Hi,

The initialize_data.py program is failing like this:

$ python /mnt/isilon/cbmi/variome/bin/SplicePlot-1.1/initialize_data.py 5:36953863 5:36877280-36953720,5:36877280-36955574 \
> --vcf CDL-217-05P-gatk-haplotype-annotated.vcf.gz \
> --gtf ref-transcripts_exons_sorted.gtf.gz \
> --mf map_file.txt \
> --output CDL-217-05P.p
Failed

I am not sure why it is failing because there is no error message. How do I debug this?

Hello!
The example files provided with SplicePlot do not work any longer with the latest dependencies.
The error is:

jens@KI-V0205:~/spliceplot$ spliceplot.py --output test test_files/test.p pickle settings_file 
Reading settings from settings_file...
Parsing settings for hive plot...
Parsing settings for structure plot...
Parsing sashimi plot settings...
Done reading settings.
Traceback (most recent call last):
  File "/mnt/software/x86_64/packages/spliceplot/1.1/spliceplot.py", line 115, in <module>
    data_frame = pickle.load(pickle_file)
TypeError: ('_reconstruct: First argument must be a sub-type of ndarray', <built-in function _reconstruct>, (<class 'pandas.indexes.base.Index'>, (0,), 'b'))

The issue arises because of a backwards incompatibility of pandas:
http://stackoverflow.com/questions/27950991/pandas-backwards-compatibility-issue-with-pickle-0-14-1-and-0-15-2

Since the new pd.read_pickle takes the filename as string it's now impossible to recover the panda data frames that are in the example files without installing an older version of pandas.
A possible solution is to fix the pickle file to contain only one pickle object, e.g. as a list (in initialize_data.py):

pickle_file = open('{0}{1}'.format(stem,tail),'wb')
pickle_list = [args.varpos, args.junc, genotype_averages_dict, mRNA_info_object, data_frame, filtered_genotypes_list]
pickle.dump(pickle_list,pickle_file)
pickle_file.close()

or to have the pickles in independent files. Can you provide me with either of the solutions?

Best,
Jens

I am using this command
python //SplicePlot/junction_from_window.py chr4:170314426-chr4-170533780 /mnt/NGS/RNAseq_Data/Spliceplot_output/map_file.txt

and my map file is having path of the bam files
//NM1.bam
//AF2.bam

but no table file is getting generated, error is coming
File "/mnt/NGS/RNAseq_Data/SplicePlot/junction_from_window.py", line 8, in get_bam_locations
bam_path = line.strip('\n').split()[1]
IndexError: list index out of range

not getting the error, I have the *.bam.bai in both the path.