how to ask SINA to save taxonomy search results from multiple runs into 1 file, but not save alignments?

[l-yampolsky]

If I do

for f in *.fasta; do [PATH2SINA]/sina -i $f \ -r [PATH2SILVA.arb] \ -o outfile \ -t --search --search-max-result=1 --lca-fields=tax_slv --meta-fmt=csv >> silvaResults.csv ; done;

-clearly it overwrites the outfile each time and nothing goes into silvaResults.csv.

If I do

for f in *.fasta; do [PATH2SINA]/sina -i $f \ -r [PATH2SILVA.arb] \ -o - \ #of omit -o altogether -t --search --search-max-result=1 --lca-fields=tax_slv --meta-fmt=csv >> silvaResults.csv ; done;

then, instead of appending to silvaResults.csv, SINA appends to -.csv. There are two problems with that: 1)everything gets dumped into -.csv, inlcuding the alignments and 2) the file -csv has to be manually renamed before it can be used in scripts.

Is there a way to suppress output of the alignments and to give the default output file some other name?

Thanks!!

[epruesse]

What you want will work with 1.6.1 more easily. There, you can just say

sina .... -o output1.csv

It might just be easiest to wait until then.

[epruesse]

Considering duplicate of #10