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biocore / wol

Reference Phylogeny for Bacterial and Archaeal Genomes
BSD 3-Clause "New" or "Revised" License
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gOTU_from_maps.py 'NoneType' object has no attribute 'lower' #33

Closed jgarbe256 closed 4 years ago

jgarbe256 commented 4 years ago

When I run gOTU_from_maps.py without specifying a method I get this error:

gOTU_from_maps.py alignments gOTU Samples to read: 1. Traceback (most recent call last): File "/home/umgc-staff/jgarbe/dev/software/shogun-scripts/gOTU_from_maps.py", line 235, in main() File "/home/umgc-staff/jgarbe/dev/software/shogun-scripts/gOTU_from_maps.py", line 97, in main data[sample] = parse_map(f, args.method, sbj2g) File "/home/umgc-staff/jgarbe/dev/software/shogun-scripts/gOTU_from_maps.py", line 131, in parsemap m = method.lower() AttributeError: 'NoneType' object has no attribute 'lower'

It seems that the parse_map function should check if the method is None before attempting to convert it to lowercase:

if method is None: return parsesimple(f, 1, sbj2g) m = method.lower() if m_ == 'centrifuge': return parsecentrifuge(f, sbj2g) elif m == 'bowtie2': return parsesimple(f, 2, sbj2g) elif m is None: return parse_simple(f, 1, sbj2g) else: raise ValueError('Unsupported method: %s.' % method)

qiyunzhu commented 4 years ago

Hello @jgarbe256 Thanks for reporting this bug! I have fixed it and updated the repository (#35). By the way, we are working on a new program: Woltka, which replaces / formalizes the data analysis protocols mentioned in this tutorial. It is in alpha release status. Feel free to try!

jgarbe256 commented 4 years ago

I'll check it out, thanks!

On Sun, May 31, 2020 at 12:25 PM Qiyun Zhu notifications@github.com wrote:

Hello @jgarbe256 https://github.com/jgarbe256 Thanks for reporting this bug! I have fixed it and updated the repository (#35 https://github.com/biocore/wol/pull/35). By the way, we are working on a new program: Woltka https://github.com/qiyunzhu/woltka, which replaces / formalizes the data analysis protocols mentioned in this tutorial. It is in alpha release status. Feel free to try!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/biocore/wol/issues/33#issuecomment-636501621, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEOV6A7RJYAUDF2NWTCDI2DRUKHJ7ANCNFSM4NICBZAQ .

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John Garbe, Ph.D. Informatics Lead | University of Minnesota Genomics Center | genomics.umn.edu University of Minnesota | umn.edujgarbe@umn.edu | 612-807-3379