blaiseli

`bioawk` segfaults when asked to parse an empty files ```bash $ touch test.fastq $ gzip test.fastq $ bioawk -c fastx '{print}' test.fastq.gz Segmentation fault ``` Actually, it also segfaults on...

Possibility to source a script and passing arguments to it

2

Is it possible to pass arguments to a script using docopt when sourcing this script? I tried redefining commandArgs as suggested in http://stackoverflow.com/a/14526329/1878788, but this fails. for instance, my docopt...

I'm using `bedtools intersect` (v2.27.1-1-gb87c465-dirty compiled from git latest source) on two bed filed that seem normal (http://paste.ubuntu.com/p/GxPWFb9Vby/ and http://paste.ubuntu.com/p/3Ndz5jkmrW/), and I get a strange error: ``` $ bedtools intersect...

Spurious strand indication in fasta header with option -nameOnly of getfasta

3

I expect the fasta header to only contain the name with option `-nameOnly` of `getfasta`, but there is an extra strand between parentheses: ``` $ head tmp.GFP_mRNA/mm6.minus.bed GFP_mRNA 0 21...

I added an option so sort by sequence size. It seems to work. This might be useful.

Consider the following usage description: ``` Usage: qaf_demux.jl [-i | --input_fastq ] (-o | --output_dir ) -b -s [-m ] -h --help Show this help message and exit. -i --input_fastq...

dontprint icon not appearing even on suggested test arxiv article

3

I tried to install dontprint on Firefox under Xubuntu 16.04. After re-starting the browser, I started following the "getting started" thing, but I can't find a dontprint icon allowing me...

Add documentation and example about IO operations

3

I'm surprised how hard it is for me to understand how to write a simple program that reads from stdin or from a file and processes the data line by...

**Describe the bug** The documentation lacks examples of how to generate seqlogos when ambiguous nucleotides are present. I have sequences made of A, C, G, T and N, for which...

How should one proceed to generate a valid empty gzip file using CodecZlib? Here is what I tried: ``` import CodecZlib gz = CodecZlib fh = gz.GzipCompressorStream(open("test_out.gz", "w")) close(fh) ```...