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| author | Pjotr Prins | 2020-08-24 10:31:24 +0100 |
|---|---|---|
| committer | Pjotr Prins | 2020-08-24 10:31:24 +0100 |
| commit | 7fabc4f9427856600e237c6cacd710f49b88d45d (patch) | |
| tree | 23fc807559c84ca618ec0145233f76bc6ba64fd5 /doc/blog/using-covid-19-pubseq-part3.org | |
| parent | b50c13cab729327490a9976727a95af81d629f23 (diff) | |
| download | bh20-seq-resource-7fabc4f9427856600e237c6cacd710f49b88d45d.tar.gz bh20-seq-resource-7fabc4f9427856600e237c6cacd710f49b88d45d.tar.lz bh20-seq-resource-7fabc4f9427856600e237c6cacd710f49b88d45d.zip | |
Genbank upload
Diffstat (limited to 'doc/blog/using-covid-19-pubseq-part3.org')
| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part3.org | 12 |
1 files changed, 12 insertions, 0 deletions
diff --git a/doc/blog/using-covid-19-pubseq-part3.org b/doc/blog/using-covid-19-pubseq-part3.org index b1ab90d..fda7be8 100644 --- a/doc/blog/using-covid-19-pubseq-part3.org +++ b/doc/blog/using-covid-19-pubseq-part3.org @@ -236,3 +236,15 @@ The web interface using this exact same script so it should just work We also use above script to bulk upload GenBank sequences with a [[https://github.com/arvados/bh20-seq-resource/blob/master/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py][FASTA and YAML]] extractor specific for GenBank. This means that the steps we took above for uploading a GenBank sequence are already automated. + +The steps are: from the +~bh20-seq-resource/scripts/download_genbank_data/~ directory + +#+BEGIN_SRC sh +python3 from_genbank_to_fasta_and_yaml.py +dir_fasta_and_yaml=~/bh20-seq-resource/scripts/download_genbank_data/fasta_and_yaml +ls $dir_fasta_and_yaml/*.yaml | while read path_code_yaml; do + path_code_fasta=${path_code_yaml%.*}.fasta + bh20-seq-uploader --skip-qc $path_code_yaml $path_code_fasta +done +#+END_SRC |