class Bio::Blast::RPSBlast::Report

NCBI RPS Blast (Reversed Position Specific Blast) default output parser.

It supports defalut (-m 0 option) output of the “rpsblast” command.

Because this class inherits Bio::Blast::Default::Report, almost all methods are eqaul to Bio::Blast::Default::Report. Only DELIMITER (and RS) and few methods are different.

By using Bio::FlatFile, (for example, Bio::FlatFile.open), rpsblast result generated from multiple query sequences is automatically splitted into multiple Bio::BLast::RPSBlast::Report objects corresponding to query sequences.

Note for multi-fasta results WITH using Bio::FlatFile: Each splitted result is concatenated with header of the result which describes RPS-BLAST version and database information, if possible.

Note for multi-fasta results WITHOUT using Bio::FlatFile: When parsing an output of rpsblast command running with multi-fasta sequences WITHOUT using Bio::FlatFile, each query's result is stored as an “iteration” of PSI-Blast. This behavior may be changed in the future.

Note for nucleotide results: This class is not tested with nucleotide query and/or nucleotide databases.

Constants

DELIMITER

Delimter of each entry for RPS-BLAST.

DELIMITER_OVERRUN

(Integer) excess read size included in DELIMITER.

FLATFILE_SPLITTER

Flatfile splitter for RPS-BLAST reports. It is internally used when reading RPS-BLAST report. Normally, users do not need to use it directly.

Note for Windows: RPS-BLAST results generated in Microsoft Windows may not be parsed correctly due to the line feed code problem. For a workaroud, convert line feed codes from Windows(DOS) to UNIX.

Public Class Methods

new(str) click to toggle source

Creates a new Report object from a string.

Using Bio::FlatFile.open (or some other methods) is recommended instead of using this method directly. Refer Bio::Blast::RPSBlast::Report document for more information.

Note for multi-fasta results WITHOUT using Bio::FlatFile: When parsing an output of rpsblast command running with multi-fasta sequences WITHOUT using Bio::FlatFile, each query's result is stored as an “iteration” of PSI-Blast. This behavior may be changed in the future.

Note for nucleotide results: This class is not tested with nucleotide query and/or nucleotide databases.

    # File lib/bio/appl/blast/rpsblast.rb
173 def initialize(str)
174   str = str.sub(/\A\s+/, '')
175   # remove trailing entries for sure
176   str.sub!(/\n(RPS\-BLAST.*)/m, "\n") 
177   @entry_overrun = $1
178   @entry = str
179   data = str.split(/(?:^[ \t]*\n)+/)
180 
181   if data[0] and /\AQuery\=/ !~ data[0] then
182     format0_split_headers(data)
183   end
184   @iterations = format0_split_search(data)
185   format0_split_stat_params(data)
186 end

Public Instance Methods

query_def() click to toggle source

Returns definition of the query. For a result of multi-fasta input, the first query's definition is returned (The same as iterations.first.query_def).

    # File lib/bio/appl/blast/rpsblast.rb
191 def query_def
192   iterations.first.query_def
193 end
query_len() click to toggle source

Returns length of the query. For a result of multi-fasta input, the first query's length is returned (The same as iterations.first.query_len).

    # File lib/bio/appl/blast/rpsblast.rb
198 def query_len
199   iterations.first.query_len
200 end