mdehoon
mdehoon
This PR adds the gap scores and substitution matrix for blastn, megablast, and blastp as scoring options when initializing a `PairwiseAligner` object. - [X] I hereby agree to dual licence...
Whitespace is removed from `seq` by calling `"".join(str(seq).split())`. But it's not necessary to do this, as any whitespace in `seq` will be caught as a `KeyError` anyway. With this PR,...
- [X] I hereby agree to dual licence this and any previous contributions under both the _Biopython License Agreement_ **AND** the _BSD 3-Clause License_. - [X] I have read the...
Some cleanup in CodonAdaptationIndex. Note that `islower` returns whether all letters in the sequences are lower case; this should have been `not isupper`. However, just using `upper` always makes the...
In `CodonAdaptationIndex`, use a count of 0.5 for codons that do not appear in the reference sequences. See #243. - [X] I hereby agree to dual licence this and any...
This PR adds `isupper()`, `islower()` to the `SeqRecord` class (which already contains `upper()` and `lower()`). - [X] I hereby agree to dual licence this and any previous contributions under both...
This PR replaces duplicated code in `Bio.SwissProt._read_ft` and `Bio.GenBank._pos` by a factory function for position objects in `Bio.SeqFeature`, and removes `_make_position` from `Bio.SeqIO.SwissIO.py` as it is not being used. See...
I am finding code to parse GenBank-style location strings into `SeqFeature` objects in multiple places in Biopython: - In `Bio/SwissProt/__init__.py`, in the `_read_ft` function; - In `Bio/SeqIO/SwissIO.py`, in the `_make_position`...
`Bio.codonalign` was added to Biopython about 8 years ago. Currently this module is still considered to be experimental, and prints a `BiopythonExperimentalWarning` when imported: ```python >>> from Bio import codonalign...
There is some inconsistency in exception handling between Python and Biopython when parsing files. This is what happens in Python (using the binary file `310.ab1` in `Tests/Abi` as an example):...