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Created postprocessing script for amended files
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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 |
|---|---|---|
| @@ -0,0 +1,71 @@ | ||
| #CLEAN | ||
| if test -f all_samples_completo.txt; then rm all_samples_completo.txt; fi | ||
| if test -d A_*; then rm -rf A_*; fi | ||
| if test -d B; then rm -rf B; fi | ||
| if test -d C; then rm -rf C; fi | ||
| if test -d D; then rm -rf D; fi | ||
|
|
||
| cat ../samples_id.txt | while read sample; do | ||
| FLUSUBTYPE=$(ls ${sample}/*H*.fasta | cut -d '/' -f2 | cut -d '.' -f1 | cut -d '_' -f1,3 | sort -u) | ||
| FLUTYPE=$(ls ${sample}/*H*.fasta | cut -d '/' -f2 | cut -d '.' -f1 | cut -d '_' -f1 | sort -u) | ||
| mkdir -p $FLUSUBTYPE | ||
| 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 | ||
| 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 | ||
| 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 | ||
| 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 | ||
| 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 | ||
| 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 | ||
| 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 | ||
| 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 | ||
| 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 | ||
| 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 | ||
| 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 | ||
| 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 | ||
| 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 | ||
| 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 | ||
| else | ||
| echo "The sample $sample has a segment with number $fragment, but I don't know which segment it is." | ||
| fi | ||
| done | ||
| done |