I would like to remove characters from column 7 so that from an input file looking like this:
>HWI-EAS422_12:4:1:69:89 GGTTTAAATATTGCACAAAAGGTATAGAGCGT U0 1 0 0 ref_chr8.fa 6527777 F DD
I get something like that in an output file:
... (13 Replies)
I have a large text-file with tab-delimited genetic data that looks like:
KSC112 KSC234 0 0 1 1 A G C T
I simply wan to delete the first column, but since the file has 600 000 columns, it is not possible with awk (seems to be limited at 32k columns).
Does anyone have an idea how to do this? (2 Replies)
I want to add a new column to a tab delimited text file. It will be the first column and it will just be 1's. How do I go about doing that? Thanks! (1 Reply)
Hi all,
I'm new to Unix and work primarily in bioinformatics. I am in need of a script which will allow me to replace "1" with "chr1" in only the first column of a file which looks like such:
1 10327 rs112750067 T C . PASS ASP;RSPOS=10327;... (4 Replies)
I have a file which looks like this:
73450 articles and news developmental psychology 2006-03-30 16:22:40 1 http://www.usnews.com
73450 articles and news developmental psychology 2006-03-30 16:22:40 2 http://www.apa.org
73450 articles and news developmental psychology 2006-03-30... (1 Reply)
I have a file having the following entries:
test1 test2 test3
11 22 33
22 44 66
99 99 44
---
I want to add a column so that the above file becomes:
test1 test2 test3 notest
11 22 33 *
22 44 66 *
99 99 44 *
---
Thanks (6 Replies)
I am fairly new to programming and trying to resolve this problem. I have the file like this.
CHROM POS REF ALT 10_sample.bam 11_sample.bam 12_sample.bam 13_sample.bam 14_sample.bam 15_sample.bam 16_sample.bam
tg93 77 T C T T T T T
tg93 79 ... (4 Replies)
Hi all ,
I have a file having 12 columns tab delimited .
I need to read this file and remove the column 3 and column 4 and insert a word in column 3 as "AVIALABLE "
Is there a way to do this . I am trying like below
Thanks
DJ
cat $FILENAME|awk -F"\t" '{ print $1 "\t... (3 Replies)
Hello Everyone..
I want to replace the retail col from FileI with cstp1 col from FileP if the strpno matches in both files
FileP.txt
... (2 Replies)
Discussion started by: YogeshG
2 Replies
LEARN ABOUT DEBIAN
devel::refcount
Devel::Refcount(3pm) User Contributed Perl Documentation Devel::Refcount(3pm)NAME
"Devel::Refcount" - obtain the REFCNT value of a referent
SYNOPSIS
use Devel::Refcount qw( refcount );
my $anon = [];
print "Anon ARRAY $anon has " . refcount($anon) . " reference
";
my $otherref = $anon;
print "Anon ARRAY $anon now has " . refcount($anon) . " references
";
DESCRIPTION
This module provides a single function which obtains the reference count of the object being pointed to by the passed reference value.
FUNCTIONS
$count = refcount($ref)
Returns the reference count of the object being pointed to by $ref.
COMPARISON WITH SvREFCNT
This function differs from "Devel::Peek::SvREFCNT" in that SvREFCNT() gives the reference count of the SV object itself that it is passed,
whereas refcount() gives the count of the object being pointed to. This allows it to give the count of any referent (i.e. ARRAY, HASH,
CODE, GLOB and Regexp types) as well.
Consider the following example program:
use Devel::Peek qw( SvREFCNT );
use Devel::Refcount qw( refcount );
sub printcount
{
my $name = shift;
printf "%30s has SvREFCNT=%d, refcount=%d
",
$name, SvREFCNT($_[0]), refcount($_[0]);
}
my $var = [];
printcount 'Initially, $var', $var;
my $othervar = $var;
printcount 'Before CODE ref, $var', $var;
printcount '$othervar', $othervar;
my $code = sub { undef $var };
printcount 'After CODE ref, $var', $var;
printcount '$othervar', $othervar;
This produces the output
Initially, $var has SvREFCNT=1, refcount=1
Before CODE ref, $var has SvREFCNT=1, refcount=2
$othervar has SvREFCNT=1, refcount=2
After CODE ref, $var has SvREFCNT=2, refcount=2
$othervar has SvREFCNT=1, refcount=2
Here, we see that SvREFCNT() counts the number of references to the SV object passed in as the scalar value - the $var or $othervar
respectively, whereas refcount() counts the number of reference values that point to the referent object - the anonymous ARRAY in this
case.
Before the CODE reference is constructed, both $var and $othervar have SvREFCNT() of 1, as they exist only in the current lexical pad. The
anonymous ARRAY has a refcount() of 2, because both $var and $othervar store a reference to it.
After the CODE reference is constructed, the $var variable now has an SvREFCNT() of 2, because it also appears in the lexical pad for the
new anonymous CODE block.
PURE-PERL FALLBACK
An XS implementation of this function is provided, and is used by default. If the XS library cannot be loaded, a fallback implementation in
pure perl using the "B" module is used instead. This will behave identically, but is much slower.
Rate pp xs
pp 225985/s -- -66%
xs 669570/s 196% --
SEE ALSO
o Test::Refcount - assert reference counts on objects
AUTHOR
Paul Evans <leonerd@leonerd.org.uk>
perl v5.14.2 2011-11-15 Devel::Refcount(3pm)