From d6bc0e78f43081c013a17f0373479e0f1b482fd2 Mon Sep 17 00:00:00 2001
From: frbot <67206072+frbot@users.noreply.github.com>
Date: Wed, 24 Jun 2020 00:02:08 +0100
Subject: [PATCH] Create tbl-from-gff-complete-genome.sh

---
 tbl-from-gff-complete-genome.sh | 70 +++++++++++++++++++++++++++++++++
 1 file changed, 70 insertions(+)
 create mode 100644 tbl-from-gff-complete-genome.sh

diff --git a/tbl-from-gff-complete-genome.sh b/tbl-from-gff-complete-genome.sh
new file mode 100644
index 0000000..ac72dd9
--- /dev/null
+++ b/tbl-from-gff-complete-genome.sh
@@ -0,0 +1,70 @@
+
+#! /bin/sh
+#Francesca Bottacini
+#f.bottacini@umail.ucc.ie
+
+#specify input
+input="$1"
+proteinID="$2"
+
+
+#Prepare directory
+mkdir tmp ;
+cp $input* tmp/ ;
+cd tmp ;
+
+cp $input.nucleotide $input.fsa ;
+
+#Extract features without sequence from gff file
+grep "ID" $input.gff > sequintmp ;
+sed -i "/ID/ s/ /:/g" sequintmp ;
+
+#Process forward and reverse strans ORFs
+awk '$7 == "+"' sequintmp > sequinfw ;
+awk '$7 == "-"' sequintmp > sequinrv ;
+
+awk '{print $4,$5,$3,$9}'  sequinfw > sequintblfw ;
+awk '{print $5,$4,$3,$9}'  sequinrv > sequintblrv ;
+cat sequintblfw sequintblrv > sequintbl ;
+sed -i "/ / s/ /\t/" sequintbl ;
+sed -i "/ / s/ /\t/" sequintbl ;
+sed -i "/ / s/ /\t/" sequintbl ;
+sed -i "/ / s/ \t/\t/g" sequintbl ;
+
+#Process products and insert proteinID
+sed -i "/ID/ s/:/ /g" sequintbl ;
+
+sed -i "/CDS/ s/CDS\tID=/CDS\tprotein_id=gnl\|${proteinID}\|/g" sequintbl ;
+sed -i "/;/ s/;/\n\t\t\t\t\t/g" sequintbl ;
+
+sed -i "/ID=/ s/ID\=/\n\t\t\t\t\tID\=/g" sequintbl ;
+sed -i "/protein_id\=/ s/protein_id\=/\n\t\t\t\t\tprotein_id\=/g" sequintbl ;
+sed -i "/=/ s/=/\t/g" sequintbl ;
+
+#Format tbl file with tabs and returns
+mv sequintbl $input.sequin ;
+
+sed ':a;{N;s/\n/;/};ba' $input.sequin > $input.tmptbl ;
+sed -e "s/CDS\n\t\t\t\t\tID\t/CDS\t;\t\t\t\t\tprotein_id\tgnl\|${proteinID}\|/g" $input.tmptbl > $input.tbl ;
+sed -i "/;/ s/;/\n/g" $input.tbl ;
+sed -i "/ID/ s/ID/locus_tag/g" $input.tbl ;
+sed -i "/\t/ s/\t\t\t\t\t/\t\t\t/g" $input.tbl ;
+sed -i "/>/ s/>.*//g" $input.tbl ;
+sed -i "1i >Feature ${input}" $input.tbl ;
+
+#Add hypotheticals to non predicted proteins (altho there should be none)
+
+sed -i "/product/ s/product\t$/product\thypothetical protein/g" $input.tbl ;
+sed -i "/CDS/ s/CDS\t$/CDS/g" $input.tbl ;
+sed -i "/gene/ s/gene\t$/gene/g" $input.tbl ;
+sed -i "/tRNA/ s/tRNA\t$/tRNA/g" $input.tbl ;
+sed -i "/rRNA/ s/rRNA\t$/rRNA/g" $input.tbl ;
+sed -i "s/ \+/ /g" $input.tbl ;
+sed -i "s/ \t/\t/g" $input.tbl ;
+
+#Move files and cleanup
+mv $input.tbl ../ ;
+mv $input.fsa ../ ;
+cd .. ;
+
+rm -fr tmp ;