Class: Bio::MAF::FASTARangeReader
- Inherits:
-
Object
- Object
- Bio::MAF::FASTARangeReader
- Defined in:
- lib/bio/maf/tiler.rb
Constant Summary collapse
- GT =
'>'.getbyte(0)
Instance Attribute Summary collapse
-
#f ⇒ Object
readonly
Returns the value of attribute f.
-
#pos ⇒ Object
readonly
Returns the value of attribute pos.
Instance Method Summary collapse
-
#initialize(fspec) ⇒ FASTARangeReader
constructor
A new instance of FASTARangeReader.
- #position_at_start ⇒ Object
- #read_interval(z_start, z_end) ⇒ Object
Constructor Details
#initialize(fspec) ⇒ FASTARangeReader
Returns a new instance of FASTARangeReader.
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# File 'lib/bio/maf/tiler.rb', line 190 def initialize(fspec) if fspec.respond_to? :seek @f = fspec else reader_class = if fspec =~ /.gz$/ Zlib::GzipReader else File end @f = reader_class.open(fspec) end position_at_start end |
Instance Attribute Details
#f ⇒ Object (readonly)
Returns the value of attribute f.
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# File 'lib/bio/maf/tiler.rb', line 188 def f @f end |
#pos ⇒ Object (readonly)
Returns the value of attribute pos.
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# File 'lib/bio/maf/tiler.rb', line 188 def pos @pos end |
Instance Method Details
#position_at_start ⇒ Object
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# File 'lib/bio/maf/tiler.rb', line 206 def position_at_start first = f.readline raise "expected FASTA comment" unless first =~ /^>/ @pos = 0 end |
#read_interval(z_start, z_end) ⇒ Object
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# File 'lib/bio/maf/tiler.rb', line 212 def read_interval(z_start, z_end) if z_start < pos position_at_start end data = '' region_size = z_end - z_start in_region = false f.each_line do |line_raw| if line_raw.getbyte(0) == GT raise "unexpected description line: #{line_raw.inspect}" end line = line_raw.strip end_pos = pos + line.size if (! in_region) && pos <= z_start && z_start < end_pos offset = z_start - pos end_offset = [(offset + region_size), line.size].min data << line.slice(offset...end_offset) in_region = true elsif in_region need = region_size - data.size raise "should not happen: region #{region_size}, data #{data.size}, need #{need}" if need < 0 if need > line.size data << line else # last line data << line.slice(0, need) break end end @pos = end_pos end return data end |