Mercurial > repos > abims-sbr > orthogroups_tool

comparison scripts/format_transdecoder_headers.sh @ 0:d33ad52f59bc draft default tip

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planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
author abims-sbr
date Fri, 01 Feb 2019 10:25:10 -0500
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-1:000000000000 0:d33ad52f59bc
1 #/bin/bash
2
3 # v2 - this script modifies the 'Orthogroups.txt' file in order to make it easily readable by the following script, filter_orthofinder.py
4 #Example :
5 #OG0000001: Gene.117__As119_1/1_1.000_543__g.117__m.117 Gene.157__As170_1/1_1.000_1203__g.157__m.157
6 #Becomes :
7 #As119_1/1_1.000_543 As170_1/1_1.000_1203
8
9 # removes 'OGxxxxxxx: '
10 sed -E 's/OG[0-9]{7,}:\s//' $1 > $2
11 # removes things like Gene.119__
12 sed -i -E 's/Gene\.[0-9]{1,}\_\_/>/g' $2
13 # removes things like __g.117__m.117
14 sed -i -E 's/\_\_g\.[0-9]{1,}\_\_m\.[0-9]{1,}//g' $2
15
16 # Old version
17
18 # removes 'OGxxxxxxx '
19 #sed -E 's/OG[0-9]{7}:\s//' $1 > $2
20 # replace _+_ by (+) because '_' causes bugs
21 #sed -i 's/_+_/(+)/g' $2
22 # Replaces everything by '>'
23 #sed -i -E 's/m\.[0-9]{1,}[^()]+\(\+\)\s*/>/g' $2
24 # Removes terminal '(+)'
25 #sed -i 's/(+)//g' $2
26 # Removes last suite of unwanted numbers, underscore and dash
27 #sed -i -E 's/\_[0-9]{1,}-[0-9]{1,}//g' $2