Comments (2)
Will use curl to send login information to JGI's form, and create a cookie, as a named temporary file. Then using that cookie file, will fetch XML tree. Then, for each selected XML file, will use the cookie file to fetch the gzipped FASTA sequence.
Messier, but should work, as it is "officially supported" by JGI.
from bad_mutations.
Fixed in 6067403
from bad_mutations.
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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