Damien Goutte-Gattat
bbba5cb341
Change error messages.
...
Don't start error messages with "error [doing...]", as argparse
already prefixes the message on the console with "error: ".
2 years ago
Damien Goutte-Gattat
c7f393b622
Add the silencing module.
...
Add a module for functions intended to help manipulating or
designing siRNA and similar objects.
2 years ago
Damien Goutte-Gattat
7ca873bd4d
Typo fix.
...
There is no "Translate" method in the Bio.Seq.Seq objet=ct.
2 years ago
Damien Goutte-Gattat
d8b876455d
Fix indexing of fragment specifiers.
...
Fragment specifiers in USAs are 1-based, while Biopython uses 0-based
indexes.
2 years ago
Damien Goutte-Gattat
4a8f91a86c
Add MANIFEST.in file.
...
Make sure the test modules and data files are included in the source
archive.
2 years ago
Damien Goutte-Gattat
7f316ffc0d
Fix handling of fragment specifiers for list USAs.
2 years ago
Damien Goutte-Gattat
9a8d194270
Add test case for file-based USAs.
2 years ago
Damien Goutte-Gattat
d8b4f988dd
Add tests for the USA module.
2 years ago
Damien Goutte-Gattat
69a7dfd006
Rework handling of formats and fragments.
2 years ago
Damien Goutte-Gattat
03dab6cb95
Change representation of a USA list.
...
Represents a file-of-filenames (FOFN) USA as a separate USA type
instead of a generic list of USAs.
2 years ago
Damien Goutte-Gattat
b81528e9d2
Start documenting the USA module.
...
Add docstrings to components of the public interface of the
incenp.bio.seq.usa module.
2 years ago
Damien Goutte-Gattat
8fc014dacf
Overhaul the USA module.
...
Re-write the USA module completely to proceed in two steps: a parsing
step to build a representation of the USA(s), and a reading step to
actually fetch the sequences from the USA(s).
2 years ago
Damien Goutte-Gattat
4fa63e7638
Fix imports.
2 years ago
Damien Goutte-Gattat
791909feee
Typo fixes.
2 years ago
Damien Goutte-Gattat
4b3eb6a6ee
Remove _die function.
...
Use argparse's error method instead of an internal _die function.
2 years ago
Damien Goutte-Gattat
9ff12f00d4
Initial commit.
...
This is incenp.bioutils, a package of command line utilities and
helper Python modules for computational biology, mostly built on
top of Biopython.
2 years ago
Damien Goutte-Gattat