Comments (4)
Hi Torsten, first of all, sorry for the slow response!
Is this expected behaviour?
Well... In a way ;) After reproducing and looking at the code I found that it's expected behavior, but a very unhelpful error message, which we should improve: bionode-ncbi
expects you to pass some arguments, e.g. bionode ncbi search taxonomy solenopsis
. See the README.md for more usage examples.
I hope this fixes your problem!
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Do you want me to submit a new issue to improve the error message?
Here's some suggestions on improving the interface: http://www.gigasciencejournal.com/content/2/1/15
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Thanks for the link. I talked to @bmpvieira last night about replacing the library that is currently used for argument parsing so that we can easily have things like usage info, argument validation, etc. I'll create a new issue later, probably against bionode/bionode as this affects all sub-projects.
from bionode-ncbi.
Thanks @tseemann. This is one of those obvious issues that should have been fixed by now but hasn't due to lack of time and also because of the minimal library used for parsing arguments (minimist). As @c089 said, we'll switch to a more full-blown parser (yargs) and add this.
Since it's not limited to bionode-ncbi
, I'm closing this and you can follow the new issue at bionode/bionode#25.
In the meantime, you can check each module's README.md which links to the documentation (e.g., bionode-ncbi docs) and the global docs at doc.bionode.io, resulting from the concatenation of all individual html docs (WIP: bionode/bionode#27).
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Related Issues (20)
- Implement efetch API
- Download the GFF file of the Cycas taitungensis mitochondrion HOT 9
- Uncaught, unspecified "error" event HOT 1
- How to look up metadata for an SRR file HOT 1
- Tests are broken because of NCBI side metadata changes (again) HOT 2
- rna_from_genomic instead of genomic.fna
- geo is not searchable HOT 5
- download in the examples printing too much info HOT 3
- We need a smaller assembly from NCBI for testing HOT 3
- Git rid of git-lfs
- Error handling when NCBI connection is lost HOT 4
- User-friendly CLI
- Modularize lib structure.
- Output some warning to terminal when there is no output
- Add Blast API HOT 2
- Use progress bar on download HOT 5
- Downloading one run download the whole Bioproject
- TypeError: Cannot create property 'Run' on string ' ' HOT 1
- Dependencies error: Prototype Pollution (lodash dependencies)
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