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Classify lines in file using perl

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Top Forums Shell Programming and Scripting Classify lines in file using perl
# 15  
Old 04-10-2017
I am adding the below condition to change the classification of line 3 to Likely Benign. If $Score was 20 and the PopFreqMax being what it is 0.003 it would follow the default rule.
However, because in the GeneDetailIDPrefGene section the digit 50, that is stripped off of the >50 is greater than 10, so classification is Likely Benign. I know the code that strips of the 50 works, but am I doing something else wrong? Thank you Smilie.

Code:
if ($FuncIDPrefGene !~/exonic/i && $Score < 5 && $GeneDetailIDPrefGene=~/^\D(\d+)$/;) {   # capture the digits after any non-digit into $1
        $1 > 10   # Reclassify intronic variants (with distance only) based on score less than 5 to Likely Benign
        $classification = 'Likely Benign';
    }
else {
             my $scored = $FuncIDPrefGene !~/exonic/i && $Score < 5 && $GeneDetailIDPrefGene=~/\.\d+[\+\-](\d+)/;   # capture the digits after . and (+/-) into $1
                if $scored < 5;    # Reclassify intronic variants (with c.) less than 5 based on score
       $classification =  'Likely Benign';
}
syntax error at /home/cmccabe/Desktop/NGS/scripts/classifier.pl line 45, near "}"

Execution of /home/cmccabe/Desktop/NGS/scripts/classifier.pl aborted due to compilation errors.

Last edited by cmccabe; 04-10-2017 at 09:58 AM.. Reason: fixed format
# 16  
Old 04-10-2017
Let me remove all the extra around what you posted and highlight the syntax issues.
Quote:
Originally Posted by cmccabe
[...]

Code:
# remove ;
if ($FuncIDPrefGene !~/exonic/i && $Score < 5 && $GeneDetailIDPrefGene=~/^\D(\d+)$/;) {  
        if ($1 > 10) {
             $classification = 'Likely Benign';
        }
    }
else {
             my $scored = $FuncIDPrefGene !~/exonic/i && $Score < 5 && $GeneDetailIDPrefGene=~/\.\d+[\+\-](\d+)/;   
                if ($scored < 5) {  
                       $classification =  'Likely Benign';
                }
}

This User Gave Thanks to Aia For This Post:
cmccabe
# 17  
Old 04-10-2017
Below is the updated code along with attempt to fix the message. The sections in bold were updated accordingly, however the new message seems to give a different message but allows the script to run. I am a little confused as this line seems to be important but the script ignores it/ or skips it? Thank you Smilie.


Code:
# Change to Likely Benign if either of these two conditions occurs.
    if ($Score < 5 || $PopFreqMax > 0.011) {
        $classification = 'Likely Benign';
    }
    # GeneDetail condition
    if ($FuncIDPrefGene !~/exonic/i && $Score < 5 && $GeneDetailIDPrefGene=~/^\D(\d+)$/) {
        $1 > 10
        $classification = 'Likely Benign';
    }
    else {
           if ($FuncIDPrefGene !~/exonic/i && $Score < 5 && $GeneDetailIDPrefGene=~/\.\d+[\+\-](\d+)/)
              $1 > 10
              $classification =  'Likely Benign';
    }

# token 55 is classification.
    $f[55] = $classification;

    # display results and update @f.
    print join "\t", @f;
}   # end conditional block
Scalar found where operator expected at /home/cmccabe/Desktop/NGS/scripts/classifier.pl line 34, near "$classification"
	(Missing semicolon on previous line?)
Scalar found where operator expected at /home/cmccabe/Desktop/NGS/scripts/classifier.pl line 38, near ")
              $1"
	(Missing operator before $1?)
Scalar found where operator expected at /home/cmccabe/Desktop/NGS/scripts/classifier.pl line 39, near "$classification"
	(Missing semicolon on previous line?)
syntax error at /home/cmccabe/Desktop/NGS/scripts/classifier.pl line 34, near "$classification "
syntax error at /home/cmccabe/Desktop/NGS/scripts/classifier.pl line 38, near ")
              $1 "
Execution of /home/cmccabe/Desktop/NGS/scripts/classifier.pl aborted due to compilation errors.


adding the ; indicated by the message but the script does execute
Code:
# Change to Likely Benign if either of these two conditions occurs.
    if ($Score < 5 || $PopFreqMax > 0.011) {
        $classification = 'Likely Benign';
    }
    # GeneDetail condition
    if ($FuncIDPrefGene !~/exonic/i && $Score < 5 && $GeneDetailIDPrefGene=~/^\D(\d+)$/) {
        $1 > 10;
        $classification = 'Likely Benign';
    }
    else {
           if ($FuncIDPrefGene !~/exonic/i && $Score < 5 && $GeneDetailIDPrefGene=~/\.\d+[\+\-](\d+)/)
              $1 > 10;
              $classification =  'Likely Benign';
    }

# token 55 is classification.
    $f[55] = $classification;

    # display results and update @f.
    print join "\t", @f;
}   # end conditional block
Useless use of numeric gt (>) in void context at /home/cmccabe/Desktop/NGS/scripts/classifier.pl line 33.
Useless use of numeric gt (>) in void context at /home/cmccabe/Desktop/NGS/scripts/classifier.pl line 38.

Last edited by cmccabe; 04-10-2017 at 02:03 PM.. Reason: adding bold and highlighting to make it easier to read
# 18  
Old 04-10-2017
Hi cmccabe,
Please, take a look again at post #16. I highlighted for you how it needs to be if you mean it as such.
$1 > 10; It is useless as the message says.
It would be the equivalent of _the sky is blue_. So what? No flow control, there.
If the code runs it would always be $classification = 'Likely Benign' as soon as the if is met.
This User Gave Thanks to Aia For This Post:
cmccabe
# 19  
Old 04-10-2017
I apologize I read the post incorrectly. I am not sure why line 1 in the attached file.txt should be VUS set by the default classification. That is correct. However, when the two conditions below are added the first behaves as expected. The second (after the else) changes the first line to Likely Benign. However, it should not be applied as $FuncIDPrefGene does not equal exonic. Is there something wrong with my logic? Thank you for all your help Smilie.

Code:
# GeneDetail condition
    if ($FuncIDPrefGene !~/exonic/i && $Score < 5 && $GeneDetailIDPrefGene=~/^\D(\d+)$/) {  
        if ($1 > 10) {
            $classification = 'Likely Benign';
        }
    }
        else {
             my $transcript = $FuncIDPrefGene !~/exonic/i && $GeneDetailIDPrefGene=~/\.\d+[\+\-](\d+)/;   
             if ($transcript > 10) {  
                 $classification =  'Likely Benign';
            }
    }

desired classification
Code:
VUS     ----- default classification
Likely Benign   -----  portion before the else $Score < 5
Likely Benign    ---- portion after the else >50 is used to be Likely Benign

file.txt (1.3 KB) 
# 20  
Old 04-10-2017
Quote:
Originally Posted by cmccabe
Is there something wrong with my logic?
You decide.

This is not necessary,
Code:
    if ($FuncIDPrefGene !~/exonic/i && $Score < 5 && $GeneDetailIDPrefGene=~/^\D(\d+)$/) {  
        if ($1 > 10) {
            $classification = 'Likely Benign';
        }
    }

its mission is to make $classification = 'Likely Benign', however the condition above does that job already since the $Score is less than 5, regardless if it is not exonic nor the $GeneDetailIDPrefGene is more than 10.
Code:
    if ($Score < 5 || $PopFreqMax > 0.011) {
        $classification = 'Likely Benign';
    }



Code:
        else {
             my $transcript = $FuncIDPrefGene !~/exonic/i &&$GeneDetailIDPrefGene=~/\.\d+[\+\-](\d+)/;   
             if ($transcript > 10) {  
                 $classification =  'Likely Benign';
            }
    }

The highlighted part does not work for >50 which is what the last line has.

Perhaps this might help, instead

Code:

    if ($Score < 5 || $PopFreqMax > 0.011) {
        $classification = 'Likely Benign';
    }

    if ($FuncIDPrefGene !~ /exonic/i) {
        # Get a numeric value if exist.
        my ($transcript) = ($GeneDetailIDPrefGene) =~ /(?:\.\d+[+-]|\D)(\d+)/;
        # Give it a value of zero if no numeric value was found.
        $transcript //= 0;
        $classification = 'Likely Benign' if $transcript > 10;
    }

Last edited by Aia; 04-11-2017 at 12:49 AM..
This User Gave Thanks to Aia For This Post:
cmccabe
# 21  
Old 04-11-2017
Using the lines below I am trying to update the $classification by using the rules in the description, but can not get the desired output. Thank you for all your help, I really appreciate it Smilie.

Code:
35	chr1	154562623	154562625	CCG	-	intronic	ADAR	>50	.	.	.	rs779843196	0.0003	.	.	.	.	.	.	0.0001	0.0003	0.0001	.	.	0.0001	.	0.0003	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Pathogenic|Likely Pathogenic	.	.	.	.	.	.	.	20	VUS	.	.
35	chr1	154562623	154562625	CCG	-	intronic	ADAR	>50	.	.	.	rs779843196	0.0003	.	.	.	.	.	.	0.0001	0.0003	0.0001	.	.	0.0001	.	0.0003	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Benign|other|unknown	.	.	.	.	.	.	.	20	VUS	.	.
35	chr1	154562623	154562625	CCG	-	intronic	ADAR	>50	.	.	.	rs779843196	0.0003	.	.	.	.	.	.	0.0001	0.0003	0.0001	.	.	0.0001	.	0.0003	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Uncertain signiffigance	.	.	.	.	.	.	.	20	VUS	.	.

Description:
In the first line classification updated toPathogenic because it follows the rules of the second else statement
In the second line the first else statement is used to update classification
In the third line the first if statement is used to update classification because it is a single entry with no |

ClinSig ---- only allow single entries in classification ----
Code:
Benign is single entry
Benign|Likely benign|Unknown is a multiple entry

Since a | (pipe) character is always presents for multiple entries, maybe: (seems to execute but nothing changes in classification)-

Code:
if ($ClinSig !~/untested|unknown|not provided|other/i && $ClinSig ne "." && $ClinSig ne "|") {
           $classification = $ClinSig;
         }
     }
   else {
        if ($ClinSig !~/Pathogenic|Likely pathogenic|Uncertain significance/i || $ClinSig eq ".") {
             $classification = 'Likely Benign';
   }
        }

   else {
        if ($ClinSig eq "Pathogenic|Likely pathogenic|Uncertain significance" && $ClinSig ne ".") {
                 #$classification = 'Pathogenic';
   }
        }

desired classification
Code:
Pathogenic
Likely Benign
Uncertain signiffigance

Last edited by cmccabe; 04-11-2017 at 11:11 AM.. Reason: fixed format
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