[BioRuby] mask on Ilumina-format
遠藤大二
daijiendoh at gmail.com
Mon Mar 28 23:45:55 UTC 2011
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
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