0.3.4

For this release, seqpoet is public. This also means that the documentation is available at http://seqpoet.readthedocs.org. Some other stuff has also happened:

• A summary of the results is presented on the command line
• Some issues with operon/match coordinates were fixed
• Various small bug fixes

0.3.3

This update brings improved handling of GenBank LOCUS lines. Previously it would fail with a cryptic traceback if the header line was malformed. Now it will try to salvage what it can, and if it completely fails, a proper error message is printed.

0.3.2

Small updates and bug fixes. The most major was a bug related to --no-revcomp where the results on the minus strand from operon extraction would be reverse complemented twice.

0.3.1

This is a very minor update. I just forgot to update the package name in the README.

0.3.0

The major things in this update is a name change, a couple of new command line arguments, updates to the GenBank parser and finally some documentation.

Name change

The package is now called seqpoet.

Command line arguments

• --no-revcomp: seqpoet now reverse complements results that are found on the reverse strand by default. To disable this, use this flag.
• --upstream and --downstream: extend a match a number of bases upstream or downstream for operon extraction. This can be useful in case a probe/primer pair designed for intergenic regions is used.

Bug fixes/improvements

• Fixed a critical bug in the operon extraction where features on the wrong strand would be extracted in some cases.
• Join locations are now handled.
• Multi-line GenBank location strings are now parsed properly.
• Lots of other small fixes related to GenBank parsing.

0.2.0

The reason why this first release is 0.2.0 is that 0.1.0 was used for the initial development, but not actually released. This to avoid confusion (are you confused now?).

Basically everything has changed from (the unreleased) 0.1.0, so I won't write a changelog.