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jorvis / biocode

Bioinformatics code libraries and scripts
MIT License
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problem with compare_gene_structures.py #37

Closed lfaino closed 7 years ago

lfaino commented 8 years ago

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 commented 8 years ago

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 commented 7 years ago

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