77 lines
2.0 KiB
Bash
77 lines
2.0 KiB
Bash
#!/usr/bin/env bash
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# Bash version of the Nextflow script that should run faster
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output_file="Glycine_max_duplicate_genes_KaKs.tsv"
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proteome_fasta="/home/sortion/Documents/course/master/M2/S1/comparative_genomics/project/tmp/proteome_filtered.fa"
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cds_fasta="/media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Glycine_max.Glycine_max_v2.1.cds.all.fa"
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set -euo pipefail
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mkdir -p tmp
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echo "seqfile = ./tmp/cds.ali.phy
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outfile = ./tmp/yn
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verbose = 0
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icode = 0
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weighting = 0
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commonf3x4 = 0" > yn00.ctl
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compute_kaks() {
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local gene_id_1
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local gene_id_2
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gene_id_1=$1
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gene_id_2=$2
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# Extract the proteins
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./scripts/extract_fasta_records.sh $gene_id_1 $gene_id_2 ${proteome_fasta} "./tmp/prot.fst"
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# Extract the CDS
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./scripts/extract_fasta_records.sh $gene_id_1 $gene_id_2 ${cds_fasta} "./tmp/cds.fst"
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# Run clustalw2
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clustalw2 -quiet -align -infile="./tmp/prot.fst" -outfile="./tmp/prot.ali.aln"
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# Run Pal2Nal
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pal2nal.pl "./tmp/prot.ali.aln" "./tmp/cds.fst" -output paml > "./tmp/cds.ali.phy"
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# Run yn00
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yn00
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# Extract Ka/Ks
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awk '
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BEGIN {
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on_good_section=0
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skip=0
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}
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$1 == "(B)" {
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skip=8
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on_good_section=1
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}
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on_good_section == 1 {
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if (skip == 0) {
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Ka=$8
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Ks=$11
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print Ka, Ks
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exit
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} else {
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skip -= 1
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}
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}
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' "./tmp/yn"
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}
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echo "gene_a,gene_b,ka,ks" > "${output_file}"
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input="/media/data/sync/Documents/course/master/M2/S1/comparative_genomics/project/tmp/Glycine_max_duplicate_gene_pairs.tsv"
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n=$(wc -l "${input}")
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i=0
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while IFS= read -r line
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do
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echo $i / $n
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gene_a=$(echo $line | awk '{print $1}')
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gene_b=$(echo $line | awk '{print $2}')
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i=$(expr $i + 1)
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kaks=$(compute_kaks $gene_a $gene_b | tail -1 | awk 'NF == 2')
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if [[ ! -z $kaks ]]
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then
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arr=(${kaks//\t/ })
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echo "${gene_a},${gene_b},${arr[0]},${arr[1]}" >> "${output_file}"
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fi
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done < "${input}"
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