Shell Programming and Scripting

Input Variant    Errors    Chromosomal Variant    Coding Variant(s)
NM_004992.3:c.274G>T        NC_000023.10:g.153297761C>A    XM_005274683.1:c.-6G>T    XM_005274682.1:c.-6G>T    XM_005274681.1:c.274G>T    LRG_764t2:c.274G>T    NM_004992.3:c.274G>T    LRG_764t1:c.310G>T    NM_001110792.1:c.310G>T

perl -ne 'next if $. == 1;
    if(/.*del([A-Z]+)ins([A-Z]+).*NC_0+([^.]+)\..*g\.([0-9]+)_([0-9]+)/)   # indel
    {
            print join("\t", $3, $4, $5, $1, $2), "\n";
            }
              else
{
            while (/\t*NC_(\d+)\.\S+g\.(\d+)(\S+)/g) {                                            # conditional parse
                ($num1, $num2, $common) = ($1, $2, $3);
                $num3 = $num2;
                if    ($common =~ /^([A-Z])>([A-Z])$/)   { ($ch1, $ch2) = ($1, $2) }              # SNP
                elsif ($common =~ /^del([A-Z])$/)        { ($ch1, $ch2) = ($1, "-") }             # deletion
                elsif ($common =~ /^ins([A-Z])$/)        { ($ch1, $ch2) = ("-", $1) }             # insertion
                elsif ($common =~ /^_(\d+)del([A-Z]+)$/) { ($num3, $ch1, $ch2) = ($1, $2, "-") }  # multi deletion
                elsif ($common =~ /^_(\d+)ins([A-Z]+)$/) { ($num3, $ch1, $ch2) = ("-", $1, $2) }  # multi insertion
                printf ("%d\t%d\t%d\t%s\t%s\n", $num1, $num2, $num3, $ch1, $ch2);                 # output
                map {undef} ($num1, $num2, $num3, $common, $ch1, $ch2);
            }
}' numeric

23    153297761    153297761    C    A tab-delimeted

Input Variant    Errors    Chromosomal Variant    Coding Variant(s)
NM_004992.3:c.274G>T        NC_0000X.10:g.153297761C>A    XM_005274683.1:c.-6G>T    XM_005274682.1:c.-6G>T    XM_005274681.1:c.274G>T    LRG_764t2:c.274G>T    NM_004992.3:c.274G>T    LRG_764t1:c.310G>T    NM_001110792.1:c.310G>T
Same script produces a blank output file after it executes.

X    153297761    153297761    C    A

 while (/\t*NC_(\d+)\.\S+g\.(\d+)(\S+)/g) {

 while (/\t*NC_(\w+)\.\S+g\.(\d+)(\S+)/g) {

printf ("%d\t%d\t%d\t%s\t%s\n", $num1, $num2, $num3, $ch1, $ch2);

printf ("%s\t%d\t%d\t%s\t%s\n", $num1, $num2, $num3, $ch1, $ch2);

000023    153297761    153297761    C    A

0000X    153297761    153297761    C    A

cat example.txt
Input Variant    Errors    Chromosomal Variant    Coding Variant(s)
NM_004992.3:c.274G>T        NC_000023.10:g.153297761C>A    XM_005274683.1:c.-6G>T    XM_005274682.1:c.-6G>T    XM_005274681.1:c.274G>T    LRG_764t2:c.274G>T    NM_004992.3:c.274G>T    LRG_764t1:c.310G>T    NM_001110792.1:c.310G>
NM_004992.3:c.274G>T        NC_0000X.10:g.153297761C>A    XM_005274683.1:c.-6G>T    XM_005274682.1:c.-6G>T    XM_005274681.1:c.274G>T    LRG_764t2:c.274G>T    NM_004992.3:c.274G>T    LRG_764t1:c.310G>T    NM_001110792.1:c.310G>T

perl -nale '@f = $F[1] =~ /NC_0+(\w+)\.\d+:g\.(\d+)(\w)>(\w)/; print join "\t", @f[0,1],$f[1],@f[2,3]' example.txt

23      153297761       153297761       C       A
X       153297761       153297761       C       A

#!/usr/bin/perl
# extract.pl
use strict;
use warnings;

{
    local $, = "\t";
    while(<>) {
        my @fields = split /\t+/;
        my @u = $fields[1] =~ /NC_0+(\w+)\.\d+:g\.(\d+)(\w)>(\w)/;
        print @u[0,1],$u[1],@u[2,3] . "\n" if @u;
    }
}

perl extract.pl example.txt
23      153297761       153297761       C       A
X       153297761       153297761       C       A