Mercurial > repos > abims-sbr > orthogroups_tool
comparison 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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| -1:000000000000 | 0:f3600c96e961 |
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| 1 #/bin/bash | |
| 2 | |
| 3 | |
| 4 #This script contains regex to re-write the outputs of transdecoder to the original AdaptSearch format | |
| 5 #Example : | |
| 6 #OG0007971: m.35 g.35 ORF g.35 m.35 type_internal len_307 _+_ Th132_1/1_1.000_923_1-924_+_ | |
| 7 #Becomes : | |
| 8 #Th132_1/1_1.000_923 | |
| 9 | |
| 10 # removes 'OGxxxxxxx ' | |
| 11 sed -i -E 's/OG[0-9]{7}:\s//' $1 | |
| 12 # replace _+_ by (+) because '_' causes bugs | |
| 13 sed -i 's/_+_/(+)/g' $1 | |
| 14 # Replaces everything by '>' | |
| 15 sed -i -E 's/m\.[0-9]{1,}[^()]+\(\+\)\s*/>/g' $1 | |
| 16 # Removes terminal '(+)' | |
| 17 sed -i 's/(+)//g' $1 | |
| 18 # Removes last suite of unwanted numbers, underscore and dash | |
| 19 sed -i -E 's/\_[0-9]{1,}-[0-9]{1,}//g' $1 |