owlcollab / owlcollab/owltools
Duplicated entries after map2slim
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Description
Hi,
I am mapping with to a go slim with the following command
java -jar $owlTools $oboBasic --gaf $input_gaf --map2slim -u unmapped.gaf \
--idfile $goSlim --write-gaf my_Slimgo_terms_plant.txt
After the mapping I have several duplicated entries (entire lines) in the mapped output:
wc -l my_Slimgo_terms_plant.txt
#633907
sort my_Slimgo_terms_plant.txt | uniq | wc -l
#612897
I don't have any duplicated entries in the my input_gaf.
Version:
java -jar /home/kgagalova/src/owltools --version
git-revision-sha1 f90176d5849278d8fc01e839e444408c8e9445be
git-revision-url https://github.com/owlcollab/owltools/commit/f90176d5849278d8fc01e839e444408c8e9445be
git-branch origin/master
git-dirty true
Is there any reason why there are those entries?
Thanks in advance for the repply
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- Fork the repository and make your change on a branch.
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Research direction
Start by reproducing the reported map2slim command with the supplied owlTools revision and compare my_Slimgo_terms_plant.txt using sort and uniq. Then trace the map2slim command's output handling to determine why identical lines are emitted; done means the cause is identified and duplicate output is either prevented or clearly explained.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- java
- Domain
- cli
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100