19 lines
617 B
Bash
Executable File
19 lines
617 B
Bash
Executable File
#! /bin/bash
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set -e
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TMP=${TMP:-"$PROJECTHOME/tmp"}
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if [ "$#" -ne 3 ]; then
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echo "Usage: $0 <transcripts_fasta> <swissprot_database> <output_directory>"
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echo "Predict coding sequences (CDS) from transcripts using TD2 and MMseqs2"
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exit 1
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fi
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transcripts=$1
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sprot=$2
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outdir=$3
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mkdir -p "$outdir"
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TD2.LongOrfs -t "$transcripts" --precise -@ 8 -O "$outdir"
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mmseqs easy-search "$outdir/longest_orfs.pep" "$sprot" "$outdir/mmseqs.m8" "$TMP" -s 7.0 --threads 16
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TD2.Predict -t "$transcripts" --precise -O "$outdir" --retain-mmseqs-hits "$outdir/mmseqs.m8"
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echo "CDS prediction completed. Results are in $outdir"
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