seqm

Python utilities for sequence comparison, quantification, and feature extraction.

Installation

~$ pip install seqm

Documentation

Documentation for the package can be found here.

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

Sequence Quantification

Function	Metric
seqm.polydict	Length of longest homopolymer for all bases in sequence.
seqm.polylength	Length of longest homopolymer in sequence.
seqm.entropy	Shannon entropy for bases in sequence.
seqm.gc_percent	Percentage of GC bases in sequence relative to all bases.
seqm.gc_skew	GC skew for sequence: (#G - #C)/(#G + #C).
seqm.gc_shift	GC shift for sequence: (#A + #T)/(#G + #C)
seqm.dna_weight	Molecular weight for sequence with DNA backbone.
seqm.rna_weight	Molecular weight for sequence with RNA backbone.
seqm.aa_weight	Molecular weight for amino acid sequence.
seqm.tm	Melting temperature of sequence.
seqm.zipsize	Compressibility of sequence.

Domain Conversion

Function	Conversion
seqm.revcomplement	Length of longest homopolymer for all bases in sequence.
seqm.complement	Length of longest homopolymer in sequence.
seqm.aa	Shannon entropy for bases in sequence.
seqm.wrap	Percentage of GC bases in sequence relative to all bases.
seqm.likelihood	GC skew for sequence: (#G - #C)/(#G + #C).
seqm.qscore	GC shift for sequence: (#A + #T)/(#G + #C)

Distance Metrics

Function	Distance Metric
seqm.hamming	Hamming distance between sequences.
seqm.edit	Edit (levenshtein) distance between sequences

Utilities

Function	Utility
seqm.random_sequence	Generate random sequence.
seqm.wrap	Newline-wrap sequence

Questions/Feedback

File an issue in the GitHub issue tracker.