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Diffstat (limited to 'doc/blog/using-covid-19-pubseq-part3.org')
| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part3.org | 13 |
1 files changed, 12 insertions, 1 deletions
diff --git a/doc/blog/using-covid-19-pubseq-part3.org b/doc/blog/using-covid-19-pubseq-part3.org index e8fee36..fda7be8 100644 --- a/doc/blog/using-covid-19-pubseq-part3.org +++ b/doc/blog/using-covid-19-pubseq-part3.org @@ -146,7 +146,6 @@ instead on https and entity instead of wiki) the submission went through. Reload the page (it won't empty the fields) to re-enable the submit button. - * Step 4: Check output The current pipeline takes 5.5 hours to complete! Once it completes @@ -237,3 +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 |