are corrected in the help text (from the ACD
	file) and in the documentation. The citation errors were traced to
	the original primer3_core documentation which has now been
	corrected.

	Wordmatch could confuse overlapping matches. It occasionally
	extended the wrong match and missed a corresponding new match.

	Seqmatchall results were correct with the default output
	format which reports match positions, but gave incorrect results
	with some other local alignment formats that include the sequence.
	Seqmatchall now stores alignments in the same way as other local
	alignment applications, and the alignment internals are corrected
	to ensure other applictaiopns will not have the same problem.

	Emma was officially supporting clustalw 1.83. Issues with clustalw
	2.0 are now resolved and this version is supported if clustalw2 is
	installed. Emma executes an applications called clustalw (not
	clustalw2) so version 2.0 must be installed under this name or an
	environment variable EMBOSS_CLUSTALW needs to be defined to point
	to the executable clustalw2 file.

	Sequence format "selex" allows invalid sequence data files to be
	accepted as input. Selex format is still available but is no
	longer included in the formats that can be automatically
	detected. When reading selex format data, users need to put
	"-sformat selex" on the command line, or specify "selex::" at the
	from of the USA. See the HMMER (old version EMBASSY package)
	documentation for examples. HMMERNEW (recommended) examples use
	Stockholm format and so are unchanged.

	Program dbxfasta now defaults to a filename of "*.fasta"
	The previous default "*.dat" is not commonly used for FASTA format
	databases.

	Program msbar block mutations were 1 longer than the specified
	block and may crash if the block size was fixed (minimum and
	maximum block sizes the same). This off-by-one error is now
	corrected.

	In GenBank output format, multiple line KEYWORD sections were not
	formatted correctly.

	ACD list and select values (the menus that appear in the user
	prompt) can now have ACD variables. Although useful for local
	application development these are not used in EMBOSS distributed
	ACD files because the variables are difficult for web and GUI
	interfaces to resolve when presenting the menu text.

	List and Table internal data structures are now cached so that
	creating and deleting temporary lists and tables is more efficient.

	In emboss.default database definitions the filename and exclude
	values can be delimited by spaces, commas or semicolons. Previous
	releases used only spaces. Parsing is now consistent with the
	fields definition which allowed all the above characters.

	Protein sequences with pyrrolysine ('O') had 'O' converted to a
	gap because this was a gap character in early versions of
	Phylip. This was patched in 5.0.0 to allow 'O' in UniProt release
	13. The gap character is upper case only, so 'o' was correctly
	read as pyrrolysine.

	Wordfinder used the same descriptions for two pairs of qualifiers.
	The descriptions are changed to make their meaning clear in
	commandline help and in web interfaces.

	New function ajTimeDiff returns the difference in seconds between
	two time values.

	Profiling tests showed that file reading and string handling can
	be made faster. String handling called functions many levels
	deep. Making this code inline and using macro versions improved
	performance for applications (e.g. database indexing) that use
	many string calls. File input requires each input line to be
	copied. Using copy-by-reference (ajStrAssignRef) often makes this
	more efficient. Existing macros now test for undefined strings:
	MAJSTRGETLEN, MAJSTRGETPTR, MAJSTRGETRES and MAJSTRGETUSE. New
	macros are added for string handling: MAJSTRDEL,
	MAJSTRGETUNIQUESTR, MAJSTRCMPC and MAJSTRCMPS.

	Memory management includes new macros AJCRESIZE0 and AJRESIZE0
	provide resize functions that guarantee new memory is set to
	zero. The functions must be given the original allocated size.

	Using the GNU C run-time library, calls to mcheck and mprobe are
	available to test for memory corruption by examining the bytes
	before and after an address allocated by malloc. This can be
	turned on for any application, including Unix commands, with the
	environment variable MALLOC_CHECK_ which has values 0, 1, 2 or
	3. 1 writes to standard error when a problem is found, 2 aborts
	the programs, 3 does both and 0 ignores errors. No recompilation
	is needed for this simple method. EMBOSS now has a ./configure
	option --enable-mprobe which enables two new
	functions. ajMemProbe, passed an address from malloc (AJNEW0,
	AJCNEW0, etc.) tests the bytes before and after and reports any
	errors. The advantage of using ajMemProbe rather than mprobe is
	that a macro MAJMEMPROBE also reports the file and line number
	where ist was called. To avoid large numbers of messages (when
	code has problems) a limit can be set with ajMemCheckSetLimit
	after which the program will exit. Note that enable-mprobe is
	incompatible with using valgrind to test for memory leaks - as
	mprobe and mcheck have to look at illegal bytes before and after
	allocated memory blocks. Memory checking is turned on by a call to
	mcheck, passing the function ajMemCheck, in ajnam.c before the
	first memory allocation. If any program calls malloc before
	calling embInit or embInitP this call will fail and issue a
	warning (if compiled with --enable-mprobe). A special call
	ajStrProbe tests any string with mprobe. Special calls ajListProbe
	and ajListProbeData test lists and their contents. For more
	details see http://www.gnu.org/software/libc/manual/

	Protein sequences from the Staden package were read as nucleotide
	because they were missing information on the ID line to identify
	EMBL of SWISSPROT format. The sequences are now tested and
	correctly typed.

	Wordcount now accepts protein sequences as input. Previous
	releases only allowed nucleotide sequences.

	Wordfinder options had the same information prompt. These have
	been changed from "limit" to "minimum" and "maximum" to make their
	function clear.

	Prompting for values from the user now includes a test for
	standard input in use as an input file. If standard input is open,
	the default response is accepted and a message is written to the
	user. This is to avoid problems with command lines that use
	"stdin" as an input and do not include -auto.

	The acdpretty utility can now preserve comments in ACD files.
	Comments are maintained in blocks with blank lines before and
	after. Inline comments are started in column 50 unless they are
	exceptionally long. Comments themselves have white space cleaned
	up but otherwise are not reformatted.

	A new function ajAcdGetValueDefault is added to return the default
	value of an ACD qualifier. This can be combined with
	ajAcdIsUserdefined in wrappers to test for values changed by the
	user.

	Infile qualifiers in ACD have a new attribute "trydefault" which
	allows the default filename to fail. Any filename provided by the
	user has to exist. This was added to support the behaviour of the
	MIRA EMBASSY package. To allow an infile to fail the attribute
	"nullok" also must be set to "Y"

	Applications which produce an output file or graphics often
	created an empty output file when the plot was selected.
	The ACD files have been corrected to only create the file if it
	will be written to. Applications changed are charge, dan,
	freak, hmoment, iep and tcode.

	Whichdb only writes to its output file if -get is false.
	With -get it creates sequences. The outfile is no longer created
	when whichdb is in -get mode.

	String functions corrected so that Case in the name always means
	case-insensitive and works by converting to upper case. Some
	functions were defined the wrong way, with "Case" for the
	case-insensitive form.

	GFF3 format is now the default feature output.

	A new function ajFeatIsCds identifies protein coding nucleotide
	features (CDS) using the SO identifier. A new function
	ajFeattagIsNote identifies feature tags that are for the default
	feature tag.

	Protein features now use the new Sequence Ontology terms defined
	by BioSapiens. These are not yet accepted by GFF3 validators. The
	new SO identifiers are added to protein feature definitions and
	used internally.

	Feature format definitions (the Efeatures and Etags files)
	now allow #include references to other files. This allows a
	standard EMBL and Swissprot feature table definition to be
	included by the internal and GFF definitions. Redefinitions are
	allowed using + and - prefxes to add and remove tags for existing
	feature types.

	GFF3 format feature (and report) output is added.

	A new application "density" has been added. This reports the
	A+C+G+T and AT+GC densities of nucleic acid sequences within
	an adjustable sliding window. Plots of A+C+G+T or AT+GC are
	optionally produced.

	Molecular weight programs (e.g. digest, mowse) now have a
	-mono switch to allow use of monoisotopic weights.
	By default, average molecular weights are used.

	The Eamino.dat format has changed. Molecular weight information
	has been removed and put in its own Emolwt.dat file. This latter
	now allows specification of average and monoisotopic weights. Values
	for hydrogen and oxygen are specified as well as the amino acid weights.

	The library representation of amino acid property information
	has been changed. The EmbPropTable global table has been
	removed and replaced with EmbPPropAmino and EmbPPropMolwt objects.

	Pepcoil now produces a report (replacing a text output) in "motif"
	format. The default is changed to not report non coiled-coil
	regions as they are hard to distinguish in this format.

	The "motif" report format is extended to allow two score positions
	marked with "*" and "+" and labelled internally as "pos" and
	"pos2". No application uses pos2 (it was added for pepcoil, but
	both score maximum positions are always the same)

	A new function ajAcdIsUserdefined allows wrappers to test which
	qualifiers have values changed by the user so that they can use
	shorter command lines to launch the wrapped application.

	jaspscan application added. Scans sequences for transcription
	factors using the JASPAR matrices.

	jaspextract application added to move the JASPAR matrices into the
	EMBOSS data area subdirectories.

	Alignment format "trace" used to display internal data content, is
	renamed to "debug" to be consisten with other formats. A "debug"
	format is added for feature output.

	Application documentation has been updated to remove obsolete
	references to EMBL database identifiers. These are replaced with
	the correct accession numbers.

	Two new entries have been added to the "tembl" test EMBL database
	for use in the QA tests.

	Report output now checks the sequence and feature table type. Is
	the sequence is not a valid protein, protein-only formats (pir,
	swiss) will fail with an error message. Similarly, if the sequence
	is not a valid nucleotide sequence then nucleotide-only formats
	(embl, genbank) will fail with an error message.

	Garnier now uses the correct SwissProt and internal feature keys
	for protein secondary structure. The results will appear much
	better for example as a swissprot feature table. This required
	rewriting of the internals by recoding the secondary structure
	features with a "garnier" tag replacing the previous "helix",
	"sheet", "turns" and "coil" tags. The default output is
	unchanged. The results in other report formats will be changed.

	Silent no longer reports the "Dir" column. This is replaced by the
	new "Strand" column which reports "+" for a forward feature and
	"-" for a reverse feature.

	The following programs have changed default report output, with
	the strand included for nucleotide sequences: equicktandem,
	etandem, fuzznuc, fuzztran, recoder, restrict, silent, tcode,
	twofeat. The strand column can be removed with the new commandline
	associated qualifier -norstrandshow.

	Reports for nucleotide sequences have confusing ways to represent
	the start and end positions for features on the complementary
	strand. A strand column has been added to these reports,
	controlled by a new -rstrandshow qualifier and attribute. By
	default the strand is shown for all nucleotide reports (see a list
	of changed program outputs above). The start position is always
	lower than the end position for features on the complementary
	strand indicating the region that should be reversed. In past
	releases the seqtable report format (fuzznuc, dreg, dan)
	confusingly reversed start and end positions to indicate the
	unreported strand. For all report formats (nametable, table) the
	start and end positions are now consistent with nucleotide feature
	formats (gff, embl, genbank).

	Reports from dreg incorrectly reported sequences reversed with the
	-sreverse qualifier.

	Report headers now include the text "(Reversed)" when the input
	sequence(s) are reverse complemented.

	Phylogenetic trees in newick format are now parsed into internal
	trees and converted back for use by Phylip. This allows us to
	read other tree formats and pass them to Phylip (e.g. Nexus)

	Some ACD data types did not allow the input to be NULL because
	extra tests were carried out on the results. These are all cleaned
	up and tested so that they can safely be set to nullok and missing
	in local applications.

	New sequence reading formats for PDB files. By default the ATOM
	records are used (format "pdb"). An alternative format "pdbseq"
	will read the SEQRES records which give the original sequence. The
	ATOM records give the sequence determined from the structure.

	Improved the help text for the -stdout and -filter options to
	explain output files are written to standard output. Some users
	expected graphics output (from plplot) to be controlled.