error in differential analysis using splAdder

Question

[bisht20diksha]

Hello. I am trying to use splAdder for alternative splicing analysis. I have three replicates of barley both for control and treated respectively i.e c1, c2,c3 and t1, t2, t3. I ran splAdder successfully and got the output. I have quantified and confirmed alternative splicing events based on the RNA-Seq data. But, now to perform differential analysis, I did GLM test using script spladder_test.py with command line:

python2.7 spladder_test.py -o splAdder_result -a c1.bam, c2.bam, c3.bam -b t1.bam, t2.bam, t3.bam

The following error appears:

FutureWarning: The pandas.core.datetools module is deprecated and will be removed in a future version. Please use the pandas.tseries module instead.
  from pandas.core import datetools
/home/aasim/.local/lib/python2.7/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters
Traceback (most recent call last):
  File "spladder_test.py", line 873, in <module>
    main()
  File "spladder_test.py", line 757, in main
    gene_counts, gene_strains, gene_ids = get_gene_expression(CFG, fn_out=CFG['fname_exp_hdf5'], strain_subset=condition_strains)
  File "spladder_test.py", line 171, in get_gene_expression
    gene_counts[gidx, :] = IN['segments'][seg_idx, :][strain_idx] * seg_lens[seg_idx, 0] / CFG['read_length']
IndexError: index 1 is out of bounds for axis 0 with size 1

How to fix it?

[Matteo Schiavinato]

This is a python error, whenever you get an IndexError in such a situation it usually means that your file is not formatted as it should. How is a line of your file structured? Are all of them like that?