20251125

99.scripts/workflow/orthology_inference/01.orthofinder_sc_align.sh

@@ -0,0 +1,8 @@
+#! /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"

99.scripts/workflow/orthology_inference/02.hmmbuild.sh

@@ -0,0 +1,8 @@
+#! /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"

99.scripts/workflow/orthology_inference/03.hmmsearch.sh

@@ -0,0 +1,8 @@
+#! /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"

99.scripts/workflow/orthology_inference/04.pep_align.sh

@@ -0,0 +1,8 @@
+#! /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"

99.scripts/workflow/orthology_inference/05.pal2nal.sh

@@ -0,0 +1,8 @@
+#! /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"

99.scripts/workflow/orthology_inference/06.trim_alignment.sh

@@ -0,0 +1,8 @@
+#! /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"

99.scripts/workflow/orthology_inference/07.fasttree.sh

@@ -0,0 +1,8 @@
+#! /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"

99.scripts/workflow/orthology_inference/08.treeshrink.sh

@@ -0,0 +1,11 @@
+#! /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

99.scripts/workflow/orthology_inference/09.filter_ogs.sh

@@ -0,0 +1,12 @@
+#! /usr/bin/env bash
+total_taxon=11
+min_seq_length=300
+mkdir -p final_ogs
+for i in treeshrink/* ; do
+    j=$(basename "$i")
+    seqlen=$(seqkit fx2tab -C ATCG "$i"/output.fasta | awk '{print $3}' | sort -n | head -n 1)
+    seqnum=$(grep -c ">" "$i"/output.fasta)
+    if [[ $seqnum -eq $total_taxon && $seqlen -ge $min_seq_length ]]; then
+        cp -l "$i"/output.fasta final_ogs/"${j}.fa"
+    fi
+done