included postprocessing script in lablog

Author: svarona

bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/04-irma/lablog

@@ -9,31 +9,6 @@ cat ../samples_id.txt | while read in; do echo "srun --partition short_idx --cpu
 
 echo 'bash create_irma_stats.sh' > _02_create_stats.sh
 
-echo "ls */*HA*.fasta | cut -d '/' -f2 | cut -d '.' -f1 | sort -u | cut -d '_' -f3  | sed '/^\$/d' | sed 's/^/A_/g' > HA_types.txt" > _03_post_processing.sh
+echo 'bash postprocessing.sh' > _03_post_processing.sh
 
-echo 'cat HA_types.txt | while read type; do if test -d ${type}; then rm -rf ${type}; fi; done; if test -d B ; then rm -rf B; fi; if test -d C; then rm -rf C; fi' >> _03_post_processing.sh
-
-echo 'if test -f all_samples_completo.txt; then rm all_samples_completo.txt; fi' >> _03_post_processing.sh
-
-echo "cat HA_types.txt | while read in; do mkdir \${in}; done" >> _03_post_processing.sh
-
-echo "if grep -qw 'B__' irma_stats.txt; then mkdir B; fi" >> _03_post_processing.sh
-
-echo "if grep -qw 'C__' irma_stats.txt; then mkdir C; fi" >> _03_post_processing.sh
-
-echo "ls */*.fasta | cut -d '/' -f2 | cut -d '.' -f1 | cut -d '_' -f1,2 | sort -u | grep 'A_' > A_fragment_list.txt" >> _03_post_processing.sh
-
-echo "ls */*.fasta | cut -d '/' -f2 | cut -d '.' -f1 | cut -d '_' -f1,2 | sort -u | grep 'B_' > B_fragment_list.txt" >> _03_post_processing.sh
-
-echo "ls */*.fasta | cut -d '/' -f2 | cut -d '.' -f1 | cut -d '_' -f1,2 | sort -u | grep 'C_' > C_fragment_list.txt" >> _03_post_processing.sh
-
-echo 'cat HA_types.txt | while read type; do grep ${type} irma_stats.txt | cut -f1 | while read sample; do cat A_fragment_list.txt | while read fragment; do if test -f ${sample}/${fragment}*.fasta; then cat ${sample}/${fragment}*.fasta | sed "s/^>/\>${sample}_/g" | sed 's/_H1//g' | sed 's/_H3//g' | sed 's/_N1//g' | sed 's/_N2//g' | sed s@-@/@g | sed s/_A_/_/g ; fi >> ${type}/${fragment}.txt; done; done; done' >> _03_post_processing.sh
-
-echo 'grep -w 'B__' irma_stats.txt | cut -f1 | while read sample; do cat B_fragment_list.txt | while read fragment; do if test -f ${sample}/${fragment}*.fasta; then cat ${sample}/${fragment}*.fasta | sed "s/^>/\>${sample}_/g" | sed s/_H1//g | sed s/_H3//g | sed s/_N1//g | sed s/_N2//g | sed s@-@/@g | sed s/_B_/_/g ; fi >> B/${fragment}.txt; done; done' >> _03_post_processing.sh
-
-echo 'grep -w 'C__' irma_stats.txt | cut -f1 | while read sample; do cat C_fragment_list.txt | while read fragment; do if test -f ${sample}/${fragment}*.fasta; then cat ${sample}/${fragment}*.fasta | sed "s/^>/\>${sample}_/g" | sed s/_H1//g | sed s/_H3//g | sed s/_N1//g | sed s/_N2//g | sed s@-@/@g | sed s/_C_/_/g ; fi >> C/${fragment}.txt; done; done' >> _03_post_processing.sh
-
-echo 'cat ../samples_id.txt | while read in; do cat ${in}/*.fasta | sed "s/^>/\>${in}_/g" | sed 's/_H1//g' | sed 's/_H3//g' | sed 's/_N1//g' | sed 's/_N2//g' | sed 's@-@/@g' | sed 's/_A_/_/g' | sed 's/_B_/_/g' | sed 's/_C_/_/g' >> all_samples_completo.txt; done' >> _03_post_processing.sh
-
-echo 'sed "s/__//g" irma_stats.txt > clean_irma_stats.txt' >> _03_post_processing.sh
-echo 'sed "s/_\t/\t/g" irma_stats.txt > clean_irma_stats.txt' >> _03_post_processing.sh
+echo 'sed "s/__//g" irma_stats.txt | sed "s/_\t/\t/g" > clean_irma_stats.txt' >> _03_post_processing.sh