34 lines
739 B
Bash
34 lines
739 B
Bash
#!/bin/bash
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while getopts s:o: option
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do
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case "${option}"
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in
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s) FILE1=${OPTARG};;
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o) FILE2=${OPTARG};;
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esac
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done
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for i in $(cat $FILE1); do
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if [[ $(grep "Possible" ${i}*alleles) && $(grep "*" ${i}*alleles) ]]; then
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paste <(echo ${i}) <(grep "*" ${i}*alleles) <(grep "Possible" ${i}*alleles) | column -s $'\t' -t -o $'\t' >> $FILE2
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elif [[ $(grep "*" ${i}*alleles) ]]; then
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paste <(echo ${i}) <(grep "*" ${i}*alleles) | column -s $'\t' -t -o $'\t' >> $FILE2
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elif [[ $(grep "Possible" ${i}*alleles) ]]; then
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paste <(echo ${i}) <(grep "Possible" ${i}*alleles) | column -s $'\t' -t -o $'\t' >> $FILE2
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else
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paste <(echo ${i}) <(echo No_call) | column -s $'\t' -t -o $'\t' >> $FILE2
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fi
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done
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