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Rewrite sed to perl or run sed in perl

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Top Forums Shell Programming and Scripting Rewrite sed to perl or run sed in perl
# 8  
Old 04-09-2015
Well, I don't.

This exact program:

Code:
next if $. == 1;

if(/.*del([A-Z]+)ins([A-Z]+).*NC_0{4}([0-9]+).*g\.([0-9]+)_([0-9]+)/)
{
        print join("\t", $3, $4, $5, $1, $2), "\n";
}

running on this exact input:

Code:
Input Variant   Errors  Chromosomal Variant     Coding Variant(s)
NM_004004.5:c.592_600delGTGTCTGGAinsCAGTGTTCATGACATTC           NC_000013.10:g.20763121_20763129delinsGAATGTCATGAACACTG NM_004004.5:c.592_600delinsCAGTGTTCATGACATTC    XM_005266354.1:c.592_600delinsCAGTGTTCATGACATTC XM_005266355.1:c.592_600delinsCAGTGTTCATGACATTC XM_005266356.1:c.592_600delinsCAGTGTTCATGACATTC

Gives this output:

Code:
13      20763121        20763129        GTGTCTGGA       CAGTGTTCATGACATTC

...so you're either running very different data or very different code.
# 9  
Old 04-09-2015
Lets say there are two inputs combined into a file (out_position2), the output leaving the while statement in and removing it is attached. Leaving the while statement in results in output that is close, but the third line in it 13 20763121 20763121 C - is not needed and Im not sure why it is there. Thank you Smilie.

It looks the third line is the parsed output of the first if statement, is there a way to prevent this?
shell.zip (705 Bytes) 
Last edited by cmccabe; 04-09-2015 at 03:04 PM.. Reason: added a comment
# 10  
Old 04-09-2015
Running the code I showed on out_position2.txt gives this exact output:

Code:
13      20763121        20763129        GTGTCTGGA       CAGTGTTCATGACATTC

...and nothing else.

So please show exactly what you are doing, word for word, letter for letter, keystroke for keystroke, to get the output you are.
# 11  
Old 04-09-2015
Two variants are inputted by the user and written to one file (out_position.txt). Then the below parser is used on that file. Depending on the input line one of the parse conditions is used. So, for the "del" in line 1 of the input file the # deletion is used. For the "delins" on line 2 the # indel is used. So the resulting output of the parsed file would be two lines (it is 3 now). I am not sure how to fix it but it looks like the while may be the issue, bit removing it doesnt result in the desired output. Thank you Smilie.

Code:
 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, $2), "\n";
}
            while (/\t*NC_(\d+)\.\S+g\.(\d+)(\S+)/g) {                                            # conditional parse
                ($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);
            }
           ' C:/Users/cmccabe/Desktop/annovar/out_position.txt > C:/Users/cmccabe/Desktop/annovar/out_parse.txt

# 12  
Old 04-09-2015
So, that 'while' loop should only happen when the data doesn't match the regex from sed?

Code:
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, $2), "\n";
}
else
{
            while (/\t*NC_(\d+)\.\S+g\.(\d+)(\S+)/g) {                                            # conditional parse
                ($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);
            }
}

This User Gave Thanks to Corona688 For This Post:
cmccabe
# 13  
Old 04-10-2015
Thats it, works perfect Smilie.
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