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svaronasvarona
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Shortened code to look better
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‎bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/04-irma/postprocessing.sh

+14-28
Original file line numberDiff line numberDiff line change
@@ -12,58 +12,44 @@ cat ../samples_id.txt | while read sample; do
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ls ${sample}/amended_consensus/*.fa | cut -d '_' -f3 | cut -d '.' -f1 | while read fragment; do
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if [ $fragment == 1 ]; then
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if [ $FLUTYPE == "B" ]; then
15-
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_1/_PB1/' >> ${FLUSUBTYPE}/B_PB1.txt
16-
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_1/_PB1/' >> all_samples_completo.txt
15+
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
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else
18-
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_1/_PB2/' >> ${FLUSUBTYPE}/${FLUTYPE}_PB2.txt
19-
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_1/_PB2/' >> all_samples_completo.txt
17+
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
2018
fi
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elif [ $fragment == 2 ]; then
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if [ $FLUTYPE == "B" ]; then
23-
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_2/_PB2/' >> ${FLUSUBTYPE}/B_PB2.txt
24-
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_2/_PB2/' >> all_samples_completo.txt
21+
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
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else
26-
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_2/_PB1/' >> ${FLUSUBTYPE}/${FLUTYPE}_PB1.txt
27-
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_2/_PB1/' >> all_samples_completo.txt
23+
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
2824
fi
2925
elif [ $fragment == 3 ]; then
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if [ $FLUTYPE == "B" ] || [ $FLUTYPE == "A" ]; then
31-
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_3/_PA/' >> ${FLUSUBTYPE}/${FLUTYPE}_PA.txt
32-
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_3/_PA/' >> all_samples_completo.txt
27+
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
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else
34-
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_3/_P3/' >> ${FLUSUBTYPE}/${FLUTYPE}_P3.txt
35-
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_3/_P3/' >> all_samples_completo.txt
29+
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
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fi
3731
elif [ $fragment == 4 ]; then
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if [ $FLUTYPE == "B" ] || [ $FLUTYPE == "A" ]; then
39-
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_4/_HA/' >> ${FLUSUBTYPE}/${FLUTYPE}_HA.txt
40-
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_4/_HA/' >> all_samples_completo.txt
33+
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
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else
42-
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_4/_HE/' >> ${FLUSUBTYPE}/${FLUTYPE}_HE.txt
43-
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_4/_HE/' >> all_samples_completo.txt
35+
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
4436
fi
4537
elif [ $fragment == 5 ]; then
46-
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_5/_NP/' >> ${FLUSUBTYPE}/${FLUTYPE}_NP.txt
47-
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_5/_NP/' >> all_samples_completo.txt
38+
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
4839
elif [ $fragment == 6 ]; then
4940
if [ $FLUTYPE == "B" ] || [ $FLUTYPE == "A" ]; then
50-
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_6/_NA/' >> ${FLUSUBTYPE}/${FLUTYPE}_NA.txt
51-
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_6/_NA/' >> all_samples_completo.txt
41+
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
5242
else
53-
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_6/_MP/' >> ${FLUSUBTYPE}/${FLUTYPE}_MP.txt
54-
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_6/_MP/' >> all_samples_completo.txt
43+
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
5544
fi
5645
elif [ $fragment == 7 ]; then
5746
if [ $FLUTYPE == "B" ] || [ $FLUTYPE == "A" ]; then
58-
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_7/_MP/' >> ${FLUSUBTYPE}/${FLUTYPE}_MP.txt
59-
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_7/_MP/' >> all_samples_completo.txt
47+
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
6048
else
61-
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_7/_NS/' >> ${FLUSUBTYPE}/${FLUTYPE}_NS.txt
62-
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_7/_NS/' >> all_samples_completo.txt
49+
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
6350
fi
6451
elif [ $fragment == 8 ]; then
65-
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_8/_NS/' >> ${FLUSUBTYPE}/${FLUTYPE}_NS.txt
66-
cat ${sample}/amended_consensus/*_${fragment}.fa | sed 's/-/\//g' | sed 's/_8/_NS/' >> all_samples_completo.txt
52+
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
6753
else
6854
echo "The sample $sample has a segment with number $fragment, but I don't know which segment it is."
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fi

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