#!/bin/bash

shopt -s expand_aliases

alias ~=”:«’~bash’”

:«’~~~bash’

Usage

$ getSxPlasmidFileRef.sh \
    plasmid_file \
    genome \
    bowtie2index \
    [ext1up ext1down ext2up ext2down]

---
title: getSxPlasmidFileRef
---
flowchart TD
    PF[(
        
plasmid_file
        

            

                
adapter#0040;20bp#0041; + sgRNA#0040;20bp#0041; + scaffold#0040;83/93bp#0041; + query#0040;44bp#0041; + 3bp + RCbarcode#0040;18bp#0041; + RCprimer#0040;21bp#0041;
            
            

                
...
            
        
    )] --> GSPFR[getSxPlasmidFileRef.sh]
    GF[(
genome_file
)] --> GSPFR
    BI[(
bowtie2index
)] --> GSPFR
    EXT[(
        
extentions
        

            

                
ext1up
                
ext1down
                
ext2up
                
ext2down
            
        
    )] --> GSPFR
    GSPFR --> REF[(
        
stdout
        

            

                
start1
                
ref1
                
end1
                
start2
                
ref2
                
end2
            
            

                
...
                
...
                
...
                
...
                
...
                
...
            
        
    )]

• Extract references from the in-house plasmid_file and output to stdout.
• For NGG plasmid_file, the 44bp query can be perfectly mapped to the genome.
• For NAA plasmid_file, 17~18bp of query is TT, which should be replaced by CC in order to map genome.
• The actual cut site is inferred from mapping result.
• ref1 consists of ext1up bases upstream to the cut site and ext1down bases downstream to the cut site.
• ref2 consists of ext2up bases upstream to the cut site and ext2down bases downstream to the cut site.
• Note that for NAA plasmid_file, the retrieved reference need replace GG (query and reference have opposite strands, so CC becomes GG) back to AA.

Source

plasmid_file=$1
genome=$2
bowtie2index=$3
ext1up=${4:-50}
ext1down=${5:-0}
ext2up=${6:-10}
ext2down=${7:-100}


getSxPlasmidFileTarget.pl "${plasmid_file}" | bowtie2 --quiet --mm -x "${bowtie2index}" -r -U - 2> /dev/null | samtools view | gawk -f sxTargetSam2Bed.awk -- ${ext1up} ${ext1down} ${ext2up} ${ext2down} | bedtools getfasta -s -fi "${genome}" -bed - | sed '1~2d' | getSxRefFile.pl ${ext1up} ${ext2up} ${plasmid_file: -6:1}

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