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sequence analysis tools for flu research

Project description

Build Status

flutile

Installation

pip install flutile

Commands

compare

compare takes a multiple-sequence alignment as an input and creates a character difference table. This command is designed for preparing amino acid difference tables (although it will accept DNA as well). Below is an example output:

site A B C D E F G H
2 L M M M M M
12 N I I I T T I T
66 T K
110 S P P P P P
116 T A
140 K R R R R R
146 K E E E E
147 K M

Sequences B-H are compared to sequence A. Every difference is reported with the alternative amino acid, while identities are left blank.

compare takes two arguments (--make-consensus and --use-consensus-as-reference) which will add a consensus column as the final column in the table of as the first (in which case it is the reference column).

represent

represent takes a multiple-sequence alignment as input and removes entries that are similar in sequence and time. The function requires that headers have a date term (with format year/month/day). For example:

>A|1990-01-02
GATACA
>B|1990-02-02
CATATA

There may be gaps in the alignment. Sequences in the alignment that are separated by less than or equal to --max-day-sep and that are a sequence identity of greather than or equal to --min-pident-sep will be clustered together. A single representative is sampled from each cluster (the latest one with ties resolved by order).

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