Mercurial > repos > abims-sbr > orthogroups_tool
diff scripts/format_transdecoder_headers.sh @ 0:f3600c96e961 draft
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit f30d34a6decb05f6b7803f6d677dad4c50f9cebe
| author | abims-sbr |
|---|---|
| date | Fri, 27 Oct 2017 10:38:52 -0400 |
| parents | |
| children | 3f862f346967 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/format_transdecoder_headers.sh Fri Oct 27 10:38:52 2017 -0400 @@ -0,0 +1,19 @@ +#/bin/bash + + +#This script contains regex to re-write the outputs of transdecoder to the original AdaptSearch format +#Example : +#OG0007971: m.35 g.35 ORF g.35 m.35 type_internal len_307 _+_ Th132_1/1_1.000_923_1-924_+_ +#Becomes : +#Th132_1/1_1.000_923 + +# removes 'OGxxxxxxx ' +sed -i -E 's/OG[0-9]{7}:\s//' $1 +# replace _+_ by (+) because '_' causes bugs +sed -i 's/_+_/(+)/g' $1 +# Replaces everything by '>' +sed -i -E 's/m\.[0-9]{1,}[^()]+\(\+\)\s*/>/g' $1 +# Removes terminal '(+)' +sed -i 's/(+)//g' $1 +# Removes last suite of unwanted numbers, underscore and dash +sed -i -E 's/\_[0-9]{1,}-[0-9]{1,}//g' $1