I'm a biologist and i have to extract information from one text. The text is something like this
The thing that I need is to print de column 1, 2, 3, 4 and 6.But in the sixth column I want to extract de information of different characters that are there. I want to print the the number of c or C and g or G and t or T and a or A of each line.
The thing that I use is just
I need this and also the count of each.
If anyone could help me..
Thanks
Last edited by Corona688; 03-21-2012 at 03:36 PM..
Reason: Code tags for code, please.
I have a text file which represents a http flow like this:
HTTP/1.1 200 OK
Date: Fri, 23 Jan 2009 17:16:24 GMT
Server: Apache
Last-Modified: Fri, 23 Jan 2009 17:08:03 GMT
Accept-Ranges: bytes
Cache-Control: max-age=540
Expires: Fri, 23 Jan 2009 17:21:31 GMT
Vary: Accept-Encoding ... (1 Reply)
Hi All,
I am another biologist attempting to parse a large txt file containing several million lines like:
tucosnp 56762 T Y 228 228 60 23 .CcCcc,,..c.c,cc,,.C...
What I need to do is get the frequency of periods (.) plus commas (,) in column 9, and populate this number into another... (1 Reply)
Hi all,
I like to know how to get the count of each character in a given word. Using the commands i can easily get the output. How do it without using the commands ( in shell programming or any programming)
if you give outline of the program ( pseudo code )
i used the following commands
... (3 Replies)
Hi i have data like
abchd 124 ldskc aattggcc
each separated by tab space i want to count number of characters in 4th column and print it in new column with tabspace for every line can anyone help me how to do it.
Thanks. (3 Replies)
Hi all, I need help.
I have an input text file (input.txt) like this:
21 GTGCAACACCGTCTTGAGAGG 50
21 GACCGAGACAGAATGAAAATC 73
21 CGGGTCTGTAGTAGCAAACGC 108
21 CGAAAAATGAACCCCTTTATC 220
21 CGTGATCCTGTTGAAGGGTCG 259
Now I need to count A/T/G/C numbers at each character location in column... (2 Replies)
I have a file as follows
ATOM 5181 N AMET K 406 12.440 6.552 25.691 0.50 7.37 N
ATOM 5182 CA AMET K 406 13.685 5.798 25.578 0.50 5.87 C
ATOM 5183 C AMET K 406 14.045 5.179 26.909 0.50 5.07 C
ATOM 5184 O MET K... (14 Replies)
Hi All!
I would like to solve a problem but I have no clue of how do it!I will be grateful if someone could help me!
I have a file like this:
> genes | transcript
...sequence....
>ENSMUSG00000006638|ENSMUST00000006814
GGGAAATGGAATACCCCTACACAACCAAGATGCTGAGTTCCTCCCTGAGCCCGCAAAACG... (2 Replies)
Hello all,
I would like to ask your help here:
I've a huge file that has 2 columns. A part of it is:
sorted.txt:
kss23 rml.67lkj
kss23 zhh.6gf
kss23 nhd.09.fdd
kss23 hp.767.88.89
fl67 nmdsfs.56.df.67
fl67 kk.fgf.98.56.n
fl67 bgdgdfg.hjj.879.d
fl66 kl..hfh.76.ghg
fl66... (5 Replies)
Need to count consecutive characters in a string and give the output as below
i/p=aaaabbcaa
o/p=a4b2c1a2 (10 Replies)
Discussion started by: prasanna2166
10 Replies
LEARN ABOUT DEBIAN
html::tidy::message
HTML::Tidy::Message(3pm) User Contributed Perl Documentation HTML::Tidy::Message(3pm)NAME
HTML::Tidy::Message - Message object for the Tidy functionality
SYNOPSIS
See HTML::Tidy for all the gory details.
EXPORTS
None. It's all object-based.
METHODS
Almost everything is an accessor.
new( $file, $line, $column, $text )
Create an object. It's not very exciting.
where()
Returns a formatted string that describes where in the file the error has occurred.
For example,
(14:23)
for line 14, column 23.
The terrible thing about this function is that it's both a plain ol' formatting function as in
my $str = where( 14, 23 );
AND it's an object method, as in:
my $str = $error->where();
I don't know what I was thinking when I set it up this way, but it's bad practice.
as_string()
Returns a nicely-formatted string for printing out to stdout or some similar user thing.
file()
Returns the filename of the error, as set by the caller.
type()
Returns the type of the error. This will either be "TIDY_ERROR", or "TIDY_WARNING".
line()
Returns the line number of the error, or 0 if there isn't an applicable line number.
column()
Returns the column number, or 0 if there isn't an applicable column number.
text()
Returns the text of the message. This does not include a type string, like "Info: ".
LICENSE
This code may be distributed under the same terms as Perl itself.
Please note that these modules are not products of or supported by the employers of the various contributors to the code.
AUTHOR
Andy Lester, "<andy@petdance.com>"
perl v5.14.2 2010-02-16 HTML::Tidy::Message(3pm)