skbio.alignment.Alignment.int_map

Alignment.int_map(prefix='')[source]

Create an integer-based mapping of sequence ids

Note

Deprecated in scikit-bio 0.2.0-dev SequenceCollection.int_map will be removed in scikit-bio 0.3.0 in favor of SequenceCollection.update_ids, which provides a generalized way of updating IDs on a SequenceCollection. The default behavior of SequenceCollection.update_ids matches the behavior in int_map, except that a new SequenceCollection is returned instead of a dict.

Parameters:

prefix : str

String prefix for new integer-based ids.

Returns:

dict

Mapping of new ids to sequences.

dict

Mapping of new ids to old ids.

Notes

This is useful when writing sequences out for use with programs that are picky about their sequence ids (e.g., raXML).

The integer-based ids will be strings, for consistency (e.g., if prefix is passed) and begin at 1.

References

RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies”. In Bioinformatics, 2014