Open nr0cinu opened 5 years ago
As a workaround, removing the relative abundance
section before using iRep_filter.py
seems to fix it.
This is the command I use the process the files before merging them:
awk '/## index of replication/{ flag=1 } /## relative abundance/{ flag=0 } /## % windows passing filter/{ flag=1 } flag' a.tsv > a_tmp.tsv
Hi!
I noticed, that when iRep_filter.py is run twice (e.g., first collating genomes, then samples), the coverage information gets lost.
Here is a minimal example:
input: a.txt b.txt
when i run
iRep_filter.py -t a.txt b.txt > ab.txt
it results in ab.txtNotice how these sections are suddenly identical
It’s not shown in this example, but I have observed, that when the coverage values are replaced with the wrong "relative abundance" values, they seem to be used for coverage filtering, which can result in loosing valid iRep values.
Thanks! Bela