I am new to perl, and I am fiddiling around. I found this code online.
Here is the snippet of code:
82 process_input(q,[]).
83 process_input(n,Task) :- toptask(Task), set_new_threshold.
84 process_input(s,Task) :- suggest_task(T),
85 apply(addtoagenda,T),toptask(Task).
86 process_input(x,Task) :- print('not yet implemented'),nl,toptask(Task).
87 process_input(i,Task) :- user_task,toptask(Task).
And I am getting this error: Bareword found where operator expected near "process_input(n, Task" line 83.
Might be a runaway multi-line ,, string starting on line 82.
A 'Bareword' error is caused by a syntax error in your code. A 'runaway multi-line' usually pinpoints where the start of the error is, and usually means that a line has not been completed, often because of mismatched brackets or quote marks.
As has been pointed out by several SO-ers, that doesn't look like Perl! The Perl interpreter is balking on a syntax error because it doesn't speak that particular language!
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 is no longer valid syntax for a match operator.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.
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.
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
What does the following error mean(and I don't even have line no.83 either in .mzn or .dzn:
Error: invalid integer literal in line no. 83
Error: syntax error, unexpected ':', expecting FZ_INT_LIT in line no. 83
Is it because the numbers in my arrays are too large for the solver to handle?
I am quite new with fortran and have a question. I need to read 2 integers from the following line:
K=234, L=241, I=0
I am not interested in the last value. Just need the integers 234 and 241. I tried it with
read(20,'(3X,I3,3X,I3)')a,b
It compiles, but when I run the program I always get the error message:
At line 27 of file test.f90 (unit = 20, file = 'int_p2.dat')
Fortran runtime error: Bad value during integer read
Don't know what I am doing wrong. Can someone give me some advice?
You have strings in your line, so your READ statement ought to account for it. You should replace it with
READ(20, '(3(a2,i3,2x))') dumChar, k, dumChar, l, dumInt, dumChar
where dumChar is a character of length 2 and dumInt is an integer.
I don't see a problem in your code. (off course, your format is wrong, but should not give runtime error). Also, you are escaping chars (K,L) rather then reading them. compiler should not complain. but 3X will eat up 1 integer for K=234
Program se
Implicit None
integer :: K,L,I,a,b
open(20, file="se.in",status='old')
read(20,'(3X,I3,3X,I3)')a,b
close(20)
write(*,*)a,b
End Program se
$ cat se.in
K=234, L=241, I=0
$gfortran se.f90
$ ./a.out
34 241
If you still getting the problem, and if this are one single line you are trying to read, do
remove any space before K= in the file.
I think this is the error, as the code is reading non-integer.