ROSE_bamToGFF.py : UnboundLocalError: local variable 'newGFF' referenced before assignment

Issue #59 open
bhanratt created an issue

I am trying to run ROSE on the provided test data from the Young lab website.

I am using Python2 and the version of Samtools recommended by the documentation:

$:~/bin/young_computation-rose-feb35cb1d955/ROSE_DATA/data$ python --version 
Python 2.7.15
$:~/bin/young_computation-rose-feb35cb1d955/ROSE_DATA/data$ samtools
Program: samtools (Tools for alignments in the SAM format)
Version: 0.1.18 (r982:295)

My ROSE directory looks like this:

$:~/bin/young_computation-rose-feb35cb1d955$ ls -1
annotation
README.txt
ROSE_bamToGFF.py
ROSE_bamToGFF_turbo.py
ROSE_callSuper.R
ROSE_DATA
ROSE_DATA.zip
ROSE_geneMapper.py
ROSE_main.py
ROSE_main_turbo.py
ROSE_utils.py
ROSE_utils.pyc

Here is my command utilizing the test data:
python ROSE_bamToGFF.py -b ROSE_DATA/data/MM1S_MED1.hg18.bwt.sorted.bam -i ROSE_DATA/data/HG18_MM1S_MED1.gff -o MM1S.gff

Which returns this error:

{'matrix': None, 'extension': 200, 'floor': 0, 'sense': 'both', 'output': 'MM1S.gff', 'bam': 'ROSE_DATA/data/MM1S_MED1.hg18.bwt.sorted.bam', 'rpm': False, 'input': 'ROSE_DATA/data/HG18_MM1S_MED1.gff'}
[]
Traceback (most recent call last):
  File "ROSE_bamToGFF.py", line 247, in <module>
    main()
  File "ROSE_bamToGFF.py", line 241, in main
    ROSE_utils.unParseTable(newGFF,output,'\t')
UnboundLocalError: local variable 'newGFF' referenced before assignment

This same error was returned when I tried running on my own data. So I thought to try running with the test data and unfortunately this produced the same error. Any guidance would be appreciated. As far as I can tell I followed the documentation exactly.

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