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biocore / emperor

Emperor a tool for the analysis and visualization of large microbial ecology datasets
http://biocore.github.io/emperor/
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Compare plots fails if input directory contains files _other than_ pc.txt #323

Closed lkursell closed 9 years ago

lkursell commented 9 years ago

For some reason, the transform coordinates file posted a "Icon?" file in the output directory, leading to the error:

if not lines[0].startswith('pc vector number'): IndexError: list index out of range

Removing the non _pc.txt files solves this.

ElDeveloper commented 9 years ago

AFAIK the Icon? files are generated by OSX, so the problem is not really transform_coordinates.py it is instead the way Emperor looks for files inside a folder.

On (Dec-04-14|11:58), Luke Ursell wrote:

For some reason, the transform coordinates file posted a "Icon?" file in the output directory, leading to the error:

if not lines[0].startswith('pc vector number'): IndexError: list index out of range

Removing the non _pc.txt files solves this.

Reply to this email directly or view it on GitHub: https://github.com/biocore/emperor/issues/323

lkursell commented 9 years ago

It would also help if the documentation for make_emperor.py -h listed a more explicit explanation of doing procrustes analysis, aka the need to run transform_coordinate_matrix.py before passing into emperor.