Error in example

[jpearl01]

Hi pjotrp,

Was just trying to get some of your examples to work, and I ran into an issue, essentially I used this file 'short_trial.aln.fasta'

43617/31050-31061
accaatatcgcc
46P47B1/31054-31065
gccaatatcgcc
7169/31137-31148
gccaatatcgcc
B496/31053-31064
gccaatatcgcc
B502/31118-31129
accaatatcgcc
B503/31055-31066
gccaatatcgcc
B507/31052-31063
accaatatcgcc
B508/31057-31068
accaatatcgcc
B583/31081-31092
accaatatcgcc
B615/31109-31120
accaatatcgcc
B616/31296-31307
gccaatattatt
B617/31057-31068
accaatatcgcc
B618/31052-31063
accaatatcgcc
B619/31062-31073
gccaatatcgcc

Then ran these commands in irb:
require 'bio-alignment'
require 'bigbio' # for the Fasta reader
include Bio::BioAlignment # Namespace
aln = Alignment.new
fasta = FastaReader.new('short_trial.aln.fasta')
fasta.each do | rec |
aln.sequences << rec
end
aln[3][0]

And at this point I get the error:
irb(main):012:0> aln[3][0]
NoMethodError: undefined method []' for #<FastaRecord:0x0000000251f3e0> from (irb):12 from /usr/bin/irb:12:in

'
irb(main):013:0> aln[3]
=> #<FastaRecord:0x0000000251f3e0 @id="46P47B1/31054-31065", @Descr="46P47B1/31054-31065", @seq="gccaatatcgcc">

Am I messing this up somehow?

~josh

[pjotrp]

Hi Josh,

FastaRecord does not support indexed retrieval. You need to wrap it with a Sequence object. There are some examples in the bio-alignment README.

Pj.

[jpearl01]

Yeah, I ended up changing the line:

aln.sequence << rec

to

aln.sequences << Sequence.new(rec.descr,rec.seq)

which worked fine. I just wanted to let you know, because in the file doc/bio-alignment-design.md beginning on line 130 there is a code example that appears to do what I was doing above, but would not work.

Thanks,
~josh

[pjotrp]

I'll fix that. Note that it would be trivial to add a def [] method to FastaRecord (you can even add that yourself by just reopening the class definition in your source). The reason I don't add it in the original is that I have the policy to add minimal functionality to modules and classes - so as to keep them simple.