Add support for input of gzip files and/or stdin

[Jason Vander Heiden]

From @vrbacky :
"I'm preparing some new pipelines and I'd like to cut primers from our amplicon sequencing data. MaskPrimers seems to be good tool to do it but it'd be great if it can use fastq.gz files or STDIN/STDOUT. Do you plan to implement it?"

I think .gz should be pretty straightforward. I don't think biopython or scikit-bio have native support fastq.gz, but I'm guessing opening the file with the gzip library will work. Need to look into it.

[Jason Vander Heiden]

Got another request for this. Bio.SeqIO.index will not work with standard gzipped files though, so it would either need to be done through a temp file or only support BGZF compressed files.

[Jason Vander Heiden]

Going to close this, as it would only work for the first step in the pipeline anyway. It'd be overly slow to uncompress/recompress for every step in a pipeline, so one uncompress at the beginning seems more straightforward.