Comments (5)
zhangrengang
commented on August 27, 2024
Hi @2eYu.
Please refer to #34 (the last comment).
RunCmdsMP.py is in ~/miniconda3/envs/TEsorter/lib/python*/site-packages/TEsorter*/TEsorter/modules/, but is not found from PYTHONPATH. You can link it into PYTHONPATH or ~/miniconda3/envs/TEsorter/bin/. It should work.
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2eYu
commented on August 27, 2024
Thanks for your quick reply, I used this command
~/miniconda3/pkgs/tesorter-1.3.0-py_0/site-packages/TEsorter/modules/concatenate_domains.py HFgenome.fa.mod.LTR.intact.fa.rexdb-plant.cls.pep GAG PROT RH RT INT > HFgenome.fa.mod.LTR.intact.fa.rexdb-plant.cls.pep.full.aln2
It finally worked. Thank you!!!
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zhangrengang
commented on August 27, 2024
Hi @Juke34, can you please update the TEsorter (the last verion 1.4.6) in conda? I have fixed some bugs and added new features.
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Juke34
commented on August 27, 2024
Sure but you must make a proper release (https://github.com/zhangrengang/TEsorter/releases) with description of lastest modifications.
Oh actually I see that the version 1.4 didn't went well into bioconda (bioconda/bioconda-recipes#33660) I must first fix this one.
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zhangrengang
commented on August 27, 2024
Thanks @Juke34. I have made a new release v1.4.6.
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Related Issues (20)
- Does TEsorter results only contain positive strain? HOT 5
- keyError HOT 5
- Hi~ TEsorter can be worked in animal genoem ? HOT 2
- ValueError: invalid literal for int() with base 10: '0.5' HOT 8
- How to analyze the effect of transposons on plant traits in de novo transcriptome assembly. HOT 4
- Problem with concatenate_domains.py HOT 1
- How to identify the homology (synteny) of LTRs? HOT 10
- Insertion time calculation HOT 4
- Crash when special characters occurred in sequence IDs HOT 3
- Can TEsorter classify Class II elements(DNA transposons) into clade-level? HOT 2
- Assistance with custom installation directory HOT 5
- How to obtain the set of distances between LTRs and their adjacent genes? HOT 3
- TEsorter genome.fasta -genome -p 20 -prob 0.9 HOT 1
- Allocation into lineages for metazoan LTR-RTs HOT 4
- How to merge the TEsorter repeat libraires HOT 18
- get_full_seqs in LTR_retriever.py generate some empty sequences which should be generated. HOT 4
- Exploring the transposition profile of specific LTRs HOT 1
- TypeError HOT 2
- AttributeError: 'NoneType' object has no attribute 'groups'
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