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Check insertion and deletion blast files #13

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Check insertion and deletion blast files #13

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5a8b658
Check insertion and deletion blast files
elcortegano Mar 25, 2021
a5b9382
awk only divides when NR is not NULL
elcortegano Mar 25, 2021
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20 changes: 13 additions & 7 deletions mumandco_v2.4.2.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -162,7 +162,7 @@ echo ""
# > ""$prefix"_query".coordsg_matched

##get average quality
average_quality=$(tail -n +5 "$alignments_folder/""$prefix"_ref".delta_filter.coordsg" | awk '{sum+=$7} END{print sum/NR}')
average_quality=$(tail -n +5 "$alignments_folder/""$prefix"_ref".delta_filter.coordsg" | awk '{sum+=$7} END{if(NR){print sum/NR}}')

### filter for alignment less than 10kb (limit on translocation size)
### filter for any alignment overlapping another with more than 50bp and with lower quality
Expand Down Expand Up @@ -244,7 +244,7 @@ tail -n +5 "$alignments_folder/""$prefix"_ref".delta_filter.coordsg" |\
#

##filter any remaining alignments with less than (1.25 x standard deviation) less than the average of the remaining alignments
average_quality=$(cat ""$prefix"_pre_list.txt" | awk '{sum+=$7} END{print sum/NR}')
average_quality=$(cat ""$prefix"_pre_list.txt" | awk '{sum+=$7} END{if(NR){print sum/NR}}')

if [[ "$average_quality" == "100" ]]
then
Expand All @@ -256,7 +256,7 @@ if [[ "$average_quality" == "100" ]]

else

stdev125=$(cat ""$prefix"_pre_list.txt" | awk '{sum=sum+$7 ; sumX2+=(($7)^2)} END{print 1.25*(sqrt(sumX2/(NR) - ((sum/NR)^2)))}')
stdev125=$(cat ""$prefix"_pre_list.txt" | awk '{sum=sum+$7 ; sumX2+=(($7)^2)} END{if(NR){print 1.25*(sqrt(sumX2/(NR) - ((sum/NR)^2)))}}')
quality_filt=$(echo $average_quality - $stdev125 | bc)
cat ""$prefix"_pre_list.txt" | awk -v quality_filt="$quality_filt" '{if($7 > quality_filt) print $14"\t"$15}' | sort | uniq > ""$prefix"_chromosome_pairs.txt"

Expand Down Expand Up @@ -1082,7 +1082,13 @@ then

cat $prefix.filteredcalls | awk '{if($6!="insertion" && $6!="deletion") print $0}' > $prefix.noINDEL
echo "ref_chr query_chr ref_start ref_stop size SV_type query_start query_stop" > $prefix.SVs_all.tsv
cat $prefix.insertion_blast $prefix.deletion_blast $prefix.noINDEL | sort -k1,1 -k3V >> $prefix.SVs_all.tsv
if [ -f $prefix.insertion_blast ]; then
sort -k1,1 -k3V $prefix.insertion_blast >> $prefix.SVs_all.tsv
fi
if [ -f $prefix.deletion_blast ]; then
sort -k1,1 -k3V $prefix.deletion_blast >> $prefix.SVs_all.tsv
fi
sort -k1,1 -k3V $prefix.noINDEL >> $prefix.SVs_all.tsv

rm query_segment.fa
rm ref_segment.fa
Expand Down Expand Up @@ -1110,7 +1116,7 @@ echo ""
total=$(cat $prefix.filteredcalls | awk '{print $0}' | wc -l)
total_del=$(cat $prefix.filteredcalls | awk '/deletion/{print $0}' | wc -l)
total_ins=$(cat $prefix.filteredcalls | awk '/insertion/{print $0}' | wc -l)
#total_INDELmean=$(cat $prefix.filteredcalls | awk 'BEGIN{sum=0} !/double/&&/deletion/||/insertion/{sum+=$5} END{print sum/NR}')
#total_INDELmean=$(cat $prefix.filteredcalls | awk 'BEGIN{sum=0} !/double/&&/deletion/||/insertion/{sum+=$5} END{if(NR){print sum/NR}}')
total_dup=$(cat $prefix.filteredcalls | awk '/duplication/{print $0}' | wc -l)
total_inv=$(cat $prefix.filteredcalls | awk '/inversion/{print $0}' | wc -l)
total_trans=$(cat $prefix.filteredcalls | awk '!/complicated/&&/transloc/{print $0}' | wc -l)
Expand Down Expand Up @@ -1172,8 +1178,8 @@ then
rm $prefix.deletions
rm $prefix.blast_in
rm $prefix.blast_del
rm $prefix.deletion_blast
rm $prefix.insertion_blast
rm -f $prefix.deletion_blast
rm -f $prefix.insertion_blast
fi
fi

Expand Down