Comments (4)
mojaveazure
commented on August 16, 2024
Using the latest version from GitHub:
hoffmanp@login02 [~/sandbox/LRT_Pipeline/LRT] % ./LRT_Predict.py fetch
Traceback (most recent call last):
File "./LRT_Predict.py", line 36, in
from lrt_predict.Blast import blast_search
File "/panfs/roc/groups/9/morrellp/hoffmanp/sandbox/LRT_Pipeline/LRT/lrt_predict/Blast/blast_search.py", line 10, in
from Bio.Blast.Applications import NcbitblastxCommandline
ImportError: No module named Bio.Blast.Applications
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ChaochihL
commented on August 16, 2024
Not able to run fetch on login where we have internet access because it requires BioPython.
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TomJKono
commented on August 16, 2024
You should be able to run this package from one of the lab nodes. I'm running the 'fetch' routine right now and it is downloading CDS files.
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TomJKono
commented on August 16, 2024
At least ensembl
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Related Issues (20)
- Skip sequences with ambiguous nucleotides HOT 1
- Off-by-one error in HyPhy script? HOT 1
- Add command for dowloading in Mannual HOT 1
- Fail gracefully when no BLAST hits HOT 1
- makeblastdb HOT 1
- No output written to output dir with silent error HOT 3
- Fail nicely when "required" arguments are not specified
- Add Filtering of Species Databases
- Sanitize sequence names before alignment HOT 1
- Add Logistic Regression to Prediction
- Doesn't find HyPhy properly
- BAD_Mutations Incorrectly Back-translates from PASTA HOT 1
- The logistic P value is only valid for the 41 genomes
- Fetch XML ParseError HOT 5
- Multiple Trees in File HOT 6
- Fetch only the latest CDS for each species
- The XML document has moved HOT 2
- Compile Bug - Won't work on test data HOT 5
- Compile - include SNP names? HOT 1
- BUG: HOT 3
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