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Perl keeps telling me that '11' from my input file is not numeric. Last time I checked 11 was a number, so I'm a bit confused what the problem is here and hence where to start looking.
Interestingly, it's line 1 of my input file causing the problem, the numbers on lines 2 onwards are interpreted correctly.
Argument "11" isn't numeric in numeric eq (==) at ./extract.pl line 200, <INPUTFILE> line 1.
Line 200 is
if ($_data[0] == $_ch && !exists $_ch_sn{$_data[1]}) { $_ch_sn{$_data[1]} = undef; }
Any help much appreciated!
The error was caused by a BOM in my inputfile. Using setlocal nobomb in Vi solved the problem!
It could be that the source doesn't actually contain 11 (e.g. maybe it contains a character that resembles a one but isn't), but I suspect the warning message is incorrectly identifying the expression that's non-numeric[1].
That fact that nothing remotely resembling 11 appears on that line appears to support that[2].
So just pretend you obtained the following warning:
Argument isn't numeric in numeric eq (==) at ./extract.pl line 200, <INPUTFILE> line 1.
This means that $_data[0] or $_ch is a non-numeric string[2].
If both should be numbers, determine which one isn't, possibly using the following code:
use Data::Dumper; { local $Data::Dumper::Useqq = 1; warn(Dumper($_data[0], $_ch)); }
Once you determine which variable is wrong, debug to find out why it is that way.
If they could be legitimately be non-numeric, add appropriate checks to handle that situation.
For performance reasons, that part of the error message is deduced from the compiled code, a complicated and unreliable process.
I'm assuming the if has no elsif clause. Warnings from an elsif condition can appear to be from an if statement.
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When I try to delete a specific line number from my file, all lines that have the same pattern are deleted. This is not what I want, I want to only delete the line number itself, not similar patterns.
Here is what I am trying to do:
x = 5
Command I run now:
sed -i "${x}d" home/file.txt
You had spaces around your variable assignment
x = 5
Which would be wrong.
Try the below fix
x=5
sed -i ${x}d home/file.txt
Here is an example to delete line number 33 of your file:
sed -i '33d' home/file.txt
If you need the number to be a variable:
local line_number=5
sed -i "${line_number}d" home/file.txt
The problem with what you are doing is the spaces, x = 5, will not work while x=5 will.
Here is what I am trying to do:
x = 5
That gives me:
bash: x: command not found...
, which is what I would expect. If you did not get a similar error message then you must be in the unfortunate situation of having a program named x in your path, perhaps because of doing something unwise, such as putting . in your PATH. Or perhaps you got such a message but did not see it because you have redirected your stderr.*
In any event, the quoted line does not assign a value to any shell variable. Shell variable assignments must not have whitespace around the = operator, so if you want to assign 5 to variable x, that must be
x=5
.
It is not an error to perform parameter expansion on a name that has not been assigned any value. The result is nothing. Thus, if x has not successfully been assigned any value then "${x}d" will expand to "d". As a complete sed script, that will delete every line.
*Or if you did get such an message then why in the world didn't you at least say so?
I am trying to select the below value from database:
Reporting that one of #its many problems had been the recent# extended
sales slump in women's apparel, the seven-store retailer said it would
start a three-month liquidation sale in all of its stores.~(A) its
many problems had been the recent~(B) its many problems has been the
recently~(C) its many problems is the recently~(D) their many problems
is the recent~(E) their many problems had been the recent~
i am selecting this value in variable $ques and then selecting a text as below:
$ques=~s/^(.*?)\#(.*?)\#(.*?)$/$2/;
Now, while replacing the ~ character in the string by
$3=~s/~/\n/g; ---->line 171
and running the script, I am getting one error as:
Modification of a read-only value attempted at main.pl line 171
I want to replace all the ~ character with '\n' and print the final value. Please suggest how to do it.
*I have researched this on net, but got confused that how to handle these read only variables.
You've already got a good explanation of the problem from José Castro. But there's another solution if you're using a recent-ish version of Perl (Update: having checked more carefully, I find that means 5.14+). The /r argument to the substitution operator will copy your string, make the substitution on the copy and then return that altered value.
So you could write:
my $new_value = $3 =~ s/~/\n/rg;
It sounds like what you really want in this case is split rather than regular expression capture groups:
my #parts = split(/#/, $ques);
$parts[2] =~ s/~/\n/g;
It makes the intent of your code clearer since you are, in fact, splitting on # symbols.
Just like you say, the special variables $1, $2, etc., are read-only, and that means that you can't perform that substitution on them.
Performing the substitution on $ques will do what you need:
$ques =~ s/~/\n/g;
print $ques;
Do note that in the earlier substitution that you're performing on $ques you're getting rid of all the ~ characters.
Hi I was trying to use linkdatagen, which is a perl based tool. It requires a vcf file (using mpileup from SAMtools) and a hapmap annotation file (provided). I have followed the instructions but the moment I use the perl script provided, I get this error.
The codes I used are:
samtools mpileup -d10000 -q13 -Q13 -gf hg19.fa -l annotHapMap2U.txt samplex.bam | bcftools view -cg -t0.5 - > samplex.HM.vcf
Perl vcf2linkdatagen.pl -variantCaller mpileup -annotfile annotHapMap2U.txt -pop CEU -mindepth 10 -missingness 0 samplex.HM.vcf > samplex.brlmm
Use of uninitiated value $chr in concatenation (.) or string at vcf2linkdatagentest.pl line 487, <IN> line 1.... it goes on and on.. I have mailed the authors, and haven't heard from them yet. Can anyone here please help me? What am I doing wrong?
The perl script is :
http://bioinf.wehi.edu.au/software/linkdatagen/vcf2linkdatagen.pl
The HapMap file can be downloaded from the website mentioned below.
http://bioinf.wehi.edu.au/software/linkdatagen/
Thanks so much
Ignoring lines starting with #, vcf2linkdatagen.pl expects the first field of the first line of the VCF to contain something of the form "chrsomething", and your file doesn't meet that expectation. Examples from a comment in the code:
chr1 888659 . T C 226 . DP=26;AF1=1;CI95=1,1;DP4=0,0,9,17;MQ=49;FQ=-81 GT:PL:GQ 1/1:234,78,0:99
chr1 990380 . C . 44.4 . DP=13;AF1=7.924e-09;CI95=1.5,0;DP4=3,10,0,0;MQ=49;FQ=-42 PL 0
The warning means that a variable used in a string is not initialized (undefined). It is an indication that something might be wrong. The line in question can be traced to this statement
my $chr = $1 if ($tmp[0] =~ /chr([\S]+)/);
It is bad practice to use postfix if statements on a my statement.
As ikegami notes a workaround for this might be
my ($chr) = $tmp[0] =~ /chr([\S])/;
But since the match failed, it will likely return the same error. The only way to solve is to know more about the purpose of this variable, if the error should be fatal or not. The author has not handled this case, so we do not know.
If you want to know more about the problem, you might add a debug line such as this:
warn "'chr' value not found in the string '$tmp[0]'" unless defined $chr;
Typically, an error like this occurs when someone gives input to a program that the author did not expect. So if you see which lines give this warning, you might find out what to do about it.
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I have an array in the third element dataArr[2], I know it contains a 10 digit phone. I need to only read or print the first 6 digits. For instance if my phone is 8329001111, I need to print out the 832900. I tried to see if I can use substr but I keep reading or printing the full list. Do I need to dereference..
Try this :
$dataArr[2] =~ s/\s//g; # ensure there's no spaces
print substr($dataArr[2], 0, 6);
# ^ ^ ^
# variable | |
# offset start|
# |
# substring length
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How do I fix this Perl code so that 1.1 + 2.2 == 3.3?
I'm working on a Perl script that compares strings representing gene models and prints out a summary of the comparison. If the gene models match perfectly, I print out a very terse summary, but if they are different, the summary is quite verbose.
The script looks at the value of a variable to determine whether it should do the terse or verbose summary--if the variable is equal to 1, it should print the terse summary; otherwise, it should print the verbose summary.
Since the value is numeric (a float), I've been using the == operator to do the comparison.
if($stats->{overall_simple_matching_coefficient} == 1)
{
print "Gene structures match perfectly!\n";
}
This worked correctly for all of my tests and even for most of the new cases I am running now, but I found a weird case where the value was equal to 1 but the above comparison failed. I have not been able to figure out why the comparison failed, and stranger yet, when I changed the == operator to the eq operator, it seemed to work fine.
I thought the == was for numerical comparison and eq was for string comparison. Am I missing something here?
Update: If I print out the value right before the comparison...
printf("Test: '%f', '%d', '%s'\n", $stats->{overall_simple_matching_coefficient}, $stats->{overall_simple_matching_coefficient}, $stats->{overall_simple_matching_coefficient});
...I get this.
Test: '1.000000', '0', '1'
The first thing any computer language teacher should teach you about any computer language is that YOU CANNOT COMPARE FLOATS FOR EQUALITY. This is true of any language. Floating point arithmetic is not exact, and two floats that look like they're the same will be different in the insignificant digits somewhere where you can't see it. Instead, you can only compare that they are close to each other - like
if (abs(stats->{overall_simple_matching_coefficient)-1) < 0.0001)
What do you get if you print the value of $stats->{overall_simple_matching_coefficient} just before the comparison? If it's 1, try printf with a format of "%20.10f". I strongly suspect you have some rounding error (less then 1e-6) accumulated in the variable and it's not comparing equal numerically. However when converted to string, since the error is right of the 6th decimal place, and the default string format is to six places, it compares equal.