Shell Programming and Scripting

 
The header is skipped  and
1. 4 zeros after the NC_  (not always the case) and the digits before the .        NM_004004.5:c.34_35delGGinsT
2. g. ### (before underscore)  _### (# after the _)  ] - NC_000013.10:g.20763686_20763687delinsA
3. letters after the "del" until the “ins”
4. letters after the "ins"

Desired output: 13     20763686     20763687     GG     T

perl -ne 'next if $. == 1;
            while (/\t*NC_(\d+)\.\S+g\.(\d+)(\S+)/g) {                                            # conditional parse
                ($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);
            }
           ' out_position.txt > out_parse.txt