22 lines
721 B
Bash
22 lines
721 B
Bash
# prepare input files for orthofinder
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mkdir input_pep
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cp ../11.reference_v2/pep/primary_transcripts/*.pep.fa input_pep
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mkdir input_pep/core
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mkdir input_pep/outgroup
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mv input_pep/EA.pep.fa input_pep/outgroup
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mv input_pep/EM.pep.fa input_pep/outgroup
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mv input_pep/ZJ.pep.fa input_pep/outgroup
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mv input_pep/*.pep.fa input_pep/core
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for i in input_pep/*/*.pep.fa; do
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base=$(basename "$i" .pep.fa)
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echo "Processing $base"
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sed -i "s/>/>${base}@/g" "$i"
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done
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# run orthofinder with Hippophae genomes as backbone
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pueue add -- orthofinder -t 12 -a 4 -f input_pep/core -o orthofinder_out
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# assign outgroups
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pueue add -- orthofinder -t 12 -a 4 --assign input_pep/outgroup --core orthofinder_out/Results_Hippophae_only
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