[julia-users] Re: Bio package - open function error
Thanks!
On Sunday, January 17, 2016 at 4:49:23 AM UTC-8, Kenta Sato wrote:
>
> Hi, Elmo,
>
> Thank you for using our Bio.jl package.
>
> I guess that is because you didn't run `using Bio.Seq` before opening a
> FASTA file. Types and functions related to biological sequences are defined
> in the`Bio.Seq` module, not `Bio`.
> And, you don't have to install neither Colm nor Ragel in order to use
> Bio.jl. Those tools are required only when you need to write your own
> Ragel-based parser. The FASTA parser generated from Ragel is already
> bundled in Bio.jl.
>
> On Sunday, January 17, 2016 at 2:46:51 PM UTC+9, St Elmo Wilken wrote:
>>
>> Hi,
>>
>> I am brand new to the Bio package and wanted to play with it a bit. I
>> have some transcription data in a FASTA file which I want to read. Based on
>> the docs I tried:
>> stream = open("somefile.fasta", FASTA)
>> but all this generates is
>> ERROR: UndefVarError: FASTA not defined
>> Am I doing something wrong?
>>
>> Also, do I need to have colm and ragel installed for Bio to work?
>>
>> Thanks!
>>
>
[julia-users] Re: Bio package - open function error
Hi, Elmo,
Thank you for using our Bio.jl package.
I guess that is because you didn't run `using Bio.Seq` before opening a
FASTA file. Types and functions related to biological sequences are defined
in the`Bio.Seq` module, not `Bio`.
And, you don't have to install neither Colm nor Ragel in order to use
Bio.jl. Those tools are required only when you need to write your own
Ragel-based parser. The FASTA parser generated from Ragel is already
bundled in Bio.jl.
On Sunday, January 17, 2016 at 2:46:51 PM UTC+9, St Elmo Wilken wrote:
>
> Hi,
>
> I am brand new to the Bio package and wanted to play with it a bit. I have
> some transcription data in a FASTA file which I want to read. Based on the
> docs I tried:
> stream = open("somefile.fasta", FASTA)
> but all this generates is
> ERROR: UndefVarError: FASTA not defined
> Am I doing something wrong?
>
> Also, do I need to have colm and ragel installed for Bio to work?
>
> Thanks!
>
