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dieterich-lab / DCC

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.
https://dieterichlab.org/software/
GNU General Public License v3.0
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DCC throws value error? #103

Open mathavanpu opened 1 year ago

mathavanpu commented 1 year ago

hi, I have executed the DCC, the circular RNA counts and co-ordinates files are generated. For finding the CircSkipJunction I got the error mentioned below. Can you please guide me resolve this

Traceback (most recent call last): File "/home/mathavan/.local/bin/DCC", line 33, in sys.exit(load_entry_point('DCC==0.5.0', 'console_scripts', 'DCC')()) File "/home/mathavan/.local/lib/python3.10/site-packages/DCC-0.5.0-py3.10.egg/DCC/main.py", line 490, in main File "/home/mathavan/.local/lib/python3.10/site-packages/DCC-0.5.0-py3.10.egg/DCC/main.py", line 679, in findCircSkipJunction File "/home/mathavan/.local/lib/python3.10/site-packages/DCC-0.5.0-py3.10.egg/DCC/Circ_nonCirc_Exon_Match.py", line 281, in findcircAdjacent File "/home/mathavan/.local/lib/python3.10/site-packages/DCC-0.5.0-py3.10.egg/DCC/Circ_nonCirc_Exon_Match.py", line 222, in getAdjacent ValueError: invalid literal for int() with base 10: '8"'

tjakobi commented 1 year ago

Hi @mathavanpu,

This error seems to have been caused by an update to HTSeq. I've corrected the code in DCC to correctly work with newer HTSeq versions.

Please reinstall from GitHub and see if the error is fixed for you.

Tobias

jaanckae commented 1 year ago

Hi @tjakobi

I'm having the same issue as mentioned above:

Count CircSkip junctions Traceback (most recent call last): File "/usr/local/bin/circtools", line 18, in import circtools File "/usr/local/lib/python3.9/dist-packages/circtools/init.py", line 2, in main() File "/usr/local/lib/python3.9/dist-packages/circtools/circtools.py", line 31, in main CircTools() File "/usr/local/lib/python3.9/dist-packages/circtools/circtools.py", line 77, in init getattr(self, args.command)() File "/usr/local/lib/python3.9/dist-packages/circtools/circtools.py", line 609, in detect DCC.main(parser) File "/usr/local/lib/python3.9/dist-packages/DCC/main.py", line 490, in main CircSkipfiles = findCircSkipJunction(output_coordinates, options.tmp_dir, File "/usr/local/lib/python3.9/dist-packages/DCC/main.py", line 679, in findCircSkipJunction circStartAdjacentExons, circStartAdjacentExonsIv = CCEM.findcircAdjacent(circStartExons, Custom_exon_id2Iv, File "/usr/local/lib/python3.9/dist-packages/DCC/Circ_nonCirc_Exon_Match.py", line 281, in findcircAdjacent interval = Custom_exon_id2Iv[self.getAdjacent(ids, start=start)] File "/usr/local/lib/python3.9/dist-packages/DCC/Circ_nonCirc_Exon_Match.py", line 222, in getAdjacent exon_number = int(custom_exon_id.split(':')[1]) - 1 ValueError: invalid literal for int() with base 10: '2"'

It indeed seems that the HTSeq module is adding unwanted quotes to the modified GTF file. Is it possible to add this fix to the PyPi installation files?

Thanks Jasper

tjakobi commented 1 year ago

Hi @jaanckae,

Thank you for your report.

Are you using the master branch or a released PyPi version?

I did not yet publish a new DCC release yet, but will do so soon.

Could you please give the master branch version a try?

Thank you!

jaanckae commented 1 year ago

Hi @tjakobi

Master branch works perfect, thank you. On to the next part of the program.

kelly-sovacool commented 2 months ago

@tjakobi do you plan to release a new version with this bug fix?

tjakobi commented 2 months ago

Hi @kelly-sovacool,

DCC is now part of circtools at https://github.com/jakobilab/circtools and this repository is not updated anymore.

The issues has been fixed in circtools which is available via pip or from GitHub.

Best,

Tobias

kelly-sovacool commented 2 months ago

Great, thanks for letting us know about the new repo