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gff3 to tab seperated
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cd fasta_proteome_files/
ls
head H.m_proteome.fasta
cd ../
cat H.moselyanum_helixer.gff3 | grep "\sgene\s"
cat H.moselyanum_helixer.gff3 | grep "\sgene\s" | cut -f 1,4,5,9
cat H.moselyanum_helixer.gff3 | grep "\sgene\s" | cut -f 1,4,5,9 | sed 's/ID=//g'
cat H.moselyanum_helixer.gff3 | grep "\sgene\s" | cut -f 1,4,5,9 | sed 's/ID=//g' | awk -F '{print $1,$4,$2,$3]'
cat H.moselyanum_helixer.gff3 | grep "\sgene\s" | cut -f 1,4,5,9 | sed 's/ID=//g' | awk -F '{print $1,$4,$2,$3}'
cat H.moselyanum_helixer.gff3 | grep "\sgene\s" | cut -f 1,4,5,9 | sed 's/ID=//g' | awk '{print $1,$4,$2,$3}'
cat H.moselyanum_helixer.gff3 | grep "\sgene\s" | cut -f 1,4,5,9 | sed 's/ID=//g' | awk '{print $1,$4,$2,$3}' | sed 's/ /\t/g'
cat H.moselyanum_helixer.gff3 | grep "\sgene\s" | cut -f 1,4,5,9 | sed 's/ID=//g' | awk '{print $1,$4,$2,$3}' | sed 's/ /\t/g' > H.moselyanum_helixer-DupGeneFinder.gff
ls
cat hifiasm_M.beccarii_out.gff3 | grep "\sgene\s" | cut -f 1,4,5,9 | sed 's/ID=//g' | awk '{print $1,$4,$2,$3}' | sed 's/ /\t/g' > M.beccarii_helixer-DupGeneFinder.gff
cat M.beccarii_helixer-DupGeneFinder.gff
ls
cat H.moselyanum_helixer-DupGeneFinder.gff M.beccarii_helixer-DupGeneFinder.gff | cut - f 2 | sort -d
cat H.moselyanum_helixer-DupGeneFinder.gff M.beccarii_helixer-DupGeneFinder.gff | cut -f 2 | sort -d
cat H.moselyanum_helixer-DupGeneFinder.gff M.beccarii_helixer-DupGeneFinder.gff | cut -f 2 | sort -d | wc -l
cat H.moselyanum_helixer-DupGeneFinder.gff M.beccarii_helixer-DupGeneFinder.gff | cut -f 2 | sort -u | wc -l
wc -l M.beccarii_helixer-DupGeneFinder.gff
wc -l H.moselyanum_helixer-DupGeneFinder.gff
cat H.moselyanum_helixer-DupGeneFinder.gff M.beccarii_helixer-DupGeneFinder.gff | cut -f 2 | sort | uniq -d | wc -l
ls
head H.moselyanum_helixer-DupGeneFinder.gff
head H.moselyanum_helixer-DupGeneFinder.gff | sed 's/\t_/GGGG/g'
head H.moselyanum_helixer-DupGeneFinder.gff | sed 's/\t_/\tHm/g'
head H.moselyanum_helixer-DupGeneFinder.gff | sed 's/\t_/\tHm_/g'
sed 's/\t_/\tHm_/g' -i H.moselyanum_helixer-DupGeneFinder.gff
sed 's/\t_/\tMb_/g' -i M.beccarii_helixer-DupGeneFinder.gff
cat H.moselyanum_helixer-DupGeneFinder.gff M.beccarii_helixer-DupGeneFinder.gff | cut -f 2 | sort | uniq -d | wc -l
ls
cd fasta_proteome_files/
ls
head H.m_proteome.fasta
cat H.m_proteome.fasta | sed 's/>/>Hm/g' > H.m_proteome-DupGeneFinder.fasta
cat M.b_proteome.fasta | sed 's/>/>Mb/g' > M.b_proteome-DupGeneFinder.fasta
cat M.b_proteome.fasta
cat M.b_proteome-DupGeneFinder.fasta
cd ../
ls
H.moselyanum_helixer-DupGeneFinder.gff cat
head H.moselyanum_helixer-DupGeneFinder.gff
ls
cd fasta_proteome_files/
ls
grep ">" H.m_proteome-DupGeneFinder.fasta
grep ">" H.m_proteome-DupGeneFinder.fasta | grep -v "\.1$"
grep ">" H.m_proteome-DupGeneFinder.fasta | grep -v "\.2$"
grep ">" H.m_proteome-DupGeneFinder.fasta | sed 's/.1$//g'
sed 's/.1$//g' -i H.m_proteome-DupGeneFinder.fasta
sed 's/.1$//g' -i M.b_proteome-DupGeneFinder.fasta
head M.b_proteome-DupGeneFinder.fasta
ls
cd ../
ls
cat H.moselyanum_helixer-DupGeneFinder.gff M.beccarii_helixer-DupGeneFinder.gff > Combined-DupGeneFinder.gff
cd fasta_proteome_files/
ls