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
