Metadata-Version: 2.1
Name: flutile
Version: 0.3.1
Summary: sequence analysis tools for flu research
Home-page: https://github.com/flu-crew/flutile
Author: Zebulun Arendsee
Author-email: zebulun.arendsee@usda.gov
License: UNKNOWN
Description: [![Build Status](https://travis-ci.org/flu-crew/flutile.svg?branch=master)](https://travis-ci.org/flu-crew/flutile)
        
        # flutile
        
        ## Installation
        
        ``` sh
        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).
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
