175 lines
5.2 KiB
Bash
175 lines
5.2 KiB
Bash
#!/bin/bash
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set -euo pipefail
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export PATH="$PATH:${SCRIPTS}/bucky/bin"
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# treeshrink
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mkdir -p treeshrink
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for i in ../13.gene_phylogeny/alignments_filtered/*.fa; do
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j=$(basename "$i" .fa)
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mkdir -p treeshrink/"${j}"
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absolute_path=$(readlink -f "$i")
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ln -s "$absolute_path" "treeshrink"/"${j}"/input.fasta
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ln -s "$(readlink -f ../13.gene_phylogeny/raxml)"/"${j}/${j}".raxml.bestTree "treeshrink"/"${j}"/input.tree
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done
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pueue add -- run_treeshrink.py -f -i treeshrink/ -t input.tree -a input.fasta -m per-gene
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# treeshrink summary
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mkdir -p treeshrink_summary
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removed_sequences="treeshrink_summary/treeshrink_removed_sequences.tsv"
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removed_by_species="treeshrink_summary/treeshrink_removed_by_species.tsv"
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removed_group_summary="treeshrink_summary/treeshrink_removed_group_summary.tsv"
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printf "OG\tspecies\n" >"$removed_sequences"
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for output_fasta in treeshrink/*/output.fasta; do
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og_name=$(basename "$(dirname "$output_fasta")")
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input_fasta="$(dirname "$output_fasta")/input.fasta"
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comm -23 \
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<(awk '/^>/{sub(/^>/, ""); sub(/[[:space:]].*$/, ""); print}' "$input_fasta" | sort -u) \
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<(awk '/^>/{sub(/^>/, ""); sub(/[[:space:]].*$/, ""); print}' "$output_fasta" | sort -u) |
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while IFS= read -r species; do
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printf "%s\t%s\n" "$og_name" "$species"
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done >>"$removed_sequences"
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done
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printf "species\tfiltered_OG_count\n" >"$removed_by_species"
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awk -F '\t' 'NR > 1 {count[$2]++} END {for (species in count) print species, count[species]}' \
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OFS='\t' "$removed_sequences" | sort -k2,2nr -k1,1 >>"$removed_by_species"
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printf "group\tfiltered_OG_count\n" >"$removed_group_summary"
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awk -F '\t' '
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NR > 1 {
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if ($2 == "EA" || $2 == "EM" || $2 == "ZJ")
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outgroup[$1] = 1
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else
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ingroup[$1] = 1
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}
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END {
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for (og in outgroup) outgroup_count++
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for (og in ingroup) ingroup_count++
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print "outgroup_EA_EM_ZJ", outgroup_count + 0
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print "ingroup", ingroup_count + 0
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}
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' OFS='\t' "$removed_sequences" >>"$removed_group_summary"
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# LBS filter
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min_taxon=11
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echo -n "" >treeshrink_filtered.list
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for i in treeshrink/*/output.fasta; do
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j=$(dirname "$i")
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j=$(basename "$j")
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seqnum=$(grep -c ">" "$i")
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if [[ $seqnum -ge $min_taxon ]]; then
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echo -n ""
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else
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echo "$j" >>treeshrink_filtered.list
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fi
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done
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# data preparation
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ln -s ../13.gene_phylogeny/raxml .
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ln -s ../13.gene_phylogeny/mbsum .
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##
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## 第一套，所有基因保留，仅移除treeshrink过滤掉的基因
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##
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mkdir -p all_genes
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cd all_genes
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# aster coalescence tree
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for file in ../raxml/*/*.support; do
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gene=$(basename "$(dirname "$file")")
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if ! grep -Fqx -- "$gene" ../treeshrink_filtered.list; then
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cat "$file"
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fi
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done >all.ml.tre
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mkdir -p species_tree
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pueue add -- astral4 -t 6 -i all.ml.tre -o species_tree/coal.tre --root ZJ
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# bucky
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mkdir bucky
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for mbfile in ../mbsum/*.in; do
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gene=$(basename "$mbfile" .in)
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if ! grep -Fqx -- "$gene" ../treeshrink_filtered.list; then
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cp "$mbfile" bucky/"$gene".in
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fi
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done
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cd bucky
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tar -cf input.mb.tar -- ./*.in
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rm -- ./*.in
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pueue add -- "$SCRIPTS"/utils/bucky.pl -a 1 -o bucky_1 -s input.mb.tar
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# SNaQ
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mkdir snaq
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cd snaq
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## run snaq.jl with interactive mode
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# julia snaq.jl
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cd ../..
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##
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## 第二套，移除treeshrink过滤掉的基因和移码突变基因
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mkdir -p exclude_all_fs
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cd exclude_all_fs
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cut -f 1 ../../13.gene_phylogeny/frameshift_summary/frameshift_locus_classification.tsv | sed 1d > fs_exclude.list
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# aster coalescence tree
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for file in ../raxml/*/*.support; do
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gene=$(basename "$(dirname "$file")")
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if ! grep -Fqx -- "$gene" ../treeshrink_filtered.list fs_exclude.list; then
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cat "$file"
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fi
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done >all.ml.tre
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mkdir -p species_tree
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pueue add -- astral4 -t 6 -i all.ml.tre -o species_tree/coal.tre --root ZJ
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# bucky
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mkdir bucky
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for mbfile in ../mbsum/*.in; do
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gene=$(basename "$mbfile" .in)
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if ! grep -Fqx -- "$gene" ../treeshrink_filtered.list fs_exclude.list; then
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cp "$mbfile" bucky/"$gene".in
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fi
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done
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cd bucky
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tar -cf input.mb.tar -- ./*.in
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rm -- ./*.in
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pueue add -- "$SCRIPTS"/utils/bucky.pl -a 1 -o bucky_1 -s input.mb.tar
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mkdir snaq
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cd snaq
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## run snaq.jl with interactive mode
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# julia snaq.jl
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cd ../..
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## 第三套，移除严重移码突变基因和treeshrink过滤掉的基因
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mkdir -p exclude_severe_fs
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cd exclude_severe_fs
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grep -wv single_species_single_event ../../13.gene_phylogeny/frameshift_summary/frameshift_locus_classification.tsv | cut -f 1 | sed 1d > fs_exclude.list
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# aster coalescence tree
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for file in ../raxml/*/*.support; do
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gene=$(basename "$(dirname "$file")")
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if ! grep -Fqx -- "$gene" ../treeshrink_filtered.list fs_exclude.list; then
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cat "$file"
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fi
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done >all.ml.tre
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mkdir -p species_tree
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pueue add -- astral4 -t 6 -i all.ml.tre -o species_tree/coal.tre --root ZJ
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# bucky
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mkdir bucky
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for mbfile in ../mbsum/*.in; do
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gene=$(basename "$mbfile" .in)
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if ! grep -Fqx -- "$gene" ../treeshrink_filtered.list fs_exclude.list; then
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cp "$mbfile" bucky/"$gene".in
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fi
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done
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cd bucky
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tar -cf input.mb.tar -- ./*.in
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rm -- ./*.in
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pueue add -- "$SCRIPTS"/utils/bucky.pl -a 1 -o bucky_1 -s input.mb.tar
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mkdir snaq
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cd snaq
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## run snaq.jl with interactive mode
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# julia snaq.jl
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cd ../..
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