Download¶
Warning: We consider this version of sff_extract obsolete. The new sff_extract is included now in our tool set seq_crumbs.
sff_extract 0.3.0¶
sff_extract 0.3.0. Relased on 9-7-2012.
Changes by Bastien Chevreux :
- fixed bug in clipping points (was an error report by Ion Torrent)
- reads with partial linkers have “_part” instead of ”.part” in the name
- paired-read naming: .f,.r to /1, /2
- paired-read: segment not reversed
- -Q removed, added -A
- added compat mode “-C”
- cleaned up usage text
- run test for ssaha2 before extracting reads
sff_extract 0.2.12¶
sff_extract 0.2.12. Relased on 15-2-2012.
Changes:
- Minimun frequency option added by Francisco Pina Martins.
sff_extract 0.2.11¶
sff_extract 0.2.11. Relased on 13-1-2012.
Changes:
- Bugfix by Michael Schatz <mschatz@cshl.edu> .
sff_extract 0.2.8¶
sff_extract 0.2.8. Relased on 2-3-2010.
Changes:
- Bugfix by Bastien. Qualities were not properly reversed when doing paried ends.
sff_extract 0.2.6¶
sff_extract 0.2.6. Relased on 8-6-2009.
Changes:
- Bugfix by Bastien. Fixes a problem with some malformed sff files.
sff_extract 0.2.5¶
sff_extract 0.2.5. Relased on 6-5-2009.
Changes:
- Bugfix release. Paired ends work better now.
sff_extract 0.2.3¶
sff_extract 0.2.3. Relased on 29-12-2008.
Changes:
- Bugfix release. Clipping works again with paired ends and test for ssaha2 removed.
sff_extract 0.2.2¶
sff_extract 0.2.2. Relased on 30-10-2008.
Changes:
- It can work again with python 2.4.
sff_extract 0.2.1¶
sff_extract 0.2.1. Relased on 13-11-2008.
sff_extract 0.2 represents an important improvement over the 0.1 series. Bastian Chevreux has added support for the paried end sequencing. If you feed sff_extract with a linker sequence you will obtain the paired end sequences split. All the following changes have been coded by Bastien:
- Reads from paired-end files which are not splitted into 2 sequences now get ”.n” postfix.
- Reads that had mutliple paired-end linkers get “_mlc” in the name and no pairing information written to the XML.
- sff_extract now return 0 if everything went ok or 1 if there was a problem of any kind.
- Added left clip plausibility check: check_for_dubious_startseq(). If sequences look fishy, sff_extract prints a warning, continues to extract, but will return with 1 to the shell at the very end.
- Raises error on empty linker file.
- Error handling in reading FASTAs
- Error raised when no SFF file given on command line
- Fix: XML info now written also for clipped reads (just the clip infor is left out).
- Added short description of program purpose.
- Renamed -m to -u and inverted meaning: lowercasing clipped parts is now default.
- Added –min_left_clip.
- Added –version.
sff_extract 0.1.2¶
sff_extract 0.1.2. Relased on 30-10-2008.
Changes:
- It can work again with python 2.4.
sff_extract 0.1.1¶
sff_extract 0.1.1. Relased on 16-10-2008.
Changes:
- “o” option added to specify a common basename for all output files.
- More simple error messages thrown.
sff_extract 0.1¶
sff_extract 0.1. Relased on 14-10-2008.
Changes:
- Initial Release. Save the script, make it executable and run it.