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Merge pull request #60 from marbl/v3.1.0
V3.1.0
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#!/bin/bash | ||
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FASTA_FAI=$1 | ||
PAF=$2 | ||
COVERAGE=$3 | ||
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cat $FASTA_FAI | awk -v OFS='\t' '{print($1,"0",$2)}' > $PAF.sequences.bed | ||
cat \ | ||
<(cat $PAF | awk -v OFS='\t' '{print $1, $3, $4, "", "", $5}') \ | ||
<(cat $PAF | awk -v OFS='\t' '{print $6, $8, $9, "", "", "+"}') \ | ||
| bedtools sort | bedtools merge > $PAF.query+target.bed | ||
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echo "#seq.name" coverage | tr ' ' '\t' > $PAF.coverage.txt | ||
bedtools intersect -a $PAF.sequences.bed -b $PAF.query+target.bed -wo > $PAF.overlap.bed | ||
awk 'BEGIN{FS=OFS="\t"}{ | ||
if(NR==FNR){ | ||
len[$1]=$3-$2; coverage[$1]=0; | ||
} else { | ||
coverage[$1]+=$NF | ||
} | ||
} END{ | ||
for(seq in len){ | ||
printf("%s\t%f\n", seq, coverage[seq] / len[seq]) | ||
} | ||
}' $PAF.sequences.bed $PAF.overlap.bed >> $PAF.coverage.txt | ||
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cat \ | ||
<(head -n 1 $PAF.coverage.txt) \ | ||
<(sed '1d' $PAF.coverage.txt | sort -k 2,2nr -k 1,1) | column -t | ||
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awk -v threshold=$COVERAGE 'NR > 1 && $2 < threshold { | ||
print "Low coverage for sequence " $1 " with coverage " $2; | ||
flag = 1 | ||
} END { | ||
if (flag) exit 1 | ||
}' $PAF.coverage.txt |
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