20261002

2026-10-02 03:32:03 +08:00
parent e398109a10
commit 06954e0e49
21 changed files with 4336 additions and 8560 deletions
@@ -0,0 +1,174 @@
+#!/bin/bash
+
+set -euo pipefail
+export PATH="$PATH:${SCRIPTS}/bucky/bin"
+
+# treeshrink
+mkdir -p treeshrink
+for i in ../13.gene_phylogeny/alignments_filtered/*.fa; do
+    j=$(basename "$i" .fa)
+    mkdir -p treeshrink/"${j}"
+    absolute_path=$(readlink -f "$i")
+    ln -s "$absolute_path" "treeshrink"/"${j}"/input.fasta
+    ln -s "$(readlink -f ../13.gene_phylogeny/raxml)"/"${j}/${j}".raxml.bestTree "treeshrink"/"${j}"/input.tree
+done
+pueue add -- run_treeshrink.py -f -i treeshrink/ -t input.tree -a input.fasta -m per-gene
+
+# treeshrink summary
+mkdir -p treeshrink_summary
+removed_sequences="treeshrink_summary/treeshrink_removed_sequences.tsv"
+removed_by_species="treeshrink_summary/treeshrink_removed_by_species.tsv"
+removed_group_summary="treeshrink_summary/treeshrink_removed_group_summary.tsv"
+printf "OG\tspecies\n" >"$removed_sequences"
+for output_fasta in treeshrink/*/output.fasta; do
+    og_name=$(basename "$(dirname "$output_fasta")")
+    input_fasta="$(dirname "$output_fasta")/input.fasta"
+    comm -23 \
+        <(awk '/^>/{sub(/^>/, ""); sub(/[[:space:]].*$/, ""); print}' "$input_fasta" | sort -u) \
+        <(awk '/^>/{sub(/^>/, ""); sub(/[[:space:]].*$/, ""); print}' "$output_fasta" | sort -u) |
+        while IFS= read -r species; do
+            printf "%s\t%s\n" "$og_name" "$species"
+        done >>"$removed_sequences"
+done
+printf "species\tfiltered_OG_count\n" >"$removed_by_species"
+awk -F '\t' 'NR > 1 {count[$2]++} END {for (species in count) print species, count[species]}' \
+    OFS='\t' "$removed_sequences" | sort -k2,2nr -k1,1 >>"$removed_by_species"
+printf "group\tfiltered_OG_count\n" >"$removed_group_summary"
+awk -F '\t' '
+    NR > 1 {
+        if ($2 == "EA" || $2 == "EM" || $2 == "ZJ")
+            outgroup[$1] = 1
+        else
+            ingroup[$1] = 1
+    }
+    END {
+        for (og in outgroup) outgroup_count++
+        for (og in ingroup) ingroup_count++
+        print "outgroup_EA_EM_ZJ", outgroup_count + 0
+        print "ingroup", ingroup_count + 0
+    }
+' OFS='\t' "$removed_sequences" >>"$removed_group_summary"
+
+# LBS filter
+min_taxon=11
+echo -n "" >treeshrink_filtered.list
+for i in treeshrink/*/output.fasta; do
+    j=$(dirname "$i")
+    j=$(basename "$j")
+    seqnum=$(grep -c ">" "$i")
+    if [[ $seqnum -ge $min_taxon ]]; then
+        echo -n ""
+    else
+        echo "$j" >>treeshrink_filtered.list
+    fi
+done
+
+# data preparation
+ln -s ../13.gene_phylogeny/raxml .
+ln -s ../13.gene_phylogeny/mbsum .
+
+##
+## 第一套，所有基因保留，仅移除treeshrink过滤掉的基因
+##
+
+mkdir -p all_genes
+cd all_genes
+
+# aster coalescence tree
+for file in ../raxml/*/*.support; do
+    gene=$(basename "$(dirname "$file")")
+    if ! grep -Fqx -- "$gene" ../treeshrink_filtered.list; then
+        cat "$file"
+    fi
+done >all.ml.tre
+mkdir -p species_tree
+pueue add -- astral4 -t 6 -i all.ml.tre -o species_tree/coal.tre --root ZJ
+
+# bucky
+mkdir bucky
+for mbfile in ../mbsum/*.in; do
+    gene=$(basename "$mbfile" .in)
+    if ! grep -Fqx -- "$gene" ../treeshrink_filtered.list; then
+        cp "$mbfile" bucky/"$gene".in
+    fi
+done
+cd bucky
+tar -cf input.mb.tar -- ./*.in
+rm -- ./*.in
+pueue add -- "$SCRIPTS"/utils/bucky.pl -a 1 -o bucky_1 -s input.mb.tar
+
+# SNaQ
+mkdir snaq
+cd snaq
+## run snaq.jl with interactive mode
+# julia snaq.jl
+cd ../..
+
+##
+## 第二套，移除treeshrink过滤掉的基因和移码突变基因
+mkdir -p exclude_all_fs
+cd exclude_all_fs
+cut -f 1 ../../13.gene_phylogeny/frameshift_summary/frameshift_locus_classification.tsv | sed 1d > fs_exclude.list
+
+# aster coalescence tree
+for file in ../raxml/*/*.support; do
+    gene=$(basename "$(dirname "$file")")
+    if ! grep -Fqx -- "$gene" ../treeshrink_filtered.list fs_exclude.list; then
+        cat "$file"
+    fi
+done >all.ml.tre
+mkdir -p species_tree
+pueue add -- astral4 -t 6 -i all.ml.tre -o species_tree/coal.tre --root ZJ
+
+# bucky
+mkdir bucky
+for mbfile in ../mbsum/*.in; do
+    gene=$(basename "$mbfile" .in)
+    if ! grep -Fqx -- "$gene" ../treeshrink_filtered.list fs_exclude.list; then
+        cp "$mbfile" bucky/"$gene".in
+    fi
+done
+cd bucky
+tar -cf input.mb.tar -- ./*.in
+rm -- ./*.in
+pueue add -- "$SCRIPTS"/utils/bucky.pl -a 1 -o bucky_1 -s input.mb.tar
+
+mkdir snaq
+cd snaq
+## run snaq.jl with interactive mode
+# julia snaq.jl
+cd ../..
+
+## 第三套，移除严重移码突变基因和treeshrink过滤掉的基因
+mkdir -p exclude_severe_fs
+cd exclude_severe_fs
+grep -wv single_species_single_event ../../13.gene_phylogeny/frameshift_summary/frameshift_locus_classification.tsv | cut -f 1 | sed 1d > fs_exclude.list
+
+# aster coalescence tree
+for file in ../raxml/*/*.support; do
+    gene=$(basename "$(dirname "$file")")
+    if ! grep -Fqx -- "$gene" ../treeshrink_filtered.list fs_exclude.list; then
+        cat "$file"
+    fi
+done >all.ml.tre
+mkdir -p species_tree
+pueue add -- astral4 -t 6 -i all.ml.tre -o species_tree/coal.tre --root ZJ
+
+# bucky
+mkdir bucky
+for mbfile in ../mbsum/*.in; do
+    gene=$(basename "$mbfile" .in)
+    if ! grep -Fqx -- "$gene" ../treeshrink_filtered.list fs_exclude.list; then
+        cp "$mbfile" bucky/"$gene".in
+    fi
+done
+cd bucky
+tar -cf input.mb.tar -- ./*.in
+rm -- ./*.in
+pueue add -- "$SCRIPTS"/utils/bucky.pl -a 1 -o bucky_1 -s input.mb.tar
+
+mkdir snaq
+cd snaq
+## run snaq.jl with interactive mode
+# julia snaq.jl
+cd ../..