更新 .gitignore，添加 06.gene_trees 目录；重构 macse.sh 脚本，移除 fs_lr 参数；删除多个不再使用的脚本；添加 check_frameshift.py 和 get_og_seqs.py 脚本以处理阅读框移位和提取单拷贝OG序列；更新 pixi.toml 和 pixi.lock 文件以添加 paml 依赖。

2025-12-20 01:57:25 +08:00
parent e8ba2ed962
commit dba4833905
15 changed files with 433 additions and 117 deletions
@@ -1,51 +0,0 @@
-#! /bin/bash
-set -e
-
-if [ "$#" -ne 4 ]; then
-    echo "Usage: $0 <ogs_dir> <outdir> <proteome> <threads>"
-    echo "search homologous sequences in <proteome> using HMMs built from orthogroup alignments"
-    exit 1
-fi
-
-ogs_dir=$(readlink -f "$1")
-outdir=$2
-proteome=$(readlink -f "$3")
-threads=$4
-
-mkdir -p "$outdir"
-cd "$outdir" || exit 1
-echo "Working directory: $(pwd)"
-echo "Using OGS directory: $ogs_dir"
-echo "Using $threads threads"
-echo ""
-echo "Starting orthogroup sequence alignment..."
-mkdir -p msa
-echo -n >mafft.cmds
-for i in "$ogs_dir"/*.fa; do
-    j=$(basename "$i")
-    echo "linsi --quiet $i > msa/$j" >>mafft.cmds
-done
-xargs -t -P "$threads" -I cmd -a mafft.cmds bash -c "cmd"
-echo "Orthogroup sequence alignment completed."
-echo ""
-echo "Starting HMM building from alignments..."
-mkdir -p hmms
-echo -n >hmmbuild.cmds
-for i in msa/*.fa; do
-    j=$(basename "$i")
-    echo "hmmbuild -o hmms/${j}.hmmbuild.out --amino hmms/${j}.hmm $i" >>hmmbuild.cmds
-done
-xargs -t -P "$threads" -I cmd -a hmmbuild.cmds bash -c "cmd"
-echo "HMM building completed."
-echo ""
-echo "Starting HMM search against other proteome..."
-mkdir -p search
-echo -n >hmmsearch.cmds
-for i in hmms/*.hmm; do
-    j=$(basename "$i")
-    echo "hmmsearch --tblout search/${j}search.tblout $i $proteome > search/${j}search.rawout" >>hmmsearch.cmds
-done
-xargs -t -P "$threads" -I cmd -a hmmsearch.cmds bash -c "cmd"
-echo "HMM search completed."
-echo ""
-echo "All steps completed successfully."
@@ -0,0 +1,24 @@
+#! /bin/bash
+set -e
+THREADS=${THREADS:-12}
+EXT=${EXT:-"fa"}
+
+if [ "$#" -ne 2 ]; then
+    echo "Usage: $0 <ogs_dir> <out_dir>"
+    echo "Perform MACSE alignment for each orthologous group"
+    exit 1
+fi
+
+ogs_dir=$(readlink -f "$1")
+out_dir=$2
+
+mkdir -p "$out_dir"
+echo "Starting MACSE alignment of orthologous groups..."
+echo -n >macse.cmds
+for og_fasta in "$ogs_dir"/*."$EXT"; do
+    og_name=$(basename "$og_fasta" ."$EXT")
+    out_stem="$out_dir/$og_name"
+    echo "macse -prog alignSequences -seq $og_fasta -out_AA ${out_stem}.pal -out_NT ${out_stem}.nal > ${out_stem}.log 2>&1" >>macse.cmds
+done
+xargs -t -P "$THREADS" -I cmd -a macse.cmds bash -c "cmd" &&
+    echo "MACSE alignment completed."
@@ -1,34 +0,0 @@
-#! /bin/bash
-set -e
-SCRIPTS=${SCRIPTS:-"$PROJECTHOME/99.scripts"}
-THREADS=${THREADS:-12}
-
-if [ "$#" -ne 5 ]; then
-    echo "Usage: $0 <ogs_dir> <hmmsearch_result_dir> <all_cds.fa> <output_dir> <homolog_stem>"
-    echo "Integrate hmmsearch results to new orthologous groups directory and perform MACSE alignment"
-    exit 1
-fi
-
-ogs_dir=$(readlink -f "$1")
-search_dir=$(readlink -f "$2")
-all_cds=$(readlink -f "$3")
-out_dir=$4
-stem=$5
-
-echo "Integrating hmmsearch results to new orthologous groups directory..."
-python3 "$SCRIPTS"/miscs/hmmsearch_result_to_new_ogs_dir.py \
-    -d "$ogs_dir" \
-    -t "$search_dir" \
-    -f "$all_cds" \
-    -o "$out_dir" \
-    -s "$stem"
-echo "Integration completed."
-
-echo "Starting MACSE alignment of orthologous groups..."
-echo -n >macse.cmds
-for og_dir in "$out_dir"/ogs/*; do
-    j=$(basename "$og_dir")
-    echo "cd $og_dir && bash $SCRIPTS/miscs/macse.sh ${j}_${stem}.fa ${j}.fa $j" >>macse.cmds
-done
-xargs -t -P "$THREADS" -I cmd -a macse.cmds bash -c "cmd"
-echo "MACSE alignment completed."
@@ -0,0 +1,20 @@
+#! /bin/bash
+set -e
+THREADS=${THREADS:-12}
+if [ "$#" -ne 3 ]; then
+    echo "Usage: $0 <nal_dir> <out_dir> <ext>"
+    echo "Trim MACSE nucleotide alignments using trimal"
+    exit 1
+fi
+
+nal_dir=$(readlink -f "$1")
+out_dir=$(readlink -f "$2")
+ext=$3
+
+mkdir -p "$out_dir"
+echo -n >trimal.cmds
+for i in "$nal_dir"/*."$ext"; do
+    j=$(basename "$i" ."$ext")
+    echo "trimal -in $i -out $out_dir/${j}.trimed.fa -automated1 -resoverlap 0.5 -seqoverlap 50" >>trimal.cmds
+done
+xargs -t -P "$THREADS" -I cmd -a trimal.cmds bash -c "cmd"
@@ -0,0 +1,26 @@
+#! /bin/bash
+set -e
+THREADS=${THREADS:-12}
+
+if [ "$#" -ne 3 ]; then
+    echo "Usage: $0 <aln_dir> <out_dir> <ext>"
+    echo "Build FastTree phylogenetic trees and perform TreeShrink on trimmed MACSE nucleotide alignments"
+    exit 1
+fi
+
+aln_dir=$(readlink -f "$1")
+out_dir=$(readlink -f "$2")
+ext=$3
+
+# fasttree
+mkdir -p "$out_dir"
+echo -n >fasttree.cmds
+for i in "$aln_dir"/*."$ext"; do
+    j=$(basename "$i" ."$ext")
+    mkdir -p "$out_dir"/"${j}"
+    cp -s "$i" "$out_dir"/"${j}"/input.fasta
+    echo "FastTree -nt -gtr -quiet $out_dir/${j}/input.fasta > $out_dir/${j}/input.tree" >>fasttree.cmds
+done
+xargs -t -P "$THREADS" -I cmd -a fasttree.cmds bash -c "cmd"
+# treeshrink
+run_treeshrink.py -f -i "$out_dir"/ -t input.tree -a input.fasta >treeshrink.log
@@ -1,8 +0,0 @@
-#! /usr/bin/env bash
-mkdir -p trimed_nal
-echo -n > trimal.cmds
-for i in cds_aln/*.nal ;do
-    j=$(basename "$i")
-    echo "trimal -in $i -out trimed_nal/${j/.nal/.trimed.fa} -automated1 -resoverlap 0.5 -seqoverlap 50" >> trimal.cmds
-done
-xargs -t -P 4 -I cmd -a trimal.cmds bash -c "cmd"
@@ -1,8 +0,0 @@
-#! /usr/bin/env bash
-mkdir -p fasttree
-echo -n > fasttree.cmds
-for i in trimed_nal/*.trimed.fa ;do
-    j=$(basename "$i")
-    echo "FastTree -nt -gtr -quiet $i > fasttree/${j/.trimed.fa/.tree}" >> fasttree.cmds
-done
-xargs -t -P 8 -I cmd -a fasttree.cmds bash -c "cmd"
@@ -1,11 +0,0 @@
-#! /usr/bin/env bash
-mkdir -p treeshrink
-for i in trimed_nal/*.trimed.fa; do
-    j=$(basename "$i")
-    mkdir -p treeshrink/"${j/.trimed.fa/}"
-    cd treeshrink/"${j/.trimed.fa/}" || exit 1
-    ln -s ../../fasttree/"${j/.trimed.fa/.tree}" input.tree
-    ln -s ../../"$i" input.fasta
-    cd ../../
-done
-run_treeshrink.py -i treeshrink/ -t input.tree -a input.fasta > treeshrink.log