problem with compare_gene_structures.py

[lfaino]

Dear,
I have a problem using the code compare_gene_structures.py. I get the following error: File "/home/faino001/bin/biocode/gff/compare_gene_structures.py", line 612, in
process_files(args)
File "/home/faino001/bin/biocode/gff/compare_gene_structures.py", line 322, in process_files
for exon_1 in sorted(feat_1) :
UnboundLocalError: local variable 'feat_1' referenced before assignment

any idea why?

thanks
Luigi

[lfaino]

Hi,
well I solved the previous error but now I have compatibility issues. the new bedtools do not use -nms and -score anymore. how can I solve the problem? any suggestions?

thanks
Luigi

[jorvis]

I corrected this in 8c8c642, which replaced the -nms and -scores options with "-c 4 -o collapse". Reference:

https://groups.google.com/forum/#!topic/bedtools-discuss/pvd-Tcb3AXI