Hello there!
I'm trying to incluce For cycle in my Qiime2 full pipeline.
I already lunch multiple subsequent command with "&& " and now i trying to use for cycle because i analyze different data set in different folder.
I already successfully lunch this command line:
for i in {1..7}
do
qiime taxa collapse
--i-table right/path/ASV_table.qza
--i-taxonomy /right/path/taxonomy.qza
--p-level $i
--o-collapsed-table another/path/ASV_collapsed_Level_$i.qza
done
and that work.... so i try another one but with different usage.
i want use "$i" as part of a path.
for i in {first/path/piece,second/path/piece,third/path/piece}
do
qiime feature-classifier classify-sklearn
--i-classifier right/path/classifier.qza
--i-reads same/path/for/all/{i}/rep_seqs.qza \
--o-classification same/path/for/all/{i}/taxonomy.qza
done
but my terminal not work... no error message, no nothing.. i trying to press enter multiple time but nothing... i let it in that condition for one nigth, but nothing...
I sure i wrong something but i am a noob in python.. help me please
ps sorry for my English 