Commit 5aace6ed authored by CHEVIGNON's avatar CHEVIGNON
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parent cd65b56e
#!/usr/bin/env bash
# $1 Contig_1_Bonamia_rRNA_operon.frequency.monomorphic.vcf.all.clean_for-missing.txt
cp $1 test.txt
awk 'NR == 1 {print$0}' test.txt > 1.tmp
gsed -i '1d' test.txt
for ((i=1;i<=5599;i++))
do
echo ""$i"_5599"
position=`awk '$1 == '"$i"' {print$0}' test.txt`
echo "$position"
lineBefore=`awk 'NR == '"$i"'-1 {print$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10}' test.txt | gsed 's/\t/_/g'`
echo "$lineBefore"
if [[ -z "$position" ]]
then
gsed -i ''$i'i'$i' '$lineBefore'' test.txt
gsed -i 's/_/\t/g' test.txt
gsed -i 's/ /\t/g' test.txt
gsed -i 's/\t\+/\t/g;s/^\t//' test.txt
fi
done
cat 1.tmp test.txt > $1_final.txt
rm 1.tmp
rm test.txt
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