happykhan/bincrisp

Find CRISPRS in genomes using pilercr & draws a matrix

bincrisp's Issues

Different output when the order of input genomes change

Hi Nabil,

I tried your tool here, great potential as there aren't any other tools out there to visualize and compare spacers between genomes. But I found a bug (I think).

In an attempt to identify spacers in a dataset, I had my input genomes ordered as they appear in the phylogeny (orderNum_strainName.fna). To do that, I had to sort the files being read by altering:

for name in sorted(files):
into
for name in sorted(files, key=lambda x: int(x.split('_')[0])):
It worked perfectly until I realised that the output before ordering is very different to after ordering. It could be an issue with the part of the script which parses pilercr report because I looked at the drawarray and found that for strain X, ordered vs. non-ordered has different number of spacers. It could also be an issue in the drawing code, because drawarray predicts for example 10 spacers for strain X, but the resulting svg shows only 2 spacers (in the case of ordered input).

Now I know this tool may not be supported anymore, but just a shot in the dark.

Thanks,
Areej

Error in bincrisp.py

Hello sir,
I started using bincrisp in ubuntu in virtualbox but I am not able to do so, its showing error in every print command as--

(base) aakash@aakash-VirtualBox:~/binCrisp$ python binCrisp.py findcr -d /home/aakash/ecolik12/ proutput File "binCrisp.py", line 70 print 'Comparing CR files' ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print('Comparing CR files')?
"
Could you guide me on this?