addBowtieAlignSingle

#!/bin/bash

out=$1
shift
bt2s=($*)

total=0
unpair=0
align0=0
align1=0
alignM=0

for bt2 in ${bt2s[@]}
do
    echo $bt2
    T=$(grep -P "^\d+ reads;" $bt2 | awk '{ print $1 }')
    U=$(grep -P "^  \d+ .[\d.]+%. were unpaired" $bt2 | awk '{ print $1 }')
    N=$(grep -P "^    \d+ .[\d.]+%. aligned 0" $bt2 | awk '{ print $1 }')
    S=$(grep -P "^    \d+ .[\d.]+%. aligned exactly" $bt2 | awk '{ print $1 }')
    M=$(grep -P "^    \d+ .[\d.]+%. aligned \>1" $bt2 | awk '{ print $1 }')
    total=$(echo "$total+$T" | bc)
    unpair=$(echo "$unpair+$U" | bc)
    align0=$(echo "$align0+$N" | bc)
    align1=$(echo "$align1+$S" | bc)
    alignM=$(echo "$alignM+$M" | bc)
done

pctU=$(printf "%0.2f" $(echo "scale=3; 100*$unpair/$total" | bc))
pct0=$(printf "%0.2f" $(echo "scale=3; 100*$align0/$total" | bc))
pct1=$(printf "%0.2f" $(echo "scale=3; 100*$align1/$total" | bc))
pctM=$(printf "%0.2f" $(echo "scale=3; 100*$alignM/$total" | bc))
rate=$(printf "%0.2f" $(echo "scale=3; 100*($align1+$alignM)/$total" | bc))

echo -e "$total reads; of these:
  $unpair ($pctU%) were unpaired; of these:
    $align0 ($pct0%) aligned 0 times
    $align1 ($pct1%) aligned exactly 1 time
    $alignM ($pctM%) aligned >1 times
$rate% overall alignment rate" > $out