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Parse two patterns and print next few characters following the pattern

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# 1  
Old 01-31-2012
Question Parse two patterns and print next few characters following the pattern
Hi all,

I have many large files with data like following in each line:
Code:
1    822381    rs116091741    C    T    .    PASS    ASP;G5;G5A;GMAF=0.014308426073132;KGPilot123;RSPOS=822381;SAO=0;

I want output like this:
rs116091741 0.014308426073132

I tried some of the commands unsuccessfully, for example:

Code:
sed -n 's/.*rs//p' dbsnp_132.b37.vcf

I am very much new to linux and learning basics so please forgive me if it seems to be simple question....but I am not able to understand how to parse both the pattern and print characters following 'rs' including 'rs' itself and print values followed by 'GMAF=' excluding GMAF= itself.
# 2  
Old 01-31-2012
Try:
Code:
perl -lane '/GMAF=([^;]+)/;print "$F[2] $1"' dbsnp_132.b37.vcf

This User Gave Thanks to bartus11 For This Post:
pirates.genome
# 3  
Old 01-31-2012
MySQL
Quote:
Originally Posted by bartus11
Try:
Code:
perl -lane '/GMAF=([^;]+)/;print "$F[2] $1"' dbsnp_132.b37.vcf

Thanks bartus11,

your code worked like a charm...

it will be really helpful if you can explain the code a little bit...I am learning languages and would like to know more...
# 4  
Old 01-31-2012
perl -lautomatically add newline to the print commands (among other things)
asplit every line ($_) into @F array, using one or more whitespace characters (space, tab) as delimiter
nload each line of the file into $_ for further processing, don't print the line at the end of the procesing (-p is working similarly, but it prints the line)
eexecute code that follows
'/GMAF=([^;]+)/;match string that is between "GMAF=" and ";" into variable "$1"
print "$F[2] $1"'print 3rd field from each line (see -a option), followed by string matched in the previous regular expression
This User Gave Thanks to bartus11 For This Post:
pirates.genome
# 5  
Old 01-31-2012
MySQL
Quote:
Originally Posted by bartus11
perl -lautomatically add newline to the print commands (among other things)
asplit every line ($_) into @F array, using one or more whitespace characters (space, tab) as delimiter
nload each line of the file into $_ for further processing, don't print the line at the end of the procesing (-p is working similarly, but it prints the line)
eexecute code that follows
'/GMAF=([^;]+)/;match string that is between "GMAF=" and ";" into variable "$1"
print "$F[2] $1"'print 3rd field from each line (see -a option), followed by string matched in the previous regular expression
Thank you very much bartus11....that is really very helpful...
can you also suggest me how to learn such PERL?? Any book or anything else which starts at very basic and takes to this level??
# 6  
Old 01-31-2012
I started with that book: Learning Perl, 3rd Edition-O'Reilly Media
This User Gave Thanks to bartus11 For This Post:
pirates.genome
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