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
Source
# 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
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.
Public Instance Methods
Source
# File lib/bio/appl/blast/rpsblast.rb 191 def query_def 192 iterations.first.query_def 193 end
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).
Source
# File lib/bio/appl/blast/rpsblast.rb 198 def query_len 199 iterations.first.query_len 200 end
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).