Re: [Seqan-dev] readRecord error

[Bartha Dániel <daniel.bartha@gmail.com>]

Hi Manuel,
Thank you for the answer. I check this when i arrive in the laboratory. The documentation was a bit misleading, because of the converting (or not...) ambigous character to n in dna5. But thank you very much, and have a nice day!

Daniel

2013.07.17. 9:41, "Holtgrewe, Manuel" <manuel.holtgrewe@fu-berlin.de> ezt írta:

Hi Daniel,

I think the problem is that you have non-CGATN characters in your file (W in your case). This leads to an error when reading at the moment, sadly in an uncommunicative way. We plan to improve this in the future (i.e. your pick of error or convert to N).

You can fix your problem by loading your sequences into a CharString and then assigning it into a Dna5String if you need the encoding of 0-4 for indices, for example. Otherwise, you can just load it into CharString and process it from there.

Cheers,
Manuel
________________________________________
From: Bartha Dániel [daniel.bartha@gmail.com]
Sent: Tuesday, July 16, 2013 10:10 AM
To: SeqAn Development
Subject: Re: [Seqan-dev] readRecord error

Hi Manuel and other list members,

thank you for your help. I attached the only source file, the results
i get and the input file i use (it's gzipped only for the attachment).

I think, its possible that i make something wrong, but why does it
work for the first two records, and why not for the others? I tried
formerly the basic IO features of the library (just read and dump),
and everything went proper.

And this is the v1.4.0.

Thanks again, and sorry if my problem would be too banal.

Daniel
Live long and prosper
Bartha Dániel
MTA-VMRI, 2013


2013/7/15 Holtgrewe, Manuel <manuel.holtgrewe@fu-berlin.de>:
> Hi Daniel,
>
> if possible then please use English.
>
> Can you send the FASTA file (or a part that gives you problems) to the list together with the .cpp program so we can have a look?
>
> Thanks,
> Manuel
> ________________________________________
> From: Bartha Dániel [daniel.bartha@gmail.com]
> Sent: Monday, July 15, 2013 5:34 PM
> To: seqan-dev@lists.fu-berlin.de
> Subject: [Seqan-dev] readRecord error
>
> Greetings Everyone,
>
> i am quite new by sequan, and i have a problem.
>
> I want to use the the readRecord function. I the tutorials and the
> documentation, and made a simple program:
>
>    SequenceStream inStream(argv[1]);
>     if ( isGood(inStream) )
>     {
>     while ( !atEnd(inStream) )
>     {
>     String<char> id;
>     String<Dna5> seq;
>     if (readRecord(id, seq, inStream) != 0){std::cerr << "ERROR:
> readRecord\n";return 1;}
>
>         (...)
>     }
>     }
>
> I read from a fasta file, and make something with the sequences at
> character level, it doesn't matter, what. The two first sequences
> are readed, but then i get my error message, independent from the
> content of the third record, for example even if i copy the first
> record after the second, it is the same.
>
> is there a special behaviour of the fasta parsing i have to know, or
> do i make something wrong? I use linux, i wrote a simple console
> application, and the its input independent as far as i see.
>
> And an other question: is the german language allowed on this mailing list?
>
> Many-many thanks!
>
> Daniel
>
> Live long and prosper
> Bartha Dániel
> MTA-VMRI, 2013
>
> _______________________________________________
> seqan-dev mailing list
> seqan-dev@lists.fu-berlin.de
> https://lists.fu-berlin.de/listinfo/seqan-dev
>
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