[EMBOSS] EMBOSS 4.0.0 Latest Fixes

[Peter Rice]

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.