02-11-2013
Grep for a range of numbers?
I am trying to extract specific information from a large *.sam file (it's originally 28Gb).
I want to extract all lines that are on chr3 somewhere in the range of 112,937,439-113,437,438.
Here is a sample line from my file so you can get a feel for what each line looks like:
seq.4 0 chr10 82951725 25 50M * 0 0 GCCACTTCATTATTTTGGGGACTATCTCCCTAGTCATCACAAGAAATTAA bbbeeeeegggggiiiiiiiihiiiiihiiihighiiihiiiihhiehii XO:A:F MD:Z:50 NM:i:0 IH:i:1 HI:i:1
Any suggestions?
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LEARN ABOUT OSX
svk::log::filter::grep
SVK::Log::Filter::Grep(3) User Contributed Perl Documentation SVK::Log::Filter::Grep(3)
SYNOPSIS
SVK::Log::Filter::Grep - search log messages for a given pattern
DESCRIPTION
The Grep filter requires a single Perl pattern (regular expression) as its argument. The pattern is then applied to the svn:log property
of each revision it receives. If the pattern matches, the revision is allowed to continue down the pipeline. If the pattern fails to
match, the pipeline immediately skips to the next revision.
The pattern is applied with the /i modifier (case insensitivity). If you want case-sensitivity or other modifications to the behavior of
your pattern, you must use the "(?imsx-imsx)" extended pattern (see "perldoc perlre" for details). For example, to search for log messages
that match exactly the characters "foo" you might use
svk log --filter "grep (?-i)foo"
However, to search for "foo" without regards for case, one might try
svk log --filter "grep foo"
The result of any capturing parentheses inside the pattern are not available. If demand dictates, the Grep filter could be modified to
place the captured value somewhere in the stash for other filters to access.
If the pattern contains a pipe character ('|'), it must be escaped by preceding it with a '' character. Otherwise, the portion of the
pattern after the pipe character is interpreted as the name of a log filter.
STASH
/PROPERTY MODIFICATIONS
Grep leaves all properties and the stash intact.
perl v5.10.0 2008-08-04 SVK::Log::Filter::Grep(3)