add commands.sh

knightlab-analyses · Nov 16, 2021 · c9a8ca4 · c9a8ca4
1 parent 701bc49
commit c9a8ca4
Showing 1 changed file with 14 additions and 0 deletions.
diff --git a/data/qiime2-artifacts-for-qiita/commands.sh b/data/qiime2-artifacts-for-qiita/commands.sh
@@ -0,0 +1,14 @@
+trim_lengths="90 100 150"
+
+for tl in `echo $trim_lengths`; do
+  for s in `grep -v '>' ../newbloom.all.fna | cut -c 1-${tl} | sort | uniq`; do
+    echo -e ">$s\n$s" >> blooms-${tl}.fna
+  done ;
+done
+
+for fna in `ls *.fna`; do
+  qiime tools import \
+    --input-path ${fna} \
+    --output-path ${fna/fna/qza} \
+    --type FeatureData[Sequence]
+done