[BioRuby-ja] mask on illumina-data

[遠藤大二]

Dear All
I start to use illumina-formated data.

On the start, data was parsed as below.

Data*****
@ILLUMINA-554790:34:6:107:18082:1570#0/1
AATCGTTGTAGATTCATTACTGCTCCTGAGCGGTTTACAGGAGTAAGTGTAGACGTTGAGAAATGATATTTGTGAA
+ILLUMINA-554790:34:6:107:18082:1570#0/1
efgggfffffffffffggaggggggggg[ggg[gggggagfdfafffaff_aadc^dfYaffcffKaca_^aXcBB
@ILLUMINA-554790:34:6:107:18268:1571#0/1
AGCAAGCAATCGCCAGCAGCAGAGTGCCAAGACGCCCCAGCGCAAACCACAGTCTGCCCGCTTTGCTGTTGCTGGT
+ILLUMINA-554790:34:6:107:18268:1571#0/1
cccSc]\LYSaYYbKcc[ccccccacY_c^aRaZSca\\OYaaaaJR`X\]]FHX^aQaHR\PWSaaccaaaILca
@ILLUMINA-554790:34:6:107:18774:1566#0/1
CCAGGCAAAGAGATCGCGCATAGCGGTAAATTTATTCGACAACAGCAGCCAGATAGCAAAATCACGCAGCAGCCAG
+ILLUMINA-554790:34:6:107:18774:1566#0/1
hhhhhhhhhhhghggghfhhhehhhhffhfhhhhhhhdahghchfaggafhcah[ffhefhcehffahhaffdh_a

Parsing script*****

require 'bio'
quality_threshold = 60
Bio::FlatFile.open('text.txt').each do |entry|
	p entry.format
	p entry.entry_id
	p entry.seq
	hq_seq = entry.mask(quality_threshold, mask_char='n')
end

*******************

But,
p entry.format   returns nil
and
entry.mask    returns    undefined method `mask' for
#<Bio::Fastq:0x7f1eb5d9dc28> (NoMethodError)

How I set format to FASTQ_ILLUMINA and use 'mask' method.
'http://bioruby.open-bio.org/rdoc/'  is so difficult for me and need
help to use it.

With best wishes,
Daiji Endoh