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Search for the two patterns and print everything in between

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# 1  
Old 01-16-2012
Search for the two patterns and print everything in between
Hi all,
I have a file having data:
Code:
@HWUSI-EAS1727:19:6:1:3674:984:0:1#GTTAATA
NTTGGGTTTTCT
@HWUSI-EAS1727:19:6:1:3674:984:0:1#GTTA...
NTTGGGTTTTCT
@HWUSI-EAS1727:19:6:1:3674:984:0:1#.....CT
NTTGGGTTTTCT

I want to print everything starting from # till line ends.
can you please help me how to do that??
I am trying in perl, able to parse "#......." pattern but not able to understand how to make it print??

Thanks...
Last edited by Franklin52; 01-17-2012 at 03:16 AM.. Reason: Please use code tags for code and data samples, thank you
# 2  
Old 01-16-2012
Code:
awk -F'#' '{ print "#"$2 }' inputfile > outputfile

If not on linux, try nawk or gawk.
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# 3  
Old 01-16-2012
In sh or ksh or bash
Code:
IFS="#"
while read a b
echo "$b"
done <inputfile

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# 4  
Old 01-16-2012
Code:
sed -n 's/.*#//p' infile

Code:
GTTAATA
GTTA...
.....CT

or do you need to combine the next line?
Code:
sed -n 'N;s/\n//;s/.*#//p' infile

Code:
GTTAATANTTGGGTTTTCT
GTTA...NTTGGGTTTTCT
.....CTNTTGGGTTTTCT

This User Gave Thanks to Scrutinizer For This Post:
pirates.genome
# 5  
Old 01-16-2012
Bug
Finally I used this code...by Scrutinizer...
thank you very much for replies...

I didnt know sed can be so useful and easy...now along with perl need to learn sed...

Quote:
Originally Posted by Scrutinizer
Code:
sed -n 's/.*#//p' infile

Last edited by jim mcnamara; 01-16-2012 at 11:09 PM.. Reason: [/quote]
# 6  
Old 01-17-2012
Using Perl, you could search for all text from "#" to end of line and replace the entire line by the result -

Code:
$
$ cat f31
@HWUSI-EAS1727:19:6:1:3674:984:0:1#GTTAATANTTGGGTTTTCT
@HWUSI-EAS1727:19:6:1:3674:984:0:1#GTTANTTGGGTTTTCT
@HWUSI-EAS1727:19:6:1:3674:984:0:1#CTNTTGGGTTTTCT
$
$
$ perl -lne 's/^.*#(.*)$/$1/ and print' f31
GTTAATANTTGGGTTTTCT
GTTANTTGGGTTTTCT
CTNTTGGGTTTTCT
$
$

Or you could remove everything up to and including the "#" character from each line -

Code:
$
$ perl -lne 's/^.*#// and print' f31
GTTAATANTTGGGTTTTCT
GTTANTTGGGTTTTCT
CTNTTGGGTTTTCT
$
$

Or you could split each line on "#" as the delimiter, assign the chunks to an array and print just the 2nd element of the array -

Code:
$
$ perl -lne '@x = split/#/ and print $x[1]' f31
GTTAATANTTGGGTTTTCT
GTTANTTGGGTTTTCT
CTNTTGGGTTTTCT
$
$
$ # Or more succintly...
$
$ perl -lne 'print ((split/#/)[1])' f31
GTTAATANTTGGGTTTTCT
GTTANTTGGGTTTTCT
CTNTTGGGTTTTCT
$
$ # Or even more succintly...
$
$ perl -plne '$_=(split/#/)[1]' f31
GTTAATANTTGGGTTTTCT
GTTANTTGGGTTTTCT
CTNTTGGGTTTTCT
$
$

Or you could even find out the index of the "#" character in each line, extract the substring of each line that starts from that index onwards, and then print that substring, like so -

Code:
$
$
$ perl -lne 'print substr($_,index($_,"#")+1)' f31
GTTAATANTTGGGTTTTCT
GTTANTTGGGTTTTCT
CTNTTGGGTTTTCT
$
$

tyler_durden
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