Entering edit mode
3.2 years ago
justinian458
•
0
I am trying to run DoGFinder (https://github.com/shalgilab/DoGFinder), a tool to find and quantify downstream-of-gene (DoG)-containing transcripts.
After installing it, I ran a test (python setup.py test) and I get a whole string of errors:
running test
WARNING: Testing via this command is deprecated and will be removed in a future version. Users looking for a generic test entry point independent of test runner are encouraged to use tox.
running egg_info
writing requirements to DoGFinder.egg-info/requires.txt
writing DoGFinder.egg-info/PKG-INFO
writing top-level names to DoGFinder.egg-info/top_level.txt
writing dependency_links to DoGFinder.egg-info/dependency_links.txt
reading manifest file 'DoGFinder.egg-info/SOURCES.txt'
writing manifest file 'DoGFinder.egg-info/SOURCES.txt'
running build_ext
Running tests:
Get_loci_annotation -out /home/user/Documents/scripts/DoGFinder/tests/data -gtf /home/user/Documents/scripts/DoGFinder/tests/data/test_gtf.gtf
-----------------------------------------------------Get Annotation-------------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/bin/Get_loci_annotation", line 87, in <module>
df_merge_annot.columns=['chrom','start','end','strand','name'];
File "/home/user/.local/lib/python2.7/site-packages/pandas/core/generic.py", line 5080, in __setattr__
return object.__setattr__(self, name, value)
File "pandas/_libs/properties.pyx", line 69, in pandas._libs.properties.AxisProperty.__set__
File "/home/user/.local/lib/python2.7/site-packages/pandas/core/generic.py", line 638, in _set_axis
self._data.set_axis(axis, labels)
File "/home/user/.local/lib/python2.7/site-packages/pandas/core/internals/managers.py", line 155, in set_axis
'values have {new} elements'.format(old=old_len, new=new_len))
ValueError: Length mismatch: Expected axis has 4 elements, new values have 5 elements
Pre_Process -bam /home/user/Documents/scripts/DoGFinder/tests/data/HS.bam,/home/user/Documents/scripts/DoGFinder/tests/data/UN.bam -ref /home/user/Documents/scripts/DoGFinder/tests/data/loci_annotation.bed
-----------------------------------------------------Pre_Process-------------------------------------------------------------------------
Ref. file: /home/user/Documents/scripts/DoGFinder/tests/data/loci_annotation.bed
Cores available: 48 Cores usage: 1
Processing and counting bam files...
Traceback (most recent call last):
File "/home/user/.local/bin/infer_experiment.py", line 48, in <module>
from bx.bitset import *
ImportError: /home/user/.local/lib/python2.7/site-packages/bx/bitset.so: undefined symbol: _Py_ZeroStruct
No index file at : /home/user/Documents/scripts/DoGFinder/tests/data/HS.bam.bai... Sorting and indexing...
Traceback (most recent call last):
File "/home/user/.local/bin/infer_experiment.py", line 48, in <module>
from bx.bitset import *
ImportError: /home/user/.local/lib/python2.7/site-packages/bx/bitset.so: undefined symbol: _Py_ZeroStruct
No index file at : /home/user/Documents/scripts/DoGFinder/tests/data/UN.bam.bai... Sorting and indexing...
/home/user/Documents/scripts/DoGFinder/tests/data/HS.bam : Not Paired-End, Not stranded, with 0.045284 mapped Mreads
/home/user/Documents/scripts/DoGFinder/tests/data/UN.bam : Not Paired-End, Not stranded, with 0.00284 mapped Mreads
Bam file: /home/user/Documents/scripts/DoGFinder/tests/data/UN.bam has smallest number of mapped reads: 0.00284 Mreads
Downsampling...
No index file at : /home/user/Documents/scripts/DoGFinder/tests/data/HS.bam.bai... Sorting and indexing...
No index file at : /home/user/Documents/scripts/DoGFinder/tests/data/UN.bam.bai... Sorting and indexing...
/home/user/Documents/scripts/DoGFinder/tests/data/HS.sorted_DS.bam : after downsample 0.004265 mapped Mreads
/home/user/Documents/scripts/DoGFinder/tests/data/UN.sorted_DS.bam : after downsample 0.00284 mapped Mreads
Done
Get_DoGs -out /home/user/Documents/scripts/DoGFinder/tests/data -bam /home/user/Documents/scripts/DoGFinder/tests/data/HS.sorted_PE.sorted_DS.bam -a /home/user/Documents/scripts/DoGFinder/tests/data/loci_annotation.bed -suff HS
No annotation file in : /home/user/Documents/scripts/DoGFinder/tests/data/loci_annotation.bed
Get_DoGs -out /home/user/Documents/scripts/DoGFinder/tests/data -bam /home/user/Documents/scripts/DoGFinder/tests/data/UN.sorted_PE.sorted_DS.bam -a /home/user/Documents/scripts/DoGFinder/tests/data/loci_annotation.bed -suff UN
No annotation file in : /home/user/Documents/scripts/DoGFinder/tests/data/loci_annotation.bed
Union_DoGs_annotation -dog /home/user/Documents/scripts/DoGFinder/tests/data/Final_Dog_annotation_HS.bed,/home/user/Documents/scripts/DoGFinder/tests/data/Final_Dog_annotation_UN.bed -out /home/user/Documents/scripts/DoGFinder/tests/data
No DoG annotation file in : /home/user/Documents/scripts/DoGFinder/tests/data/Final_Dog_annotation_HS.bed
Common_DoGs_annotation -comm /home/user/Documents/scripts/DoGFinder/tests/data/Final_Dog_annotation_HS.bed,/home/user/Documents/scripts/DoGFinder/tests/data/Final_Dog_annotation_UN.bed -out /home/user/Documents/scripts/DoGFinder/tests/data
No DoG annotation file in : /home/user/Documents/scripts/DoGFinder/tests/data/Final_Dog_annotation_HS.bed
Get_DoGs_rpkm -out /home/user/Documents/scripts/DoGFinder/tests/data -bam /home/user/Documents/scripts/DoGFinder/tests/data/HS.sorted_PE.sorted_DS.bam -dog /home/user/Documents/scripts/DoGFinder/tests/data/union_dog_annotation.bed -s
No annotation file in : /home/user/Documents/scripts/DoGFinder/tests/data/union_dog_annotation.bed
----------------------------------------------------------------------
Ran 0 tests in 0.000s
OK
My data was aligned to hg38 so I would need to make a new annotation file with Get_loci_annotation -out /annotationdir -gtf /home/user/Documents/gtf/hg38/Homo_sapiens.GRCh38.106.chr_patch_hapl_scaff.gtf, but I get the following error:
-----------------------------------------------------Get Annotation-------------------------------------------------------------------------
sys:1: DtypeWarning: Columns (0) have mixed types. Specify dtype option on import or set low_memory=False.
Traceback (most recent call last):
File "/usr/local/bin/Get_loci_annotation", line 66, in <module>
df_gtf_annot=pd.DataFrame(df_gtf_annot.loc[~df_gtf_annot['seqname'].str.contains('random')])
File "/home/niek/.local/lib/python2.7/site-packages/pandas/core/generic.py", line 1465, in __invert__
arr = operator.inv(com.values_from_object(self))
TypeError: bad operand type for unary ~: 'float'
Has anyone used this tool successfully, and could tell me how to overcome all these errors?
