comparison correct.sh @ 18:e4d75f9efb90 draft

planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
author nick
date Thu, 02 Feb 2017 18:44:31 -0500
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17:836fa4fe9494 18:e4d75f9efb90
1 #!/usr/bin/env bash
2 if [ x$BASH = x ] || [ ! $BASH_VERSINFO ] || [ $BASH_VERSINFO -lt 4 ]; then
3 echo "Error: Must use bash version 4+." >&2
4 exit 1
5 fi
6 set -ue
7
8 INITIAL_BARCODES_DEFAULT=20
9
10 Usage="Usage: \$ $(basename $0) [barcodes to try]"
11
12 function main {
13 if [[ $# -ge 1 ]] && [[ $1 == '-h' ]]; then
14 fail "$Usage"
15 fi
16
17 initial_barcodes="$INITIAL_BARCODES_DEFAULT"
18 if [[ $# -ge 1 ]]; then
19 initial_barcodes=$1
20 fi
21
22 cat border-families.txt | paste - - | shuf --random-source=border-families.txt \
23 | head -n $initial_barcodes | while read count1 barcode order count2 rest; do
24 echo -ne "$barcode\t$count1\t$count2\t"
25 read_name=$(grep -B 1 $barcode barcodes.fq | head -n 1 | tail -c +2)
26 echo "$read_name"
27 samtools view -f 256 barcodes.bam | awk '$1 == '$read_name' && $5 > 25 {print $3}' | while read read_name2; do
28 barcode=$(grep -A 1 -E '^@'$read_name2'$' barcodes.fq | tail -n 1)
29 done
30 done
31
32 }
33
34 function fail {
35 echo "$@" >&2
36 exit 1
37 }
38
39 main "$@"