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Shortened code to look better
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@svarona
svarona committed Sep 19, 2024
1 parent c821cab commit 41da4d5
Showing 1 changed file with 14 additions and 28 deletions.
42 changes: 14 additions & 28 deletions bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/04-irma/postprocessing.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -12,58 +12,44 @@ cat ../samples_id.txt | while read sample; do
ls ${sample}/amended_consensus/*.fa | cut -d '_' -f3 | cut -d '.' -f1 | while read fragment; do
if [ $fragment == 1 ]; then
if [ $FLUTYPE == "B" ]; then
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_1/_PB1/' >> ${FLUSUBTYPE}/B_PB1.txt
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_1/_PB1/' >> all_samples_completo.txt
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_1/_PB1/' | tee -a ${FLUSUBTYPE}/B_PB1.txt all_samples_completo.txt > /dev/null
else
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_1/_PB2/' >> ${FLUSUBTYPE}/${FLUTYPE}_PB2.txt
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_1/_PB2/' >> all_samples_completo.txt
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_1/_PB2/' | tee -a ${FLUSUBTYPE}/${FLUTYPE}_PB2.txt all_samples_completo.txt > /dev/null
fi
elif [ $fragment == 2 ]; then
if [ $FLUTYPE == "B" ]; then
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_2/_PB2/' >> ${FLUSUBTYPE}/B_PB2.txt
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_2/_PB2/' >> all_samples_completo.txt
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_2/_PB2/' | tee -a ${FLUSUBTYPE}/B_PB2.txt all_samples_completo.txt > /dev/null
else
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_2/_PB1/' >> ${FLUSUBTYPE}/${FLUTYPE}_PB1.txt
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_2/_PB1/' >> all_samples_completo.txt
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_2/_PB1/' | tee -a ${FLUSUBTYPE}/${FLUTYPE}_PB1.txt all_samples_completo.txt > /dev/null
fi
elif [ $fragment == 3 ]; then
if [ $FLUTYPE == "B" ] || [ $FLUTYPE == "A" ]; then
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_3/_PA/' >> ${FLUSUBTYPE}/${FLUTYPE}_PA.txt
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_3/_PA/' >> all_samples_completo.txt
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_3/_PA/' | tee -a ${FLUSUBTYPE}/${FLUTYPE}_PA.txt all_samples_completo.txt > /dev/null
else
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_3/_P3/' >> ${FLUSUBTYPE}/${FLUTYPE}_P3.txt
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_3/_P3/' >> all_samples_completo.txt
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_3/_P3/' | tee -a ${FLUSUBTYPE}/${FLUTYPE}_P3.txt all_samples_completo.txt > /dev/null
fi
elif [ $fragment == 4 ]; then
if [ $FLUTYPE == "B" ] || [ $FLUTYPE == "A" ]; then
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_4/_HA/' >> ${FLUSUBTYPE}/${FLUTYPE}_HA.txt
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_4/_HA/' >> all_samples_completo.txt
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_4/_HA/' | tee -a ${FLUSUBTYPE}/${FLUTYPE}_HA.txt all_samples_completo.txt > /dev/null
else
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_4/_HE/' >> ${FLUSUBTYPE}/${FLUTYPE}_HE.txt
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_4/_HE/' >> all_samples_completo.txt
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_4/_HE/' | tee -a ${FLUSUBTYPE}/${FLUTYPE}_HE.txt all_samples_completo.txt > /dev/null
fi
elif [ $fragment == 5 ]; then
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_5/_NP/' >> ${FLUSUBTYPE}/${FLUTYPE}_NP.txt
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_5/_NP/' >> all_samples_completo.txt
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_5/_NP/' | tee -a ${FLUSUBTYPE}/${FLUTYPE}_NP.txt all_samples_completo.txt > /dev/null
elif [ $fragment == 6 ]; then
if [ $FLUTYPE == "B" ] || [ $FLUTYPE == "A" ]; then
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_6/_NA/' >> ${FLUSUBTYPE}/${FLUTYPE}_NA.txt
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_6/_NA/' >> all_samples_completo.txt
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_6/_NA/' | tee -a ${FLUSUBTYPE}/${FLUTYPE}_NA.txt all_samples_completo.txt > /dev/null
else
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_6/_MP/' >> ${FLUSUBTYPE}/${FLUTYPE}_MP.txt
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_6/_MP/' >> all_samples_completo.txt
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_6/_MP/' | tee -a ${FLUSUBTYPE}/${FLUTYPE}_MP.txt all_samples_completo.txt > /dev/null
fi
elif [ $fragment == 7 ]; then
if [ $FLUTYPE == "B" ] || [ $FLUTYPE == "A" ]; then
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_7/_MP/' >> ${FLUSUBTYPE}/${FLUTYPE}_MP.txt
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_7/_MP/' >> all_samples_completo.txt
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_7/_MP/' | tee -a ${FLUSUBTYPE}/${FLUTYPE}_MP.txt all_samples_completo.txt > /dev/null
else
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_7/_NS/' >> ${FLUSUBTYPE}/${FLUTYPE}_NS.txt
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_7/_NS/' >> all_samples_completo.txt
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_7/_NS/' | tee -a ${FLUSUBTYPE}/${FLUTYPE}_NS.txt all_samples_completo.txt > /dev/null
fi
elif [ $fragment == 8 ]; then
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_8/_NS/' >> ${FLUSUBTYPE}/${FLUTYPE}_NS.txt
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_8/_NS/' >> all_samples_completo.txt
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_8/_NS/' | tee -a ${FLUSUBTYPE}/${FLUTYPE}_NS.txt all_samples_completo.txt > /dev/null
else
echo "The sample $sample has a segment with number $fragment, but I don't know which segment it is."
fi
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