[BioRuby] Fwd: mask on Ilumina-format

[遠藤大二]

Thank you Nishiyama-san and Bonnal-san

1 I use bioruby on Ubuntu10.10 with synnaptic-mediated installation.
The version is 1.40-2. So I cannot use mask. And I will install
bioruby manually.
2 To setup fastq_illumina -format I had not been know. The scripts below.

q = Bio::Fastq.new("@test\natgcgataatgc\n+test\nCCCCDDDDBXXX\n")
 q.format = :fastq_illumina

As it is very difficult for me how to make a new object with certain
format. Mr Bonnal's suggestion is very helpful for me.

Thanks again

---------- 転送メッセージ ----------
From: Raoul Bonnal <bonnal at ingm.org>
日付: 2011年3月29日16:51
件名: Re: [BioRuby] mask on Ilumina-format
To: 遠藤大二 <daijiendoh at gmail.com>
Cc: bioruby at lists.open-bio.org


>From a Goto-san's mail:
 q = Bio::Fastq.new("@test\natgcgataatgc\n+test\nCCCCDDDDBXXX\n")
 q.format = :fastq_illumina
 puts q.mask(your_quality_threshold, your_masking_char)
keep in mind mask masks the bases < your_quality_threshold
by default the format is :fastq_sanger if you call q.quality_scores (
without specify q.format)
On 29/mar/2011, at 01.45, 遠藤大二 wrote:

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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Ra
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