peak_pie.py error and doc improvement

[lucapinello]

• Launching peak_pie.py without argument generate a type error instead of reporting the usage (TypeError: 'NoneType' object is not iterable)
• The doc should be improved a little bit. It is not clear where I can find a GFF with all the annotations categories (especially the introns) as the one you have in the example. If you use the GTF file for example from Genome Browser or from Ensemble and convert to GFF you only have CDS and exon. Could you explain in the doc how to get an annotated GFF file?

BTW thanks for this nice library and for keeping improving it.

Luca

[daler]

Thanks for pointing this out. The peak_pie.py help issue is fixed in d67a7f8.

For your second question, that's kind of beyond the scope of pybedtools . . . but see gffutils for much more on manipulating GFF/GTF files. I should probably add a "add intron annotations" method to gffutils for cases like this.

[lucapinello]

Thanks for you very very fast response!

I will take a look to your other project.

Thanks again,

Luca