seqm 0.1.0

Usage

The seqm module contains functions for calculating sequence-related distance and complexity metrics, commonly used in language processing and next-generation sequencing. It has a simple and consistent API that be used for investigating sequence characteristics:

>>> import seqm
>>> seqm.hamming('ATTATT', 'ATTAGT')
1
>>> seqm.edit('ATTATT', 'ATAGT')
2
>>> seqm.polydict('AAAACCGT')
{'A': 4, 'C': 2, 'G': 1, 'T': 1}
>>> seqm.polylength('AAAACCGT')
4
>>> seqm.entropy('AGGATAAG')
1.40
>>> seqm.gc_percent('AGGATAAG')
0.375
>>> seqm.gc_skew('AGGATAAG')
3.0
>>> seqm.gc_shift('AGGATAAG')
1.67
>>> seqm.dna_weight('AGGATAAG')
3968.59
>>> seqm.rna_weight('AGGATAAG')
4082.59
>>> seqm.aa_weight('AGGATAAG')
700.8
>>> seqm.tm('AGGATAAGAGATAGATTT')
39.31
>>> seqm.zipsize('AGGATAAGAGATAGATTT')
22

It also has a Sequence object for object-based access to these properties:

>>> import seqm
>>> seq = seqm.Sequence('AAAACCGT')
>>> seq.hamming('AAAAGCGT')
1
>>> seq.gc_percent
0.375
>>> seq.revcomplement
ACGTACGT
>>> seq.dna_weight
3895.59
>>> # ... and so on ...

All of the metrics available in the repository are listed below, and can also be found in the API section of the documentation.

Finally, all functions from the seqm module can be used at the command line:

~$ # calculate distance between sequences
~$ seqm edit AAAACCGT AAAAGCGT
1

~$ # calculate gc percent of sequence
~$ seqm gc_percent AAAACCGT
0.375

~$ # generate random sequence and pipe to `wrap` command
~$ seqm random --length 10 | seqm wrap --bases 5 -
ATGGA
TATTA