search

zstephens / neat-genreads

NEAT read simulation tools
Other
95 stars 27 forks source link

matplotlib imported in genMutModel but not used #42

Closed thondeboer closed 6 years ago

thondeboer commented 6 years ago

It seems that genMutModel has an import statement for matplotlib but is never used.

import matplotlib.pyplot as mpl

thondeboer commented 6 years ago

Think I see why this happened...It looks like you added the import statement to the wrong script, since the script genSeqErrorModel.py does NOT have the import statement, but I see this code down the line...

    if PLOT_STUFF:
            mpl.rcParams.update({'font.size': 14, 'font.weight':'bold', 'lines.linewidth': 3})

            mpl.figure(1)
            Z = np.array(initQ).T
            X, Y = np.meshgrid( range(0,len(Z[0])+1), range(0,len(Z)+1) )
            mpl.pcolormesh(X,Y,Z,vmin=0.,vmax=0.25)
            mpl.axis([0,len(Z[0]),0,len(Z)])
            mpl.yticks(range(0,len(Z),10),range(0,len(Z),10))
            mpl.xticks(range(0,len(Z[0]),10),range(0,len(Z[0]),10))
            mpl.xlabel('Read Position')
            mpl.ylabel('Quality Score')
            mpl.title('Q-Score Prior Probabilities')
            mpl.colorbar()
zstephens commented 6 years ago

fixed in the latest round of small tweaks.

(in genSeqErrorModel.py there's an import right after input argument parsing if --plot is specified)