Shell Programming and Scripting

perl -ne 'next if $. == 1;
	if(/.*del([A-Z]+)ins([A-Z]+).*NC_0{4}([0-9]+).*g\.([0-9]+)_([0-9]+)/)   # indel
{
        print join("\t", $3, $4, $5, $1, $2), "\n";
}
           ' out_position.txt > out1.txt


out_position.txt > out2.txt

Input Variant	Errors	Chromosomal Variant	Coding Variant(s)
NM_003924.3:c.*18_*19delGCinsAA		NC_000004.11:g.41747805_41747806delinsTT	LRG_513t1:c.*18_*19delinsAA	NM_003924.3:c.*18_*19delinsA

4	41747805	41747806	GC	AA

Input Variant	Errors	Chromosomal Variant	Coding Variant(s)
NM_003924.3:c.*18_*19delGCinsAA		NC_000014.11:g.41747805_41747806delinsTT	LRG_513t1:c.*18_*19delinsAA	NM_003924.3:c.*18_*19delinsA

14     41747805     41747806     GC     AA

.*NC_0{5}([0-9]+).

.*NC_0{5}([0-9]+[A-Z]+).

$ 
$ cat input.txt
NC_000004.11
NC_000014.11
NC_00000X.11
$ 
$ perl -lne 's/NC_0+(.*?)\..*/$1/; print' input.txt
4
14
X
$ 
$

perl -ne 'next if $. == 1;
    if(/.*del([A-Z]+)ins([A-Z]+).'s/NC_0+(.*?)\..*/$1/; print')   # indel
{
        print join("\t", $3, $4, $5, $1, $2), "\n";
}
           ' out_position.txt > out.txt
Unknown regexp modifier "/N" at -e line 2, at end of line
Unknown regexp modifier "/C" at -e line 2, at end of line
Unknown regexp modifier "/_" at -e line 2, at end of line
Unknown regexp modifier "/0" at -e line 2, at end of line
syntax error at -e line 2, near "(."
Execution of -e aborted due to compilation errors.

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";
            }
                       ' out_position.txt > out.txt

.*NC_0+([^.]+)\.

.*NC_0+([^.]+)\.

perl -nle 'BEGIN{$,="\t"}/del([A-Z]{2})ins([A-Z]{2})\s+NC_0+(\w+)\.\d+:\w\.(\d+)_(\d+)/ and print $3,$4,$5,$1,$2' out_position.txt > out2.txt

cat out2.txt
14      41747805        41747806        GC      AA