sc932
commented
10 years ago The authors recommend using IGV to view the output.
http://www.broadinstitute.org/igv/
Just import the assembly, bam and ALE scores. You can convert the .ale file to a set of .wig files with ale2wiggle.py and IGV can read those directly. Depending on your genome size you may want to convert the .wig files to the BigWig format.
The internal, debugging plotter is not in active development and is no longer supported.
I'm trying to reproduce the documentation example on an Ubuntu x86_64 machine.
plotter3.py is not producing a readable pdf.
I ran the command: "plotter3.py Ecoli_first350k.ale" The output is as follows:
Reading in contig: gi|169887498|gb|CP000948.1| len 3500000
[=================100%===================] You now have a list of contigs, try contig[0].plot() Generating figures... smoothing i smoothing p smoothing k smoothing d Thresholding for i Gauss1: mu: -0.087789, std: 0.100000 Gauss2: mu: -0.087789, std: 0.100000 mean, std -0.0877893514145 0.1 Thresholding for d Gauss1: mu: 0.087185, std: 0.100000 Gauss2: mu: 0.087185, std: 0.100000 mean, std 0.0871846640937 0.1 Thresholding for p Run 0 produced invalid model, omitted. Run 1 produced invalid model, omitted. Run 2 produced invalid model, omitted. Run 3 produced invalid model, omitted. Run 4 produced invalid model, omitted. pymix failed to find mixture model, using single gaussian Gauss1: mu: -0.011573, std: 0.130456 Gauss2: mu: -0.115732, std: 0.130456 mean, std -0.0115731856381 0.130455564816 Thresholding for k Gauss1: mu: -0.026976, std: 0.100000 Gauss2: mu: -0.026976, std: 0.100000 mean, std -0.0269761111416 0.1 [] starts and ends of windowing threshold [] [] [] starts and ends of windowing threshold [] [] [] starts and ends of windowing threshold [] [] [] starts and ends of windowing threshold [] [] gi|169887498|gb|CP000948.1| had (0.000000) thresholded. saved file Ecoli_first350k.ale.pdf Executed Sucessfully
Is this a bug or possibly caused by a lack of, or old version of a dependency?
Thanks. Nick