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Dear @kblin,
I would like to use ncbi-gneome-download as a python module within my pipeline and I have been having problems to decipher the arguments to pass to the download call. I guess the readm…
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```
ncbi-acc-download MW367468
genbank_to -g MW367468.gbk --gff3 out.gff
# GEBBANK
CDS complement(join(23549..23700,1..220))
# GFF
CDS 1 23700 . -
```
This plasmid is…
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I was going through FASTA.ipynb and had troubles downloading FASTA reference. Backtracking URL I have found a README (link below, because MD rendering doesn't allow ftp URLs) and it says all content i…
duxan updated
8 years ago
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When looking at a GenBank entry there often is interesting information in the "source" feature, which actually contains several subfields. From instance below one can see the "host" information:
…
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Names in NCBI/GenBank commonly have a particularly notation that fixSpecies() currently does not handle well. Improvements are needed. Examples are:
- "Syzygium sp. DIR045"
- "Malaxis sp. TBG13270…
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Hi,
I am attempting to annotate a customized VCF file using NCBI's GFF and (fna) FASTA files for the Newcastle disease virus (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_004786615.1/). However, …
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Subtask of #2.
Use Python script from data team to do a test run as a "straw person" exercise.
Info from PK:
> Hi Nick, yes, there’s the preingestion code that I wrote sitting on the develop b…
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For reproducibility, it would be nice to be able to specify a GenBank release instead of only downloading the most recent.
Example dummy code:
`db_download(preselection = 20, release = 248)`
Th…
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If a SEED alignment contains sequences with accessions not found in Genbank or RNAcentral (for example, `AGAIN_GXP7IEG01DU42M/31-242`) we cannot use such an alignment to build an Rfam family. The idea…
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I think we need to download all `gbenv*` files from https://ftp.ncbi.nlm.nih.gov/genbank/gbenv1 e.g. `gbenv1.seq.gz - gbenv72.seq.gz`, then extract them and parse all the `VERSION AB000684.1` valu…