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count_peptides.sh
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45 lines (41 loc) · 3.36 KB
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source configure.sh
echo "Mutation NCI CD8 SNV"
grep -cE "[[:space:]]NCI[[:space:]].*[[:space:]]CD8[[:space:]].*[[:space:]]SNV[[:space:]]" $NEORANKING_RESOURCE/data/Mutation_data_org.txt
echo "Mutation TESLA CD8 SNV"
grep -cE "[[:space:]]TESLA[[:space:]].*[[:space:]]CD8[[:space:]].*[[:space:]]SNV[[:space:]]" $NEORANKING_RESOURCE/data/Mutation_data_org.txt
echo "Mutation HiTIDE CD8 SNV"
grep -cE "[[:space:]]HiTIDE[[:space:]].*[[:space:]]CD8[[:space:]].*[[:space:]]SNV[[:space:]]" $NEORANKING_RESOURCE/data/Mutation_data_org.txt
echo "Mutation NCI negative SNV"
grep -cE "[[:space:]]NCI[[:space:]].*[[:space:]]negative[[:space:]].*[[:space:]]SNV[[:space:]]" $NEORANKING_RESOURCE/data/Mutation_data_org.txt
echo "Mutation TESLA negative SNV"
grep -cE "[[:space:]]TESLA[[:space:]].*[[:space:]]negative[[:space:]].*[[:space:]]SNV[[:space:]]" $NEORANKING_RESOURCE/data/Mutation_data_org.txt
echo "Mutation HiTIDE negative SNV"
grep -cE "[[:space:]]HiTIDE[[:space:]].*[[:space:]]negative[[:space:]].*[[:space:]]SNV[[:space:]]" $NEORANKING_RESOURCE/data/Mutation_data_org.txt
echo "Mutation NCI not screened SNV"
grep -cE "[[:space:]]NCI[[:space:]].*[[:space:]]not_tested[[:space:]].*[[:space:]]SNV[[:space:]]" $NEORANKING_RESOURCE/data/Mutation_data_org.txt
echo "Mutation TESLA not screened SNV"
grep -cE "[[:space:]]TESLA[[:space:]].*[[:space:]]not_tested[[:space:]].*[[:space:]]SNV[[:space:]]" $NEORANKING_RESOURCE/data/Mutation_data_org.txt
echo "Mutation HiTIDE not screened SNV"
grep -cE "[[:space:]]HiTIDE[[:space:]].*[[:space:]]not_tested[[:space:]].*[[:space:]]SNV[[:space:]]" $NEORANKING_RESOURCE/data/Mutation_data_org.txt
echo "Neopep NCI CD8 SNV"
grep -cE "[[:space:]]NCI[[:space:]].*[[:space:]]CD8[[:space:]].*[[:space:]]SNV[[:space:]]" $NEORANKING_RESOURCE/data/Neopep_data_org.txt
echo "Neopep TESLA CD8 SNV"
grep -cE "[[:space:]]TESLA[[:space:]].*[[:space:]]CD8[[:space:]].*[[:space:]]SNV[[:space:]]" $NEORANKING_RESOURCE/data/Neopep_data_org.txt
echo "Neopep HiTIDE CD8 SNV"
grep -cE "[[:space:]]HiTIDE[[:space:]].*[[:space:]]CD8[[:space:]].*[[:space:]]SNV[[:space:]]" $NEORANKING_RESOURCE/data/Neopep_data_org.txt
echo "Neopep NCI negative SNV"
grep -cE "[[:space:]]NCI[[:space:]].*[[:space:]]negative[[:space:]].*[[:space:]]SNV[[:space:]]" $NEORANKING_RESOURCE/data/Neopep_data_org.txt
echo "Neopep TESLA negative SNV"
grep -cE "[[:space:]]TESLA[[:space:]].*[[:space:]]negative[[:space:]].*[[:space:]]SNV[[:space:]]" $NEORANKING_RESOURCE/data/Neopep_data_org.txt
echo "Neopep HiTIDE negative SNV"
grep -cE "[[:space:]]HiTIDE[[:space:]].*[[:space:]]negative[[:space:]].*[[:space:]]SNV[[:space:]]" $NEORANKING_RESOURCE/data/Neopep_data_org.txt
echo "Neopep NCI not screened SNV"
grep -cE "[[:space:]]NCI[[:space:]].*[[:space:]]not_tested[[:space:]].*[[:space:]]SNV[[:space:]]" $NEORANKING_RESOURCE/data/Neopep_data_org.txt
echo "Neopep TESLA not screened SNV"
grep -cE "[[:space:]]TESLA[[:space:]].*[[:space:]]not_tested[[:space:]].*[[:space:]]SNV[[:space:]]" $NEORANKING_RESOURCE/data/Neopep_data_org.txt
echo "Neopep HiTIDE not screened SNV"
grep -cE "[[:space:]]HiTIDE[[:space:]].*[[:space:]]not_tested[[:space:]].*[[:space:]]SNV[[:space:]]" $NEORANKING_RESOURCE/data/Neopep_data_org.txt
echo "Mutation SNV"
grep -cE "[[:space:]]SNV[[:space:]]" $NEORANKING_RESOURCE/data/Mutation_data_org.txt
echo "Neopep SNV"
grep -cE "[[:space:]]SNV[[:space:]]" $NEORANKING_RESOURCE/data/Neopep_data_org.txt