Comments (6)
Hmmm, looks like the link changed to only accept https connections. We'll have to update the script with updated links, thanks for the info
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For example: https://www.imgt.org/download/V-QUEST/IMGT_V-QUEST_reference_directory/Homo_sapiens/IG/IGHV.fasta works
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@Ch-rode @yaober I've just pushed an update to the repository that fixes all of the links in the setup script (as well as another minor bug).
I haven't gotten all of the changes pushed to pip yet but if you git clone this repository and do the local install method the setup script should work now:
git clone https://github.com/crowelab/PyIR cd PyIR/ pip3 install --user .
Let me know if something is wrong
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@reccej thanks a lot, everything is working now.
I am sorry to bother again, I was also wondering if you added the isotypes as well. I cloned the repo but i do not find them in the output.
thanks again
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I thought I did, the isotype databases are in the source but maybe they're not getting properly compiled to a BLAST library -- I'll have to confer with @myersml5 about it. I've been mostly out of the sequencing game for 3 years and he's my go-to now
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If you wanna get funky with it, look in the pyir/data/crowelab_data folder for the files 'human_gl_C.fasta' and 'human_TCR_C.fasta'. They can be used to build a BLAST database which should be able to be fed into PyIR using the --germlineC flag, but it may be a spotty implementation
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Related Issues (20)
- tempfile.mkdtemp() causing "No space left on device error" HOT 1
- Allow argument for setting IGBlast word size HOT 3
- missing FR4 with PyIR 1.3 AIRR parser HOT 1
- could we have an selection option to use blastp? HOT 5
- Example PyIR output for immunarch HOT 1
- Support for different species HOT 4
- after pyir set up, pyir still can't be used with other species HOT 2
- Add license? HOT 1
- Murine blast? HOT 1
- Stops at 9%
- IGBLAST_TSV_HEADER misalignment
- Annotation for most alpha chains missing, but not for beta HOT 2
- Isotype annotation HOT 4
- Adaptive Biotechnologies data set HOT 4
- ABhelix data HOT 1
- I get an empty output json when running blastp on TCR data. HOT 4
- empty output HOT 1
- Result difference between PyIR and IgBLAST server
- Issue of using pair-end WES data
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