Hi,
On Wed, 22 Oct 2014 10:07:44 +0100 Jorge Soares <j.s.soares@gmail.com> 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.
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.
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.
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.