marco-mariotti / pyaln Goto Github PK

Deal with:
pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.

By modifying function _counts_per_column

See also #10

This is a bottleneck in a couple of analyses, and it seems unnecessary slow.

Have a look at _counts_per_column, that's the function to be improved
(it's cached, but that's not relevant).

@maxtico

Implement explicit iterator for [id, seq], with option on whether id is the name or title

Wrap trimal methods in a .trimal() method

Biopython wrapper doesn't cut it, build from scratch

Remove same seq match from score when self if compared against itself.

Is it possible to get matrix of sequence_identity (all vs all)?

Structure tutorial in columns vs rows section

Build as method: get command line from bio align, run, return realigned seqs.
Input argument defines aligner program and options as dict.

How to deal with file handlers? If no other option, temp folder as argument (if none, get from module?)
Note: mafft is easy, as output can be piped

Implement:

• revcomp
• translate (with non-std code: download from Bio, make dict)
• align_coding_sequences

Implement method. Based on inner join of melted position map dataframes.