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 $chr;
Typically, an error like this occurs when someone gives input to a program that the author did not expect. So if you see which lines give this warning, you might find out what to do about it.
Related
When I run a file which is begin with #!/usr/bin/perl -w, I get a error:
syntax error at line 153, near "=~ ?"
I try to add "#!/bin/bash", this error is not append, but I get another
error:
"line 34: syntax error near unexpected token `('"
line 153 in my file:
($output_volume =~ ?^([\S]+).mnc?) && ($base_name = $1) ||
die "sharpen_volume failed: output volume does not appear to be"
." a minc volume.\n";
line34 in my file:
use MNI::Startup qw(nocputimes);
$output_volume =~ ?^([\S]+).mnc?
This used to be valid perl and thus might appear in old code and instructional material.
From perlop:
In the past, the leading m in m?PATTERN? was optional, but omitting it would produce a deprecation warning. As of v5.22.0, omitting it produces a syntax error. If you encounter this construct in older code, you can just add m.
That is Perl code so the first error message is meaningful.
With delimiters other than // in the match operator you must have the explicit m for it, so
$output_volume =~ m?^([\S]+).mnc?
It is only with // delimiters that the m may be omitted; from Regex Quote-Like Operators (perlop)
If "/" is the delimiter then the initial m is optional.
See perlretut for a tutorial introduction to regex and perlre for reference.
Also note that the particular delimiters of ? trigger specific regex behavior in a special case. This is discussed by the end of the documentation section in perlop linked above.
You already have two answers that explain the problem.
? ... ? is no longer valid syntax for a match operator. You need m? ... ? instead.
Until Perl 5.22, your syntax generated a warning. Now it's a fatal error (which is what you are seeing). So I assume you're now running this on a more recent version of Perl.
There are, however, a few other points it is probably worth making.
You say you tried to investigate this by changing the first line of your file from #!/usr/bin/perl -w to #!/bin/bash. I'm not sure how you think this was going to help. This line defines the program that is used to run your code. As you have Perl code, you need to run it with Perl. Trying to run it with bash is very unlikely to be useful.
The m? ... ? (or, formerly, ? ... ?) syntax triggers an obscure and specialised behaviour. It seems to me that this behaviour isn't required in your case, so you can probably change it to the more usual / ... /.
Your regex contains an unescaped dot character. Given that you seem to be extracting the basename from a filename that has an extension, it seems likely that this should be escaped (using \.) so that it matches an actual dot (rather than any character).
If you are using this code to extract a file's basename, then using a regex probably isn't the best approach. Perhaps take a look at File::Basename instead.
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.
I'm trying to run the word_align.pl script provided by CMUSphinx. I write the command as follows:
perl word_align.pl actualtext.txt batchOutputText.txt
But the terminal gives me the following errors:
Use of uninitialized value $ref_uttid in hash element at word_align.pl line 60, line 1.
Use of uninitialized value $ref_uttid in concatenation (.) or string at word_align.pl line 61, line 1.
UttID is not ignored but it could not found in any entries of the hypothesis file on line3 1 UTTID
I am not quite familiar with Perl and I can't figure out what is the problem here though I followed the instructions provided by CMUSphinx to run that script
You can find the script here
Edit: here is the reference's file link
The answer is in this error message
UttID is not ignored but it could not found in any entries of the hypothesis file on line3 1 UTTID
The reference file that you are passing is malformed, specifically its first line isn't formatted as it should be
More precisely, each line of the reference file requires a UTT ID—a unique string in parentheses like (output00000). It must be unique because it is used as a hash key. A simple digit like (1) won't work as it will be mistaken for an alternative pronunciation
The first line of your file must be different from that. You suggest
<s> text </s> (file12)
which actually works fine—I have tested it—and $ref_uttid comes out as FILE12. If you tell us what is actually in your file then I am sure we could help you better
And how do I fix it?
If I do the following:
print unpack("B8", 7) . "\n";
I get the following output:
00110111
The expected output is of course 00000111. I've checked, and it's giving me ascii "7", the string. I'm able to fix it poorly by wrapping the 7 in a chr():
print unpack("B8", chr(7)) . "\n";
Of course, this will only work if my input remains below 255, and I suspect it may go into the low thousands (I'll make the "B8" dynamic too).
I know I'm being obtuse, but I've read the docs on this and they make no mention of it. Its reverse function, pack(), seems to interpret the second argument correctly.
unpack unpacks a string of bytes into scalars with the values represented by those bytes.
$ perl -E'say for unpack("nB8", "\x12\x34\x56")'
4660
01010110
You're looking for
sprintf("%08B", 7)
I'm having a strange problem with Email:MIME. I have the following code, which is intended to parse a MIME email message piped to it:
my $parsed = Email::MIME->new(<STDIN>);
print $parsed->body;
When I run this, either by piping a sample MIME email into it, or by setting my host to pipe new email to it and sending myself one, I get the following error on the first line:
> Can't use string ("Received: from
> servera02.tk2adsm") as a HASH ref
> while "strict refs" in use at
> /usr/lib/perl5/site_perl/5.8.8/Email/Simple.pm
> line 100, <STDIN> line 71.
The line shown in the error varies according to the email but it is always the second line of the email content (so I'm really not very sure why it's claiming it's STDIN line 71). I've done some googling about this and it really seems to be unique to me - does anyone have any ideas?
I'm not a Perl expert by a long way, and I've never used Email::MIME, so I'm hoping this is something simple.
Chris
The documentation says that new() expects its argument to be a message in the form of a string. <STDIN> is an array (since an argument list is in list context).
Try converting the message to a string as you pass it: my $parsed = Email::MIME->new(join('', <STDIN>));
i mean you might not get the error if you turn off strict refs