Class: SampleReader

Inherits:
Object
  • Object
show all
Defined in:
lib/sample_reader.rb

Overview

Class containing methods for reading and checking sample information.

Defined Under Namespace

Classes: Sample

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(revcomp1, revcomp2) ⇒ SampleReader

Internal: Constructor method for SampleReader object. The given revcomp1 and revcomp2 flags are stored as instance variables.

revcomp1 - Flag indicating that index1 should be reverse-complemented. revcomp2 - Flag indicating that index2 should be reverse-complemented.

Examples

SampleReader.new(false, false)
# => <SampleReader>

Returns SampleReader object.



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# File 'lib/sample_reader.rb', line 68

def initialize(revcomp1, revcomp2)
  @revcomp1 = revcomp1
  @revcomp2 = revcomp2
end

Class Method Details

.read(file, revcomp1, revcomp2) ⇒ Object

Internal: Class method that reads sample information from a samples file, which consists of ASCII text in three tab separated columns: The first column is the sample_id, the second column is index1 and the third column is index2.

If revcomp1 or revcomp2 is set then index1 and index2 are reverse-complemented accordingly.

file - String with path to sample file. revcomp1 - Flag indicating that index1 should be reverse-complemented. revcomp2 - Flag indicating that index2 should be reverse-complemented.

Examples

SampleReader.read("samples.txt", false, false)
# => [<Sample>, <Sample>, <Sample> ...]

Returns an Array of Sample objects.



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# File 'lib/sample_reader.rb', line 51

def self.read(file, revcomp1, revcomp2)
  sample_reader = new(revcomp1, revcomp2)
  sample_reader.samples_parse(file)
end

Instance Method Details

#samples_parse(file) ⇒ Object

Internal: Method that reads sample information from a samples file, which consists of ASCII text in three tab separated columns: The first column is the sample_id, the second column is index1 and the third column is index2.

file - String with path to sample file.

Examples

samples_parse("samples.txt")
# => [<Sample>, <Sample>, <Sample> ...]

Returns an Array of Sample objects.



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# File 'lib/sample_reader.rb', line 85

def samples_parse(file)
  samples = samples_read(file)
  samples_reverse_complement(samples)
  errors = []
  errors.push(*samples_check_index_combo(samples))
  errors.push(*samples_check_uniq_id(samples))

  unless errors.empty?
    warn errors
    fail SampleReaderError, 'errors found in sample file.'
  end

  samples
end