Mercurial > repos > abims-sbr > orthogroups_tool

annotate scripts/format_transdecoder_headers.sh @ 0:f3600c96e961 draft

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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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f3600c96e961 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit f30d34a6decb05f6b7803f6d677dad4c50f9cebe
abims-sbr
parents:
diff changeset
1 #/bin/bash
f3600c96e961 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit f30d34a6decb05f6b7803f6d677dad4c50f9cebe
abims-sbr
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2
f3600c96e961 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit f30d34a6decb05f6b7803f6d677dad4c50f9cebe
abims-sbr
parents:
diff changeset
3
f3600c96e961 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit f30d34a6decb05f6b7803f6d677dad4c50f9cebe
abims-sbr
parents:
diff changeset
4 #This script contains regex to re-write the outputs of transdecoder to the original AdaptSearch format
f3600c96e961 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit f30d34a6decb05f6b7803f6d677dad4c50f9cebe
abims-sbr
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5 #Example :
f3600c96e961 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit f30d34a6decb05f6b7803f6d677dad4c50f9cebe
abims-sbr
parents:
diff changeset
6 #OG0007971: m.35 g.35 ORF g.35 m.35 type_internal len_307 _+_ Th132_1/1_1.000_923_1-924_+_
f3600c96e961 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit f30d34a6decb05f6b7803f6d677dad4c50f9cebe
abims-sbr
parents:
diff changeset
7 #Becomes :
f3600c96e961 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit f30d34a6decb05f6b7803f6d677dad4c50f9cebe
abims-sbr
parents:
diff changeset
8 #Th132_1/1_1.000_923
f3600c96e961 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit f30d34a6decb05f6b7803f6d677dad4c50f9cebe
abims-sbr
parents:
diff changeset
9
f3600c96e961 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit f30d34a6decb05f6b7803f6d677dad4c50f9cebe
abims-sbr
parents:
diff changeset
10 # removes 'OGxxxxxxx '
f3600c96e961 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit f30d34a6decb05f6b7803f6d677dad4c50f9cebe
abims-sbr
parents:
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11 sed -i -E 's/OG[0-9]{7}:\s//' $1
f3600c96e961 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit f30d34a6decb05f6b7803f6d677dad4c50f9cebe
abims-sbr
parents:
diff changeset
12 # replace _+_ by (+) because '_' causes bugs
f3600c96e961 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit f30d34a6decb05f6b7803f6d677dad4c50f9cebe
abims-sbr
parents:
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13 sed -i 's/_+_/(+)/g' $1
f3600c96e961 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit f30d34a6decb05f6b7803f6d677dad4c50f9cebe
abims-sbr
parents:
diff changeset
14 # Replaces everything by '>'
f3600c96e961 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit f30d34a6decb05f6b7803f6d677dad4c50f9cebe
abims-sbr
parents:
diff changeset
15 sed -i -E 's/m\.[0-9]{1,}[^()]+\(\+\)\s*/>/g' $1
f3600c96e961 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit f30d34a6decb05f6b7803f6d677dad4c50f9cebe
abims-sbr
parents:
diff changeset
16 # Removes terminal '(+)'
f3600c96e961 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit f30d34a6decb05f6b7803f6d677dad4c50f9cebe
abims-sbr
parents:
diff changeset
17 sed -i 's/(+)//g' $1
f3600c96e961 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit f30d34a6decb05f6b7803f6d677dad4c50f9cebe
abims-sbr
parents:
diff changeset
18 # Removes last suite of unwanted numbers, underscore and dash
f3600c96e961 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit f30d34a6decb05f6b7803f6d677dad4c50f9cebe
abims-sbr
parents:
diff changeset
19 sed -i -E 's/\_[0-9]{1,}-[0-9]{1,}//g' $1