AttributeError: 'pysam.calignmentfile.AlignedSegment' object has no attribute 'reference_name'

[kerendanan1511]

Hi,

I am tring to get sashimi plots for my test sample that was already aligned and sorted, after getting rmats-turbo output:

out_sa=/a/home/cc/lifesci/kerendanan1/rmats_turbo/test_N010/rmats/output_dir/sashimi_output
event=/a/home/cc/lifesci/kerendanan1/rmats_turbo/test_N010/rmats/output_dir/SE.MATS.JCEC.txt
test_bam=/a/home/cc/lifesci/kerendanan1/provide/high_quality/N010_NSSAligned.sortedByCoord.out.bam

rmats2sashimiplot --b1 $test_bam --exon_s 1 --intron_s 5 --event-type SE -e $event --l1 N010_sample_SE -o $out_sa

I get this error:

'/a/home/cc/lifesci/kerendanan1/provide/high_quality/N010_NSSAligned.sortedByCoord.out.bam' is indexed already: '/a/home/cc/lifesci/kerendanan1/provide/high_quality/N010_NSSAligned.sortedByCoord.out.bam.bai'
'pysam.calignmentfile.AlignedSegment' object has no attribute 'reference_name'
There is an exception in plot_with_eventsfile
Traceback (most recent call last):
File "/a/home/cc/lifesci/kerendanan1/.conda/envs/rmats_env/bin/rmats2sashimiplot", line 33, in
sys.exit(load_entry_point('rmats2sashimiplot==3.0.0', 'console_scripts', 'rmats2sashimiplot')())
File "/a/home/cc/lifesci/kerendanan1/.conda/envs/rmats_env/lib/python3.6/site-packages/rmats2sashimiplot-3.0.0-py3.6.egg/rmats2sashimiplot/rmats2sashimiplot.py", line 949, in main
plot_with_eventsfile(options)
File "/a/home/cc/lifesci/kerendanan1/.conda/envs/rmats_env/lib/python3.6/site-packages/rmats2sashimiplot-3.0.0-py3.6.egg/rmats2sashimiplot/rmats2sashimiplot.py", line 606, in plot_with_eventsfile
options.events_file = create_chr_aware_events_file(options)
File "/a/home/cc/lifesci/kerendanan1/.conda/envs/rmats_env/lib/python3.6/site-packages/rmats2sashimiplot-3.0.0-py3.6.egg/rmats2sashimiplot/rmats2sashimiplot.py", line 575, in create_chr_aware_events_file
ref_name = alignment.reference_name
AttributeError: 'pysam.calignmentfile.AlignedSegment' object has no attribute 'reference_name'

What should I do?

I have installed as in the README, I only want to get sashimi plots for some specific genes.
Any idea, beside that error, how could I get all the sashimi plots for all the events for specified gene symbols?

Thanks!

[EricKutschera]

Here's the line for that error: https://github.com/Xinglab/rmats2sashimiplot/blob/v3.0.0/src/rmats2sashimiplot/rmats2sashimiplot.py#L575

It's reading the alignments from the bam file using pysam and it's checking the contig name (.reference_name). Based on this issue it looks like this error message can happen if using a pysam version older than 0.8.4: CGATOxford/UMI-tools#199

I was able to reproduce the error with 0.8.3 then I updated pysam to 0.9.1 (and removed .bai files created by the old version) and it worked correctly