#!/bin/bash

shopt -s expand_aliases

alias ~=”:«’~bash’”

:«’~~~bash’

Usage

sxExtractSpliter.md csvfile >spliter1 3>spliter2

Introduction

This is an in-house script to extract spliters from the csvfile of sx and lcy. The composition of the input csvfile is

adapter(20bp) + sgRNA(20bp) + scaffold(83/93bp) + target(44bp) + 3bp + RCbarcode(18bp) + RCprimer(21bp)

Two spliters are output. spliter1 is output from fd 1 (stdout). spliter1 consists of primer and barcode. R2 is aligned to spliter1. Then 44bp target is 3bp downstream to the end of barcode in R2. spliter2 is output from fd 3. spliter2 consists of adapter, sgRNA and scaffold. R1 is aligned to spliter2.

Source

getSxCsvFilePrimer()
{
    # Usage: getSxCsvFilePrimer <csvfile
    rev | sed -r 's/^\s+//' | cut -c1-21 | dd conv=ucase 2>/dev/null | tr 'ACGT' 'TGCA'
}

getSxCsvFileBarcode()
{
    # Usage: getSxCsvFileBarcode <csvfile
    rev | sed -r 's/^\s+//' | cut -c22-39 | dd conv=ucase 2>/dev/null | tr 'ACGT' 'TGCA'
}

getSxCsvFileAdapter()
{
    # Usage: getSxCsvFileAdapter <csvfile
    cut -d, -f2 | cut -c1-20 | dd conv=ucase 2>/dev/null
}

getSxCsvFilesgRNA()
{
    # Usage: getSxCsvFilesgRNA <csvfile
    cut -d, -f2 | cut -c21-40 | dd conv=ucase 2>/dev/null
}

getSxCsvFileScaffold()
{
    # Usage: getSxCsvFileScaffold <csvfile
    cut -d, -f2 | sed -r 's/^[ACGTN]+//; s/[ACGTN]+\s+$//' | dd conv=ucase 2>/dev/null
}

getSxFaHead()
{
    # Usage: getSxFaHead <csvfile
    awk '{print ">" NR - 1}'
}

csvfile=$1
paste -d "" <(getSxCsvFilePrimer <"${csvfile}") <(getSxCsvFileBarcode <"${csvfile}") | paste -d "\n" <(getSxFaHead <"${csvfile}") - >&1

paste -d "" <(getSxCsvFileAdapter <"${csvfile}") <(getSxCsvFilesgRNA <"${csvfile}") <(getSxCsvFileScaffold <"${csvfile}") | paste -d "\n" <(getSxFaHead <"${csvfile}") - >&3

alias ~~~=":" # This suppresses a warning and is not part of source.