Class: Bio::Ngs::Fastx::FastqStats

Inherits:

Object

Object
Bio::Ngs::Fastx::FastqStats

show all

Includes:: Command::Wrapper

Defined in:: lib/bio/appl/ngs/fastx.rb

Overview

usage: fastx_quality_stats [-h] [-N] [-i INFILE] [-o OUTFILE] Part of FASTX Toolkit 0.0.13 by A. Gordon ([email protected])

[-h] = This helpful help screen.
[-i INFILE]  = FASTQ input file. default is STDIN.
[-o OUTFILE] = TEXT output file. default is STDOUT.
[-N]         = New output format (with more information per nucleotide/cycle).

The OLD output TEXT file will have the following fields (one row per column):

column  = column number (1 to 36 for a 36-cycles read solexa file)
count   = number of bases found in this column.
min     = Lowest quality score value found in this column.
max     = Highest quality score value found in this column.
sum     = Sum of quality score values for this column.
mean    = Mean quality score value for this column.
Q1  = 1st quartile quality score.
med = Median quality score.
Q3  = 3rd quartile quality score.
IQR = Inter-Quartile range (Q3-Q1).
lW  = 'Left-Whisker' value (for boxplotting).
rW  = 'Right-Whisker' value (for boxplotting).
A_Count = Count of 'A' nucleotides found in this column.
C_Count = Count of 'C' nucleotides found in this column.
G_Count = Count of 'G' nucleotides found in this column.
T_Count = Count of 'T' nucleotides found in this column.
N_Count = Count of 'N' nucleotides found in this column.
max-count = max. number of bases (in all cycles)

The NEW output format:

cycle (previously called 'column') = cycle number
max-count
For each nucleotide in the cycle (ALL/A/C/G/T/N):
  count   = number of bases found in this column.
  min     = Lowest quality score value found in this column.
  max     = Highest quality score value found in this column.
  sum     = Sum of quality score values for this column.
  mean    = Mean quality score value for this column.
  Q1  = 1st quartile quality score.
  med = Median quality score.
  Q3  = 3rd quartile quality score.
  IQR = Inter-Quartile range (Q3-Q1).
  lW  = 'Left-Whisker' value (for boxplotting).
  rW  = 'Right-Whisker' value (for boxplotting).

Method Summary

Methods included from Command::Wrapper

#class_name, #default_options, included, #initialize, #normalize_params, #options, #options=, #output, #params, #params=, #path, #path=, #pipe_ahead, #pipe_ahead=, #pipe_ahead?, #program, #reset_params, #run, #sub_program, #thor_task, #to_cmd_ary, #use_aliases?