Add Vercel configuration for rewrites and build settings

2025-12-17 17:47:45 +08:00
parent 072524e303
commit 0d31d42de4
32 changed files with 7435 additions and 289 deletions
@@ -0,0 +1,51 @@
+#! /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 "$threads" -I cmd -a hmmsearch.cmds bash -c "cmd"
+echo "HMM search completed."
+echo ""
+echo "All steps completed successfully."
@@ -1,8 +0,0 @@
-#! /usr/bin/env bash
-mkdir -p msa
-echo -n > mafft.cmds
-for i in ogs/*.fa ; do
-    j=$(basename "$i")
-    echo "linsi --quiet $i > msa/$j" >> mafft.cmds
-done
-xargs -t -P 8 -I cmd -a mafft.cmds bash -c "cmd"
@@ -1,8 +0,0 @@
-#! /usr/bin/env bash
-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 $i" >> hmmbuild.cmds
-done
-xargs -t -P 8 -I cmd -a hmmbuild.cmds bash -c "cmd"
@@ -0,0 +1,34 @@
+#! /bin/bash
+set -e
+SCRIPTS=${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."
@@ -1,8 +0,0 @@
-#! /usr/bin/env bash
-mkdir -p hmmsearch
-echo -n > hmmsearch.cmds
-for i in hmms/*.hmm ; do
-    j=$(basename "$i")
-    echo "hmmsearch --tblout hmmsearch/${j}search.tblout $i ../../01.reference/Zju.pep.fa > hmmsearch/${j}search.rawout" >> hmmsearch.cmds
-done
-xargs -t -P 8 -I cmd -a hmmsearch.cmds bash -c "cmd"
@@ -1,8 +0,0 @@
-#! /usr/bin/env bash
-mkdir -p pep_aln
-echo -n > mafft.cmds
-for i in raw_ogs/pep/*.fa; do
-    j=$(basename "$i")
-    echo "linsi --quiet $i > pep_aln/${j/.fa/.pal}" >> mafft.cmds
-done
-xargs -t -P 8 -I cmd -a mafft.cmds bash -c "cmd"
@@ -1,8 +0,0 @@
-#! /usr/bin/env bash
-mkdir -p cds_aln
-echo -n > pal2nal.cmds
-for i in pep_aln/*.pal; do
-    j=$(basename "$i")
-    echo "pal2nal.pl $i raw_ogs/cds/${j/.pal/.fa} -output fasta > cds_aln/${j/.pal/.nal}" >> pal2nal.cmds
-done
-xargs -t -P 8 -I cmd -a pal2nal.cmds bash -c "cmd"