annotate CAPS2gff.sh @ 2:ea2117a7b363 draft

Uploaded CAPS marker design workflow for 454 Data
author john-mccallum
date Sun, 09 Sep 2012 23:16:56 -0400
parents 21053f7f9ed1
children b321e0517be3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
1 #!/bin/sh
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
2 ##convert output of CAPS detection tool to GFF3
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
3 #Copyright 2012 John McCallum
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
4 #New Zealand Institute for Plant and Food Research
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
5
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
6 #This program is free software: you can redistribute it and/or modify
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
7 # it under the terms of the GNU General Public License as published by
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
8 # the Free Software Foundation, either version 3 of the License, or
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
9 # (at your option) any later version.
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
10 #
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
11 # This program is distributed in the hope that it will be useful,
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
12 # but WITHOUT ANY WARRANTY; without even the implied warranty of
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
13 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
14 # GNU General Public License for more details.
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
15 #
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
16 # You should have received a copy of the GNU General Public License
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
17 # along with this program. If not, see <http://www.gnu.org/licenses/>.
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
18
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
19 inputfile=$1
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
20 outputfile=$2
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
21 awk -F '\t' 'split($4,ID,":") {print ID[1], "FINDCAPS",ID[3],ID[4],ID[4],".",".",".","ID="$1";Enzyme="$5";Phase="$6}' $inputfile > $outputfile