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Full Discussion: Fasta header modification
Top Forums UNIX for Dummies Questions & Answers Fasta header modification Post 302922936 by RavinderSingh13 on Wednesday 29th of October 2014 09:11:23 AM
Old 10-29-2014
Hello Lokaps,

Following may help you in same.

Code:
awk 'FNR==NR{A[$2]="_"$3"_[cov="$4"]";next}  {V=$1;gsub(/>/,C,V)} (V in A){print $1 A[V]} !(V in A){print $0}' file2 file1

Output will be as follows.
Code:
>contig0001_11115_[cov=20.5]
agatgtagatctct
>contig0002_23412_[cov=13.5]
atcgtcat

Thanks,
R. Singh
 

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Statistics::Basic::Covariance(3pm)			User Contributed Perl Documentation			Statistics::Basic::Covariance(3pm)

NAME
Statistics::Basic::Covariance - find the covariance between two lists SYNOPSIS
Invoke it this way: my $covariance = covariance( [1,2,3], [1,2,3] ); Or this way: my $v1 = vector(1,2,3); my $v2 = vector(1,2,3); my $cov = cov($v1,$v2); And then either query the values or print them like so: print "The covariance between $v1 and $v2: $covariance "; my $cq = $cov->query; my $c0 = 0+$cov; Create a 20 point "moving" covariance like so: use Statistics::Basic qw(:all nofill); my $sth = $dbh->prepare("select col1,col2 from data where something"); my $len = 20; my $cov = cov(); $cov->set_size($len); $sth->execute or die $dbh->errstr; $sth->bind_columns( my ($lhs, $rhs) ) or die $dbh->errstr; my $count = $len; while( $sth->fetch ) { $cov->insert( $lhs, $rhs ); if( defined( my $c = $cov->query ) ) { print "Covariance: $c "; } # This would also work: # print "Covariance: $cov " if $cov->query_filled; } METHODS
This list of methods skips the methods inherited from Statistics::Basic::_TwoVectorBase (things like query(), insert(), and ginsert()). new() Create a new Statistics::Basic::Covariance object. This function takes two arguments -- which can either be arrayrefs or Statistics::Basic::Vector objects. This function is called when the covariance() shortcut-function is called. query_vector1() Return the Statistics::Basic::Vector for the first vector. query_vector2() Return the Statistics::Basic::Vector object for the second vector. query_mean1() Returns the Statistics::Basic::Mean object for the first vector. query_mean2() Returns the Statistics::Basic::Mean object for the second vector. OVERLOADS
This object is overloaded. It tries to return an appropriate string for the calculation or the value of the computation in numeric context. In boolean context, this object is always true (even when empty). AUTHOR
Paul Miller "<jettero@cpan.org>" COPYRIGHT
Copyright 2012 Paul Miller -- Licensed under the LGPL SEE ALSO
perl(1), Statistics::Basic, Statistics::Basic::_TwoVectorBase, Statistics::Basic::Vector perl v5.14.2 2012-01-23 Statistics::Basic::Covariance(3pm)
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