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