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authorAndreaGuarracino2020-09-29 18:46:49 +0200
committerAndreaGuarracino2020-09-29 18:46:49 +0200
commitb3a671f04743dc2bf48049b413d7d1f20d31bbcf (patch)
tree05a6f0f15564f1da8e858551e644543865700ae8 /doc/blog
parentc72dab2788d010153d5406f2d5ecbe3824571931 (diff)
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esr_samples script refactoring; added a reference of the esr_samples script in the blog as an example of how to parse metadata
Diffstat (limited to 'doc/blog')
-rw-r--r--doc/blog/using-covid-19-pubseq-part3.org16
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diff --git a/doc/blog/using-covid-19-pubseq-part3.org b/doc/blog/using-covid-19-pubseq-part3.org
index 4d70e7c..abc260c 100644
--- a/doc/blog/using-covid-19-pubseq-part3.org
+++ b/doc/blog/using-covid-19-pubseq-part3.org
@@ -21,6 +21,7 @@
- [[#bulk-sequence-uploader][Bulk sequence uploader]]
- [[#run-the-uploader-cli][Run the uploader (CLI)]]
- [[#example-uploading-bulk-genbank-sequences][Example: uploading bulk GenBank sequences]]
+ - [[#example-preparing-metadata][Example: preparing metadata]]
* Uploading Data
@@ -232,6 +233,7 @@ Guix package manager).
The web interface using this exact same script so it should just work
(TM).
+
** Example: uploading bulk GenBank sequences
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
@@ -250,3 +252,17 @@ ls $dir_fasta_and_yaml/*.yaml | while read path_code_yaml; do
bh20-seq-uploader --skip-qc $path_code_yaml $path_code_fasta
done
#+END_SRC
+
+
+** Example: preparing metadata
+
+Usually, metadata are available in tabular format, like spreadsheets. As an example, we provide a script
+[[https://github.com/arvados/bh20-seq-resource/tree/master/scripts/esr_samples][esr_samples.py]] to show you how to parse
+your metadata in YAML files ready for the upload. To execute the script, go in the ~bh20-seq-resource/scripts/esr_samples
+and execute
+
+#+BEGIN_SRC sh
+python3 esr_samples.py
+#+END_SRC
+
+You will find the YAML files in the `yaml` folder which will be created in the same directory. \ No newline at end of file