[miso-users] Problem with filter_events.py

[Vincent Schulz]

Hi,

I am having a problem running filter_events.py.  It seems to work on just the first line of a
comparison file, but does not work on the whole file.  If it would be helpful I can transfer the
comparison file to you.  See material below.

Thanks,

Vince

filter_events.py --filter C9_miso_vs_C5_miso.miso_bf --num-inc 1 --num-exc 1 --num-sum-inc-exc 10
--delta-psi 0.20 --bayes-factor 10 --output-dir filtered/
Traceback (most recent call last):
   File "/usr/local/bin/filter_events.py", line 5, in <module>
     pkg_resources.run_script('misopy==0.4.7', 'filter_events.py')
   File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.34-py2.7.egg/pkg_resources.py", line
505, in run_script
     self.require(requires)[0].run_script(script_name, ns)
   File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.34-py2.7.egg/pkg_resources.py", line
1245, in run_script
     execfile(script_filename, namespace, namespace)
   File
"/usr/local/lib/python2.7/dist-packages/misopy-0.4.7-py2.7-linux-x86_64.egg/EGG-INFO/scripts/filter_events.py", 

line 405, in <module>
     main()
   File
"/usr/local/lib/python2.7/dist-packages/misopy-0.4.7-py2.7-linux-x86_64.egg/EGG-INFO/scripts/filter_events.py", 

line 402, in main
     apply_both_samples=options.apply_both)
   File
"/usr/local/lib/python2.7/dist-packages/misopy-0.4.7-py2.7-linux-x86_64.egg/EGG-INFO/scripts/filter_events.py", 

line 104, in multi_filter
     apply_both_samples=False)
   File
"/usr/local/lib/python2.7/dist-packages/misopy-0.4.7-py2.7-linux-x86_64.egg/EGG-INFO/scripts/filter_events.py", 

line 264, in filter_events
     for bf in bayes_factor:
TypeError: 'float' object is not iterable


head -n2  C9_miso_vs_C5_miso.miso_bf
event_name      sample1_posterior_mean  sample1_ci_low  sample1_ci_high sample2_posterior_mean
sample2_ci_low  sample2_ci_high diff    bayes_factor    isoforms        sample1_counts
sample1_assigned_counts sample2_counts  sample2_assigned_counts chrom   strand  mRNA_starts
mRNA_ends
ENSG00000141086 0.85,0.11,0.01,0.02     0.72,0.02,0.00,0.00     0.96,0.25,0.04,0.07
0.86,0.10,0.02,0.03     0.69,0.01,0.00,0.00     0.97,0.26,0.07,0.08     -0.00,0.01
,-0.00,-0.01    0.26,0.26,0.04,0.06
'ENST00000574481.exon6_ENST00000574481.exon5_ENST00000574481.exon4_ENST00000574481.exon3_ENST00000574481.exon2_ENST00000574481.exo
n1_ENST00000574481.exon0','ENST00000319955.exon6_ENST00000319955.exon5_ENST00000319955.exon4_ENST00000319955.exon3_ENST00000319955.exon2_ENST00000319955.exon1_ENST0000031
9955.exon0','ENST00000571044.exon5_ENST00000571044.exon4_ENST00000571044.exon3_ENST00000571044.exon2_ENST00000571044.exon1_ENST00000571044.exon0','ENST00000571605.exon5_E
NST00000571605.exon4_ENST00000571605.exon3_ENST00000571605.exon2_ENST00000571605.exon1_ENST00000571605.exon0' 

   (0,0,0,0):246,(1,0,0,0):140,(1,1,0,0):167,(1,1,0,1):77,(1,
1,1,0):34,(1,1,1,1):3   0:417,1:3,2:0,3:1
(0,0,0,0):191,(1,0,0,0):105,(1,1,0,0):119,(1,1,0,1):51,(1,1,1,0):36     0:271,1:39,2:1  chr16   -
     67963473,67963474,67963855,67963939       67966317,67965765,67965765,67965765

head -n2  C9_miso_vs_C5_miso.miso_bf > junk.miso_bf

filter_events.py --filter junk.miso_bf --num-inc 1 --num-exc 1 --num-sum-inc-exc 10 --delta-psi 0.20
--bayes-factor 10 --output-dir filtered/
Filtering
['/mnt/DataStorage1/Pat_Data/RNAseq/Tcell/misoComparisons/C9vsC5/C9_miso_vs_C5_miso/bayes-factors/junk.miso_bf'] 

into
/mnt/DataStorage1/Pat_Data/RNAseq/Tcell/misoComparisons/C9vsC5/C9_miso_vs_C5_miso/bayes-factors/filtered/junk.miso_bf.filtered
dictlist2file: serializing entries to
/mnt/DataStorage1/Pat_Data/RNAseq/Tcell/misoComparisons/C9vsC5/C9_miso_vs_C5_miso/bayes-factors/filtered/junk.miso_bf.filtered
dictlist2file: took 0.00 seconds
0/1 events pass the filter (0.00 percent).