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| author | Peter Amstutz | 2020-04-21 12:53:19 -0400 |
|---|---|---|
| committer | Peter Amstutz | 2020-04-21 12:53:19 -0400 |
| commit | 88d81f853cf04b7f28681dd9cdee775b0422f252 (patch) | |
| tree | b23f5dedc100c8508784d20edaba864f91e7444d /scripts/foreach.sh | |
| parent | 85b85b676d7ecc218d9f84357b2e7ea0133eed94 (diff) | |
| download | bh20-seq-resource-88d81f853cf04b7f28681dd9cdee775b0422f252.tar.gz bh20-seq-resource-88d81f853cf04b7f28681dd9cdee775b0422f252.tar.lz bh20-seq-resource-88d81f853cf04b7f28681dd9cdee775b0422f252.zip | |
Working on NCBI import
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Diffstat (limited to 'scripts/foreach.sh')
| -rwxr-xr-x | scripts/foreach.sh | 18 |
1 files changed, 18 insertions, 0 deletions
diff --git a/scripts/foreach.sh b/scripts/foreach.sh new file mode 100755 index 0000000..35b07b8 --- /dev/null +++ b/scripts/foreach.sh @@ -0,0 +1,18 @@ +#!/bin/sh +rm -rf validated fasta_and_yaml_* +mkdir -p validated +./from_genbank_to_fasta_and_yaml.py +fasta_files=$(find fasta_and_yaml_20200421/ -name "*.fasta") +for f in $fasta_files ; do + yaml=$(echo $f | rev | cut -c7- | rev).yaml + echo $f + echo $yaml + if bh20-seq-uploader --validate $f $yaml ; then + sz=$(stat --format=%s $f) + if test $sz -gt 20000 ; then + mv $f $yaml validated + else + echo "Fasta file too small" + fi + fi +done |