39 lines
1.2 KiB
Bash
39 lines
1.2 KiB
Bash
#!/bin/bash
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set -euo pipefail
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# 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" "$i"
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done
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# run orthofinder with Hippophae genomes as backbone
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pueue add -- orthofinder -t 12 -a 4 -f input_pep/core -o orthofinder_out
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# assign outgroups
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pueue add -- orthofinder -t 12 -a 4 --assign input_pep/outgroup --core orthofinder_out/Results_Aug03
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ln -s orthofinder_out/Results_Aug03 Hippophae_only
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ln -s orthofinder_out/Results_Aug03_1/ Hippophae_outgroup
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# get all cds into a file
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echo -ne >all_cds.fa
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for i in ../11.reference_v2/cds/*.cds.fa; do
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base=$(basename "$i" .cds.fa)
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echo "Processing $base"
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sed "s/>/>${base}@/g" "$i" >>all_cds.fa
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done
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# get og list and extract cds sequences for each og
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pueue add -- python3 "$PROJECTHOME"/99.scripts_v2/utils/get_og_seqs.py -d Hippophae_outgroup/Single_Copy_Orthologue_Sequences -a all_cds.fa -o ogs_cds
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