Description
I want to use the option --ids inside a pipeline. In case the input steps generate no output, SeqFilter will return the complete sequence set instead of an empty file.
Version
2.1.8
Expected behavior
Returning an empty sequence file
Example
cat >seq.fa <<EOF
>A
ACG
>B
HIJ
>C
KLM
EOF
# If IDs are provided via pipeline, output is as expected
grep "^>[AB]" seq.fa | SeqFilter/bin/SeqFilter --ids - seq.fa
# [17:24:14] SeqFilter/bin/SeqFilter-2.1.8
# [17:24:14] Detected FASTA format
# [17:24:14] --ids: STDIN
# [17:24:14] --in: seq.fa
# #source state reads bases max min N50 N90
# seq.fa RAW 3 9 3 3 3 3
# seq.fa FIL 2 6 3 3 3 3
# If no IDs are provided via pipeline, output contains complete sequence set
grep "^>[D]" seq.fa | SeqFilter/bin/SeqFilter --ids - seq.fa
# [17:26:09] SeqFilter/bin/SeqFilter-2.1.8
# [17:26:09] Detected FASTA format
# [17:26:09] --ids: STDIN
# [17:26:09] --in: seq.fa
# #source state reads bases max min N50 N90
# seq.fa RAW 3 9 3 3 3 3
# seq.fa FIL 3 9 3 3 3 3
Description I want to use the option
--ids
inside a pipeline. In case the input steps generate no output,SeqFilter
will return the complete sequence set instead of an empty file.Version 2.1.8
Expected behavior Returning an empty sequence file
Example