Create tbl-from-gff-complete-genome.sh

tbl-from-gff-complete-genome.sh

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+
+#! /bin/sh
+#Francesca Bottacini
+#[email protected]
+
+#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 ;