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. _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
