signalp_transdecoder.md

Running signalp on trinity/transdecoder output

Assuming we have a fasta file of proteins with ids generated from Trinity and Transdecoder called transdecoder.pep. Truncate names as follows.

cat transdecoder.pep | sed -r  's/[^:]*::/>/' > transdecoder_truncated.pep

Note that on a mac you should use -E instead of -r

Then run signalp as normal

signalp -f short transdecoder_truncated.pep > signalp_truncated.out

Finally restore the names

cat signalp_truncated.out | awk '/#/{print $0};match($0,/TRINITY_[0-9A-Z]+_c[0-9]+_g[0-9]+/){ printf("%s::%s\n",substr($0,RSTART,RLENGTH),$0)} ' > signalp.out