Re: [Seqan-dev] Problem Reading Records

[Daniel Mapleson <daniel.mapleson@tgac.ac.uk>]

That works!   Thanks for the workaround.

Dan


On 13/08/13 22:59, Holtgrewe, Manuel wrote:
> Hi Dan,
>
> this is a bug in the documentation (the behaviour used to be this way but was changed in favour of following the "do not fail silently" motto).
>
> Instead, you should load your sequence into a CharString/String<char> and then assign this to your Dna5String.
>
> We plan to make this behaviour configurable at runtime but have not made the change yet.
>
> I'm sorry for any caused confusion.
>
> Cheers,
> Manuel
> ________________________________________
> From: Daniel Mapleson [daniel.mapleson@tgac.ac.uk]
> Sent: Tuesday, August 13, 2013 12:19 PM
> To: seqan-dev@lists.fu-berlin.de
> Subject: [Seqan-dev] Problem Reading Records
>
> Hello,
>
> I work at the genome analysis centre in Norwich, UK, and am using SeqAn
> within a project primarily to load sequences from FastQ and FastA files.
>
> I have encountered a problem reading records when the record contains a
> sequence outside the DNA5 alphabet.  It was my understanding from the
> documentation that any invalid characters would be automatically
> converted to an 'N'.  Instead the file reading seems to fail with no way
> of continuing where it left off. Is this a known problem or am I doing
> something wrong here?
>
> Relevant code is as follows:
>
>           // Open file, create RecordReader and check all is well
>           std::fstream in(args->fasta_arg, std::ios::in);
>           seqan::RecordReader<std::fstream, seqan::SinglePass<> > reader(in);
>
>           // Create the AutoSeqStreamFormat object and guess the file format.
>           seqan::AutoSeqStreamFormat formatTag;
>           if (!guessStreamFormat(reader, formatTag))
>           {
>               cerr << "ERROR: Could not detect file format for: " <<
> args->fasta_arg << endl;
>               return;
>           }
>
>       ......
>
>           for (unsigned i = 0; (res == 0) && (i < BATCH_SIZE) &&
> !atEnd(reader); ++i)
>           {
>               CharString id;
>               Dna5String seq; // Supposed to auto convert chars not in
> {A,T,G,C,N} to N
>
>               res = seqan::readRecord(id, seq, reader, formatTag);
>               if (res == 0)
>               {
>                   seqan::appendValue(names, id);
>                   seqan::appendValue(seqs, seq);
>
>                   recordIndex++;
>               }
>               else
>               {
>                   cerr << endl << "ERROR: cannot finish processing all
> records in file.  Encountered an error reading file at record: " <<
> recordIndex
>                        << "; Error code: " << res << "; Last sequence ID:
> " << id << "; Continuing to process currently loaded records." << endl;
>               }
>           }
>
>
> Best regards,
> Dan Mapleson
>
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