[EMBOSS] EMBOSS 4.0.0 Latest Fixes
Michael Thon
mthon at tamu.edu
Fri Aug 25 21:31:41 UTC 2006
Hi Peter - Will you be releasing an update to the emboss distribution
that includes these changes?
cheers
Mike
On Aug 25, 2006, at 8:59 AM, Peter Rice wrote:
> I have posted some further fixes on the EMBOSS FTP site. None are
> critical. Users have been reporting interesting bugs. Some were
> also in
> release 3.0.0.
>
> The fuzznuc, fuzzpro and fuzztran reports were changed in 4.0.0 to
> always report something. Unfortunately users running searches over the
> whole database found their output files were very large. We have
> changed
> the way reports work as follows:
>
> 1. fuzznuc, fuzzpro and fuzztran again report only sequences with hits
>
> 2. when a report is closed, a default header and footer are written
> (solving the problem of empty output files)
>
> 3. for sites that had concerns about searches for trivial patterns
> taking too long and generating too much output, reports have 2 new
> associated qualifiers. -rmaxall limits the total number of matches
> reported (fuzznuc, fuzzpro and fuzztran terminate when the limit is
> reached), -rmaxseq limits the maximum number of hits for one sequence.
>
> We also have various fixes for reporting matches on the reverse
> strand,
> and for improved parsing of FASTA file IDs.
>
> To update your EMBOSS 4.0.0 release, go to:
>
> ftp://emboss.open-bio.org/pub/EMBOSS/fixes/
>
> File README.fixes (see below) lists the files and describes the fixes.
>
> Copy the files to the indicated directories and reinstall.
>
> regards,
>
> Peter Rice
>
> file README.fixes 25-aug-2006
>
> The files in this directory are bugfix replacements for files in
> the EMBOSS-4.0.0 distribution. Just drop the replacement files in
> the location shown and redo the 'make install.'
>
>
> Fix 1. EMBOSS-4.0.0/nucleus/embpatlist.c
>
> 31 Jul 2006: Fixes a problem with searching for patterns and regular
> expression in the reverse strand of nucleotide sequences. The change
> is to use ajSeqReverseForce (always reverses the sequence provided)
> instead of ajSeqReverseDo (which only reverses if the reverse flag is
> set)
>
> 9 Aug 2006: Revised to also fix a problem with reverse strand sequence
> positions.
>
>
> Fix 2. EMBOSS-4.0.0/ajax/ajfile.c
>
> 31 Jul 2006: This fixes a bug where deleting the last line of buffered
> input fails to reset the pointer to the last buffered line. This only
> affected debug traces. Unfortunately, the ajFileBuffClear function
> does call the debug trace. In practice we have only seen this bug when
> processing sequence data in EMBL format from an MRS server.
>
> Fix 3. EMBOSS-4.0.0/ajax/ajnam.c
>
> 31 Jul 3006: New database access methods MRS and DBFETCH need to be
> explicitly turned on so that showdb can report them.
>
>
> Fix 4. EMBOSS-4.0.0/ajax/ajseqdb.c
>
> 31 Jul 2006: The new MRS access method used a general search. This
> gave strange results when the ID or accession appeared in any other
> entry. It appears that MRS can search for id or accession only. This
> worked on the main MRS server at least.
>
> MRS access will be further extended in the next release. Please
> contact the developers emboss-bug at emboss.open-bio.org if you would
> like to help test new features in MRS access.
>
> 25 Aug 2006: Further change to allow multiple %s replacements in
> complex URLs for access method URL. Needed for complex SRS queries to
> resolve EMBL IDs so the following definition can be used for EMBL
> (warning, the URL may wrap badly in this email!)
>
> DB embl [
> method: "url"
> format: "embl"
> type: "N"
> url:
>
> "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-noSession+-ascii+-vn+2+-
> e+[embl-id:%s]|[embl-acc:%s]|([emblidacc-id:%s]>embl)"
> comment: "EMBL from SRS including old IDs"
> ]
>
> Fix 5. EMBOSS-4.0.0/configure
>
> 07 Aug 2006: Fix configuration problem on Intel Mac machines. Make
> sure
> this file is executable (chmod 755 configure) after downloading it.
>
> Fix 6. EMBOSS-4.0.0/ajax/ajseq.c
>
> 09 Aug 2006: Return correct USA for "asis::" sequence input.
>
> Fix 7. EMBOSS-4.0.0/emboss/dreg.c
>
> 09 Aug 2006: Correct sequence positions on the reverse strand.
>
> Fix 8. See Fix 13
>
> Fix 9. See Fix 13
>
> Fix10. EMBOSS-4.0.0/doc/programs/html/banana.1.banana.gif
> EMBOSS-4.0.0/doc/programs/html/tcode.2.tcode.gif
>
> 14 Aug 2006: These graphics example outputs were missing from the
> distribution. When you run make install they will be copied to the
> installed documentation.
>
> Fix 11. EMBOSS-4.0.0/emboss/merger.c
> EMBOSS-4.0.0/emboss/needle.c
> EMBOSS-4.0.0/emboss/prophet.c
> EMBOSS-4.0.0/emboss/water.c
>
> 14 Aug 2006: These programs calculate an internal path size from the
> lengths of the input sequences. For sequences that are too long, a
> fatal error is produced. But if the sequences are extremely long, the
> test failed and the program gave a segmentation fault. This fix tests
> in a different way that will catch all cases.
>
> Fix 12. See Fix13
>
> Fix 13. EMBOSS-4.0.0/ajax/ajacd.c
> EMBOSS-4.0.0/ajax/ajfeat.c
> EMBOSS-4.0.0/ajax/ajfeat.h
> EMBOSS-4.0.0/ajax/ajreport.c
> EMBOSS-4.0.0/ajax/ajreport.h
> EMBOSS-4.0.0/emboss/fuzznuc.c
> EMBOSS-4.0.0/emboss/fuzzpro.c
> EMBOSS-4.0.0/emboss/fuzztran.c
>
> 21 Aug 2006: This provides new qualifiers to limit report output to a
> number of hits in total (-rmaxall) or for any one sequence
> (-rmaxseq). It also fixes reversed feature locations for reports in
> EMBL format. The files fixed overlap with earlier fixes which are
> included here.
>
> 09 Aug 2006: Fix 8: In release 4.0.0 these 3 programs were changed
> to report
> even when no hits were found. The aim was to avoid empty output for a
> single sequence.
>
> Many users were running these programs over large input sets, and now
> get excessively large output files.
>
> The change has been reversed. Fix 9 makes sure a small output
> file is produced when no hits are found.
>
> 09 Aug 2006: Fix 9: When closing a report (with ajReportClose) make
> sure a
> standard report header and footer are printed if nothing has been
> reported so far. The header reports the command line. The new footer
> reports the total number of sequences and features reported.
>
> Reversed sequence positions are corrected for listfile report format.
>
> No header can be reported for some formats (EMBL, Genbank, GFF, PIR,
> Swiss, Excel, Feattable).
>
> 14 Aug 2006: Fix12: This fixes a bug where putting -ofopenfile on the
> command
> line for features output failed to set the feature output format.
>
>
> Fix 14. EMBOSS-4.0.0/ajax/ajseqread.c
> EMBOSS-4.0.0/ajax/ajseqread.h
> EMBOSS-4.0.0/ajax/ajseqwrite.c
> EMBOSS-4.0.0/emboss/dbiblast.c
> EMBOSS-4.0.0/emboss/dbifasta.c
> EMBOSS-4.0.0/emboss/dbxfasta.c
> EMBOSS-4.0.0/emboss/acd/dbiblast.acd
> EMBOSS-4.0.0/emboss/acd/dbifasta.acd
> EMBOSS-4.0.0/emboss/acd/dbxfasta.acd
>
> 24 Aug 2006: Pearson format preserves dbname:entryname style IDs
> NCBI format parsing (includes FASTA format parsing) extracts database
> name from NCBI piped ids and uses on output unless EMBOSS has defined
> some other database name.
>
> Three indexing programs call the NCBI parsing function which has an
> extra argument.
>
> Fasta parsing was also modified to allow UniProt style (yet another
> FASTA format) where the accession number is in brackets. The "idacc"
> default format now removes brackets before checking for an accession
> number or version next on the line.
>
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