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CancerRxGene / gdsctools

Tools related to the Genomics of Drug Sensitivity in Cancer (GDSC) projects (http://www.cancerrxgene.org/ )
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Bug in folder creation when tissue type is unspecified in ANOVAReport( ) #147

Closed elisabeth-chen closed 8 years ago

elisabeth-chen commented 8 years ago

Following section 12. Reproducibility on gdsctools.readthedocs,

When calling:: import wget #For python 3, wget is not default wget.download(http://www.cancerrxgene.org/gdsc1000/Data/anova/BRCA/DATA/INPUT/ANOVA_input.txt) from gdsctools import * an = ANOVA("ANOVA_input.txt", "ANOVA_input.txt") an.setttings.pvalue_correction_method = "qvalue" an.settings.equal_var_ttest = False report = ANOVAReport(an) report.settings.directory = "BRCA" report.create_html_pages()

The manova is created when defining the ANOVAReport class and is created in folder "unspecified". Setting report.settings.directory = "BRCA" creates a new folder "BRCA", where the html report is saved. However, original manova.html is still located in "unspecified/associations/manova.html", so clicking on the "MANOVA Results" link in section 3 of the html index (Explore all signfiicant results), gives a missing file error.

cokelaer commented 8 years ago

This should work as expected now within the git source code