Mercurial > repos > abims-sbr > orthogroups_tool

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d33ad52f59bc planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
abims-sbr
parents:
diff changeset
1 #/bin/bash
d33ad52f59bc planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
abims-sbr
parents:
diff changeset
2
d33ad52f59bc planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
abims-sbr
parents:
diff changeset
3 # v2 - this script modifies the 'Orthogroups.txt' file in order to make it easily readable by the following script, filter_orthofinder.py
d33ad52f59bc planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
abims-sbr
parents:
diff changeset
4 #Example :
d33ad52f59bc planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
abims-sbr
parents:
diff changeset
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
d33ad52f59bc planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
abims-sbr
parents:
diff changeset
6 #Becomes :
d33ad52f59bc planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
abims-sbr
parents:
diff changeset
7 #As119_1/1_1.000_543 As170_1/1_1.000_1203
d33ad52f59bc planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
abims-sbr
parents:
diff changeset
8
d33ad52f59bc planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
abims-sbr
parents:
diff changeset
9 # removes 'OGxxxxxxx: '
d33ad52f59bc planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
abims-sbr
parents:
diff changeset
10 sed -E 's/OG[0-9]{7,}:\s//' $1 > $2
d33ad52f59bc planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
abims-sbr
parents:
diff changeset
11 # removes things like Gene.119__
d33ad52f59bc planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
abims-sbr
parents:
diff changeset
12 sed -i -E 's/Gene\.[0-9]{1,}\_\_/>/g' $2
d33ad52f59bc planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
abims-sbr
parents:
diff changeset
13 # removes things like __g.117__m.117
d33ad52f59bc planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
abims-sbr
parents:
diff changeset
14 sed -i -E 's/\_\_g\.[0-9]{1,}\_\_m\.[0-9]{1,}//g' $2
d33ad52f59bc planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
abims-sbr
parents:
diff changeset
15
d33ad52f59bc planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
abims-sbr
parents:
diff changeset
16 # Old version
d33ad52f59bc planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
abims-sbr
parents:
diff changeset
17
d33ad52f59bc planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
abims-sbr
parents:
diff changeset
18 # removes 'OGxxxxxxx '
d33ad52f59bc planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
abims-sbr
parents:
diff changeset
19 #sed -E 's/OG[0-9]{7}:\s//' $1 > $2
d33ad52f59bc planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
abims-sbr
parents:
diff changeset
20 # replace _+_ by (+) because '_' causes bugs
d33ad52f59bc planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
abims-sbr
parents:
diff changeset
21 #sed -i 's/_+_/(+)/g' $2
d33ad52f59bc planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
abims-sbr
parents:
diff changeset
22 # Replaces everything by '>'
d33ad52f59bc planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
abims-sbr
parents:
diff changeset
23 #sed -i -E 's/m\.[0-9]{1,}[^()]+\(\+\)\s*/>/g' $2
d33ad52f59bc planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
abims-sbr
parents:
diff changeset
24 # Removes terminal '(+)'
d33ad52f59bc planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
abims-sbr
parents:
diff changeset
25 #sed -i 's/(+)//g' $2
d33ad52f59bc planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
abims-sbr
parents:
diff changeset
26 # Removes last suite of unwanted numbers, underscore and dash
d33ad52f59bc planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
abims-sbr
parents:
diff changeset
27 #sed -i -E 's/\_[0-9]{1,}-[0-9]{1,}//g' $2