65 lines
1.3 KiB
Bash
Executable File
65 lines
1.3 KiB
Bash
Executable File
#!/bin/bash
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#
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# This is a utility as part of the InterProScan v5 installation
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# get nucleotide input and generate ORFs using EMBOSS getorf
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#
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#usage: translate -i <input_file> -o <output_file>
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#
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while [[ $# -gt 1 ]]
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do
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key="$1"
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case $key in
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-i|--input)
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INPUTPATH="$2"
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shift # past argument
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;;
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-o|--output)
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OUTPUTPATH="$2"
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shift # past argument
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;;
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--default)
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DEFAULT=YES
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;;
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*)
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# unknown option
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;;
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esac
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shift # past argument or value
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done
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#echo INPUTPATH = "${INPUTPATH}"
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#echo OUTPUTPATH = "${OUTPUTPATH}"
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input_file=`realpath ${INPUTPATH}`
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output_file=`realpath ${OUTPUTPATH}`
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if [ -f $input_file ]
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then
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#echo "input is $input_file";
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timenow=`date +"%T"`
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echo "started translate at $timenow";
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else
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echo "input file not found: $input_file ";
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exit
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fi
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USER_DIR=$PWD
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INSTALL_DIR="${BASH_SOURCE[0]}"
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while [ -h "$INSTALL_DIR" ]; do
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cd "$(dirname "$INSTALL_DIR")"
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INSTALL_DIR="$(readlink "$(basename "$INSTALL_DIR")")"
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done
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cd "$(dirname "$INSTALL_DIR")"
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INSTALL_DIR="$(pwd)/"
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# set environment variables for getorf
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export EMBOSS_ACDROOT=${INSTALL_DIR}
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export EMBOSS_DATA=${INSTALL_DIR}
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${INSTALL_DIR}/getorf -sf pearson -sequence $input_file -outseq $output_file -minsize 75
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count=`grep -c '>' $output_file`
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echo "$count ORFs in $output_file"
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