class Bio::Blast::Fastacmd

DESCRIPTION¶ ↑

Retrieves FASTA formatted sequences from a blast database using NCBI fastacmd command.

This class requires ‘fastacmd’ command and a blast database

(formatted using the ‘-o’ option of ‘formatdb’).

USAGE¶ ↑

require 'bio'

fastacmd = Bio::Blast::Fastacmd.new("/db/myblastdb")

entry = fastacmd.get_by_id("sp:128U_DROME")
fastacmd.fetch("sp:128U_DROME")
fastacmd.fetch(["sp:1433_SPIOL", "sp:1432_MAIZE"])

fastacmd.fetch(["sp:1433_SPIOL", "sp:1432_MAIZE"]).each do |fasta|
  puts fasta
end

REFERENCES¶ ↑

NCBI tool ftp.ncbi.nih.gov/blast/executables/LATEST/ncbi.tar.gz
fastacmd.html biowulf.nih.gov/apps/blast/doc/fastacmd.html

Attributes

database [RW]

Database file path.

fastacmd [RW]

fastacmd command file path.

Public Class Methods

new (blast_database_file_path)

Source

   # File lib/bio/io/fastacmd.rb
80 def initialize(blast_database_file_path)
81   @database = blast_database_file_path
82   @fastacmd = 'fastacmd'
83 end

This method provides a handle to a BLASTable database, which you can then use to retrieve sequences.

Prerequisites:

You have created a BLASTable database with the ‘-o T’ option.
You have the NCBI fastacmd tool installed.

For example, suppose the original input file looks like:

>my_seq_1
ACCGACCTCCGGAACGGATAGCCCGACCTACG
>my_seq_2
TCCGACCTTTCCTACCGCACACCTACGCCATCAC
...

and you’ve created a BLASTable database from that with the command

cd /my_dir/
formatdb -i my_input_file -t Test -n Test -o T

then you can get a handle to this database with the command

fastacmd = Bio::Blast::Fastacmd.new("/my_dir/Test")

Arguments:

database

path and name of BLASTable database

Public Instance Methods

each ()

Alias for: each_entry

each_entry () { |entry| ... }

Source

    # File lib/bio/io/fastacmd.rb
129 def each_entry
130   cmd = [ @fastacmd, '-d', @database, '-D', '1' ]
131   Bio::Command.call_command(cmd) do |io|
132     io.close_write
133     Bio::FlatFile.open(Bio::FastaFormat, io) do |f|
134       f.each_entry do |entry|
135         yield entry
136       end
137     end
138   end
139   self
140 end

Iterates over all sequences in the database.

fastacmd.each_entry do |fasta|
  p [ fasta.definition[0..30], fasta.seq.size ]
end

Returns: a Bio::FastaFormat object for each iteration

Also aliased as: each

fetch (list)

Source

    # File lib/bio/io/fastacmd.rb
108 def fetch(list)
109   if list.respond_to?(:join)
110     entry_id = list.join(",")
111   else
112     entry_id = list
113   end
114 
115   cmd = [ @fastacmd, '-d', @database, '-s', entry_id ]
116   Bio::Command.call_command(cmd) do |io|
117     io.close_write
118     Bio::FlatFile.new(Bio::FastaFormat, io).to_a
119   end
120 end

Get the sequence for a list of IDs in the database.

For example:

p fastacmd.fetch(["sp:1433_SPIOL", "sp:1432_MAIZE"])

This method always returns an array of Bio::FastaFormat objects, even when the result is a single entry.

Arguments:

ids: list of IDs to retrieve from the database

Returns: array of Bio::FastaFormat objects

get_by_id (entry_id)

Source

   # File lib/bio/io/fastacmd.rb
93 def get_by_id(entry_id)
94   fetch(entry_id).shift
95 end

Get the sequence of a specific entry in the BLASTable database. For example:

entry = fastacmd.get_by_id("sp:128U_DROME")

Arguments:

id: id of an entry in the BLAST database

Returns: a Bio::FastaFormat object