sequence analysis tools for flu research
Project description
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).
trim
HA trimming is based on: Burke, Smith (2014) A Recommended Numbering Scheme for Influenza A HA Subtypes
--- | ------------------------------------------------- | ------------------- | ---------------------- | H1 | A/United Kingdom/1/1933 | MKARLLVLLCALAATDA | DTICIGYHANNS | H2 | A/Singapore/1/1957 | MAIIYLILLFTAVRG | DQICIGYHANNS | H3 | A/Aichi/2/1968 | MKTIIALSYIFCLPLG | QDLPGNDNSTATLCLGHHAVPN | * MKTIIALSYIFCLALG H4 | A/swine/Ontario/01911–2/1999 | MLSIAILFLLIAEGSS | QNYTGNPVICLGHHAVSN | H5 | A/Vietnam/1203/2004 | MEKIVLLFAIVSLVKS | DQICIGYHANNS | H6 | A/chicken/Taiwan/0705/1999 | MIAIIVIATLAAAGKS | DKICIGYHANNS | H7 | A/Netherlands/219/2003 | MNTQILVFALVASIPTNA | DKICLGHHAVSN | H8 | A/turkey/Ontario/6118/1968 | MEKFIAIAMLLASTNA | YDRICIGYQSNNS | H9 | A/swine/Hong Kong/9/1998 | MEAASLITILLVVTASNA | DKICIGYQSTNS | H10 | A/mallard/bavaria/3/2006 | MYKIVVIIALLGAVKG | LDKICLGHHAVAN | H11 | A/duck/England/1/1956 | MEKTLLFAAIFLCVKA | DEICIGYLSNNS | H12 | A/duck/Alberta/60/1976 | MEKFIILSTVLAASFA | YDKICIGYQTNNS | H13 | A/gull/Maryland/704/1977 | MALNVIATLTLISVCVHA | DRICVGYLSTNS | H14 | A/mallard/Astrakhan/263/1982 | MIALILVALALSHTAYS | QITNGTTGNPIICLGHHAVEN | H15 | A/duck/Australia/341/1983 | MNTQIIVILVLGLSMVRS | DKICLGHHAVAN | H16 | A/black-headed-gull/Turkmenistan/13/1976 | MMIKVLYFLIIVLGRYSKA | DKICIGYLSNNS | H17 | A/little-yellow-shouldered bat/Guatemala/060/2010 | MELIILLILLNPYTFVLG | DRICIGYQANQN | H18 | A/flat-faced bat/Peru/033/2010 | MITILILVLPIVVG | DQICIGYHSNNS |
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