[Biococoa-dev] Even more on sequence formats
Koen van der Drift
kvddrift at earthlink.net
Tue Apr 11 06:08:27 EDT 2006
On Apr 11, 2006, at 5:44 AM, Alexander Griekspoor wrote:
> - I've added support for reading sequence files that weren't saved
> as plain-text but as rtf, basically adding a check and converting
> the file to plain text before continuing with the normal format
That would be great addition.
> - I've changed the raw reading method such that it becomes more
> greedy. Peter's variant reads in all lines as separate entries in
> the matrix dictionary (which is probably what you want in aligned
> phylogenetic sequence files, but not in EnzymeX where people
> usually read in a single sequence file. So I remove all return
> characters first. I had one person complaining that EnzX only read
> the first line when he tried to open his nicely in 80 char columns
> formatted text file.
BCSequenceReader now works very different from the way BCReader does.
I am not using a matrixDictionary anymore (see my comments in the
previous mail, and the actual code). The current BCSequenceReader
already reads a raw file in as one whole.
BTW, be careful with what you put in your README for EnzymeX. I
noticed you wrote that it supports BEAST and TNT formats, but I don't
see those in BCReader. Unless you have a local version that does, of
course ;-) I'll have a look at the readseq code later.
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