Hi Josch,
On Thu, Oct 23, 2014 at 7:25 AM, Johannes Schauer <[email protected]> wrote: > Hi, > > On Wed, 22 Oct 2014 10:07:44 +0100 Jorge Soares <[email protected]> > wrote: > > All scripts automatically detect whether the input is a FASTA or FASTQ > file. > > Input and output files can be gzipped. > > An input file is assumed to be gzipped if its name ends with .gz. > > To gzip an output file, just name it with .gz at the end. > > You can use a minus sign for a filename to use stdin or stdout, so > scripts can be piped together. > > A developer API is also provided by this package. > > There are plenty of examples in tasks.py > > this description goes into lots of detail about how fastaq is able to > detect > whether or not the input is a fasta or fastaq file. But it does not > mention at > all what the program is actually able to do in the end. Agreed. > Going to the github > website I see that it is able to calculate the reverse complement of all > sequences in the input file. Can it do anything else? Having this > information > in the description is much more important than mentioning how it detects > gzipped input files for example. > I will change it now. > > Also, the name might be too general. The program name is the same as the > format > it reads. This makes it look as if this program is the somehow *official* > way > to read, write and manipulate fasta/fastaq files. I'm not sure I agree with this statement. If we called it fastaq-tools, this could also be seen as the *official* way to deal with fasta or fastq files. > But you don't see programs > called jpeg or odt or avi in Debian either. Maybe you should convince > upstream > to use a more unique name than the file format it operates on. > > I know exactly what you mean and I agree to a certain extent. I had actually mentioned it at the Debian Med sprint meeting as packaging fastaq was one of the actions that came out of the sprint. However we (me and upstream that sits behind me) believe this is a short name that expresses, along with a proper description, what the software does. Nowhere will we say that fastaq is the ultimate way to manipulate, write, read, season, cook or serve fasta or fastq files. We will, however, think it. :) Kind regards, Jorge
