I’d like to, though that’s been on the back burner for a while now. The problem is that some fasta/fastq files don’t conform to the ‘norm’ for their format. For instance, I’ve seen fasta’s with no description tag. I think a good solution would be to have seqdb2 try to automatically detect the file type by default, but also give the user the option to specify which loader to use.
From: [email protected] [mailto:[email protected]] On Behalf Of Namshin Kim Sent: Monday, February 09, 2009 9:22 PM To: [email protected] Subject: [pygr] Re: seqdb2 Hi Alex, It has two separate modules for fasta and fastq. Do you have any plan to merge those two functions in one module that can automatically check whether the file is fasta or fastq? Yours, Namshin Kim On Tue, Feb 10, 2009 at 8:21 AM, Alex Nolley <[email protected]> wrote: Hey everyone, I just wanted to give an update on my seqdb2 project. seqdb2 allows the user to create a database from a FASTA or FASTQ file and then query each record by name or index, retrieving sequence, description or accuracy information. Let me know what you think. available from git repo: git://iorich.caltech.edu/git/public/seqdb2 documentation: http://iorich.caltech.edu/~nolleyal/seqdb2doc.html --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
