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rgt-motifanalysis crashes with '.' FPR value in mtf file

Open charlesfeigin opened this issue 3 years ago • 0 comments

Hi, I'm trying to add a single entry to the jaspar vertebrates database. I have a correctly-formatted pwm, have created a logo and added what seems to be a correctly-formatted entry to a copy of the mtf file. However, while the instructions say that any field can be left blank by adding a '.', when I try to add this value to the FPR field for my TF of interest, I get the following error:

Traceback (most recent call last): File "/home/cfeigin/.local/bin/rgt-motifanalysis", line 33, in sys.exit(load_entry_point('RGT==0.13.1', 'console_scripts', 'rgt-motifanalysis')()) File "/home/cfeigin/.local/lib/python3.8/site-packages/rgt/motifanalysis/Main.py", line 58, in main args.func(args) File "/home/cfeigin/.local/lib/python3.8/site-packages/rgt/motifanalysis/Match.py", line 332, in main motif_set = MotifSet(preload_motifs=filter_values['database']) File "/home/cfeigin/.local/lib/python3.8/site-packages/rgt/MotifSet.py", line 93, in init self.read_mtf(self.motif_data.mtf_list) File "/home/cfeigin/.local/lib/python3.8/site-packages/rgt/MotifSet.py", line 280, in read_mtf thresholds[fpr_list[i]] = float(threshold_list[i]) ValueError: could not convert string to float: '.'

It makes sense that you can't convert a "." to a float, however the documentation and example given here (https://www.regulatory-genomics.org/motif-analysis/additional-motif-data/) seem to indicate that the program should be able to handle this. I've triple-checked that my file is otherwise formatted correctly. Thanks!

charlesfeigin avatar Apr 26 '21 22:04 charlesfeigin