[miso-users] sashimi_plot failed

[Laurent Manchon]

--Hi,

when running sashimi_plot with this command:
./sashimi_plot --plot-title "DOCK3" --plot-event "ENSG00000088538" prov 
./sashimi_plot_settings.txt --output-dir ./plots

it always failed with:

Traceback (most recent call last):
   File "./sashimi_plot", line 9, in <module>
     load_entry_point('misopy==0.5.4', 'console_scripts', 'sashimi_plot')()
   File 
"/homeniolon/miso/lib/python/misopy-0.5.4-py2.7-linux-x86_64.egg/misopy/sashimi_plot/sashimi_plot.py", 
line 276, in main
     plot_label=plot_label)
   File 
"/homeniolon/miso/lib/python/misopy-0.5.4-py2.7-linux-x86_64.egg/misopy/sashimi_plot/sashimi_plot.py", 
line 153, in plot_event
     plot_label=plot_label)
   File 
"/homeniolon/miso/lib/python/misopy-0.5.4-py2.7-linux-x86_64.egg/misopy/sashimi_plot/plot_utils/plot_gene.py", 
line 698, in plot_density_from_file
     plot_title=plot_title)
   File 
"/homeniolon/miso/lib/python/misopy-0.5.4-py2.7-linux-x86_64.egg/misopy/sashimi_plot/plot_utils/plot_gene.py", 
line 264, in plot_density
     miso_file = os.path.expanduser(miso_files[i])
IndexError: list index out of range

the index was built in prov with Homo_sapiens.GRCh37.65.gff file.

this is my sashimi_plot_settings.txt:

[data]
# directory where BAM files are
bam_prefix = ./BAM/
# directory where MISO output is
miso_prefix = ./miso_out/

bam_files = [ "5-6_3.bam","7-8_3.bam" ]

miso_files = [ "5-6_3","7-8_3" ]

[plotting]
# Dimensions of figure to be plotted (in inches)
fig_width = 7
fig_height = 5
# Factor to scale down introns and exons by
intron_scale = 30
exon_scale = 4
# Whether to use a log scale or not when plotting
logged = False
font_size = 6

bar_posteriors = True

# Max y-axis
ymax = 150

# Axis tick marks
nyticks = 3
nxticks = 4

# Whether to show axis labels
show_ylabel = True
show_xlabel = True

# Whether to plot posterior distributions inferred by MISO
show_posteriors = True

# Whether to plot the number of reads in each junction
number_junctions = True

# sample_labels = [ "DOCK3" ]

resolution = .5
posterior_bins = 40
gene_posterior_ratio = 5

# List of colors for read denisites of each sample
colors = [ "#CC0011","#FF8800" ]

# Number of mapped reads in each sample
# (Used to normalize the read density for RPKM calculation)
# coverages = [ 6830944,]

# Bar color for Bayes factor distribution
# plots (--plot-bf-dist)
# Paint them blue
bar_color = "b"

# Bayes factors thresholds to use for --plot-bf-dist
bf_thresholds = [0, 1, 2, 5, 10, 20]

##
## Names of colors for plotting
##
# "b" for blue
# "k" for black
# "r" for red
# "g" for green
#
# Hex colors are accepted too.