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ablab / rnaquast

Quality assessment of de novo transcriptome assemblies from RNA-Seq data
http://cab.spbu.ru/software/rnaquast
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name 'math' is not defined #23

Closed rasskaz closed 8 months ago

rasskaz commented 8 months ago

rnaQUAST.py --test

`Traceback (most recent call last): File "/home/eavodiasova/miniconda3/envs/quast/bin/rnaQUAST.py", line 348, in return_code = main_utils() File "/home/eavodiasova/miniconda3/envs/quast/bin/rnaQUAST.py", line 311, in main_utils separated_reports[i_transcripts].get_separated_report\ File "/home/eavodiasova/miniconda3/envs/quast/share/rnaquast-2.2.3-0/report/SeparatedReport.py", line 57, in get_separated_report DistributionReport.DistributionReport([transcripts_metrics], db_genes_metrics, self.output_dir, logger, PRECISION) File "/home/eavodiasova/miniconda3/envs/quast/share/rnaquast-2.2.3-0/report/DistributionReport.py", line 20, in init self.get_basic_plots(transcripts_metrics, db_genes_metrics, precision) File "/home/eavodiasova/miniconda3/envs/quast/share/rnaquast-2.2.3-0/report/DistributionReport.py", line 41, in get_basic_plots self.get_transcript_length_plot(db_genes_metrics, transcripts_metrics, self.output_dir, precision, short_report_visible=True) File "/home/eavodiasova/miniconda3/envs/quast/share/rnaquast-2.2.3-0/report/DistributionReport.py", line 161, in get_transcript_length_plot transcript_len_plot.plot_compare_distribution(self.short_report_plots) File "/home/eavodiasova/miniconda3/envs/quast/share/rnaquast-2.2.3-0/report/UtilsPictures.py", line 154, in plot_compare_distribution step = Plot.get_step(self.def_step, [self.isoforms_distribution], self.num_points) File "/home/eavodiasova/miniconda3/envs/quast/share/rnaquast-2.2.3-0/report/UtilsPictures.py", line 350, in get_step x_begin, x_end = cls.get_x_begins_ends_plot(distributions, False) File "/home/eavodiasova/miniconda3/envs/quast/share/rnaquast-2.2.3-0/report/UtilsPictures.py", line 316, in get_x_begins_ends_plot if not math.isinf(x_end): NameError: name 'math' is not defined

ERROR! Exception caught! ` Adding a math import to rnaquast-2.2.3-0/report/UtilsPictures.py solves the problem

andrewprzh commented 8 months ago

@rasskaz

Thanks for the report, this is known bug, which was fixed in version 2.2.4. However, I was never able to upload a newer version to bioconda due to its internal problems.

Best Andrey