I would like to extract all entries containing the following patterns: ccccta & ccccccccc from the following infile:
Thus, the desired outfile should look like this:
I am using the following codes to accomplish this task:
However, I would like to use one script only that will search for both patterns at once.
Any help will be greatly appreciated
I have a rather long csh script that works, but it's terribly ungraceful and takes a while from various loops. I only know enough code to get myself into trouble, so I'm looking for some guidance.
I have a large file that is separated at intervals by the same line, like this:
... (2 Replies)
Dear users,
I am new to AWK and have been battling with this one for close to a week now. Some of you did offer some help last week but I think I may not have explained myself very well. So I am trying again.
I have a dataset that has the following format where the datasets repeat every... (5 Replies)
Dear Members,
Problem is suppose i have 50 lines in a file, 40 lines last character is "\" and the remaining 10 lines are good(i mean these 10 lines do not have "\" character)
How can i remove this character from the file.
Thanks (1 Reply)
I have a file that is HTML encoded. Each line has something like this on each line..
<href=http://link.com/username.aspx>username </a> more info.. <a href=http://link.com/info1.aspx>info1</a> more code... <a href=http://link.com/info2.aspx>info2</a>
I have one goal really.. to clean up the... (2 Replies)
I'm trying to write a script that will do an ls of a location, echo it into a file, and then read that file and selectively delete files/folders, so it would go something like this:
cd $CLEAN_LOCN
ls >>$TMP_FILE
while read LINE
do
if LINE = $DONTDELETE
skip
elseif LINE =... (2 Replies)
Hi
I have an alignment file (.fasta) with ~80 sequences. They look like this-
>JV101.contig00066(+):25302-42404|sequence_index=0|block_index=4|species=JV101|JV101_4_0
GAGGTTAATTATCGATAACGTTTAATTAAAGTGTTTAGGTGTCATAATTT
TAAATGACGATTTCTCATTACCATACACCTAAATTATCATCAATCTGAAT... (2 Replies)
Hi,
I want to match the sequence id (sub-string of line starting with '>' and extract the information upto next '>' line ). Please help .
input
> fefrwefrwef X900
AGAGGGAATTGG
AGGGGCCTGGAG
GGTTCTCTTC
> fefrwefrwef X932
AGAGGGAATTGG
AGGAGGTGGAG
GGTTCTCTTC
> fefrwefrwef X937... (2 Replies)
I have two files. File1 is shown below.
>153L:B|PDBID|CHAIN|SEQUENCE
RTDCYGNVNRIDTTGASCKTAKPEGLSYCGVSASKKIAERDLQAMDRYKTIIKKVGEKLCVEPAVIAGIISRESHAGKVL
KNGWGDRGNGFGLMQVDKRSHKPQGTWNGEVHITQGTTILINFIKTIQKKFPSWTKDQQLKGGISAYNAGAGNVRSYARM
DIGTTHDDYANDVVARAQYYKQHGY
>16VP:A|PDBID|CHAIN|SEQUENCE... (7 Replies)
Hi i have a file in which i am doing some processing.
The code is as follows:
#!/bin/ksh
grep DATA File1.txt >> File2.txt
sed 's/DATA//' File2.txt | tr -d ‘ ‘ >> File4.xls
As you can see my output is going in a xl file.The output consist of four columns/feilds out of which the first... (20 Replies)
I have the following script:
awk 'FNR==NR{s+=$3;next;} { print $1 , $2, 100*$3/s }'
and the following file:
>P39PT-1224 Freq 900
cccctacgacggcattggtaatggctcagctgctccggatcccgcaagccatcttggatatgagggttcgtcggcctcttcagccaagg-cccccagcagaacatccagctgatcg
>P39PT-784 Freq 2... (2 Replies)
Discussion started by: Xterra
2 Replies
LEARN ABOUT DEBIAN
tree::simple::visitor::findbypath
Tree::Simple::Visitor::FindByPath(3pm) User Contributed Perl Documentation Tree::Simple::Visitor::FindByPath(3pm)NAME
Tree::Simple::Visitor::FindByPath - A Visitor for finding an element in a Tree::Simple hierarchy with a path
SYNOPSIS
use Tree::Simple::Visitor::FindByPath;
# create a visitor object
my $visitor = Tree::Simple::Visitor::FindByPath->new();
# set the search path for our tree
$visitor->setSearchPath(qw(1 1.2 1.2.2));
# pass the visitor to a tree
$tree->accept($visitor);
# fetch the result, which will
# be the Tree::Simple object that
# we have found, or undefined
my $result = $visitor->getResult() || die "No Tree found";
# our result's node value should match
# the last element in our path
print $result->getNodeValue(); # this should print 1.2.2
DESCRIPTION
Given a path and Tree::Simple hierarchy, this Visitor will attempt to find the node specified by the path.
METHODS
new There are no arguments to the constructor the object will be in its default state. You can use the "setSearchPath" and "setNodeFilter"
methods to customize its behavior.
includeTrunk ($boolean)
Based upon the value of $boolean, this will tell the visitor to include the trunk of the tree in the search as well.
setSearchPath (@path)
This is the path we will attempt to follow down the tree. We will do a stringified comparison of each element of the path and the
current tree's node (or the value returned by the node filter if it is set).
setNodeFilter ($filter_function)
This method accepts a CODE reference as its $filter_function argument and throws an exception if it is not a code reference. This code
reference is used to filter the tree nodes as they are collected. This can be used to customize output, or to gather specific
information from a more complex tree node. The filter function should accept a single argument, which is the current Tree::Simple
object.
visit ($tree)
This is the method that is used by Tree::Simple's "accept" method. It can also be used on its own, it requires the $tree argument to be
a Tree::Simple object (or derived from a Tree::Simple object), and will throw and exception otherwise.
getResult
This method will return the tree found at the specified path (set by the "setSearchPath" method) or "undef" if no tree is found.
getResults
This method will return the tree's that make up the path specified in "setSearchPath". In the case of a failed search, this can be used
to find the elements which did successfully match along the way.
BUGS
None that I am aware of. Of course, if you find a bug, let me know, and I will be sure to fix it.
CODE COVERAGE
See the CODE COVERAGE section in Tree::Simple::VisitorFactory for more inforamtion.
SEE ALSO
These Visitor classes are all subclasses of Tree::Simple::Visitor, which can be found in the Tree::Simple module, you should refer to that
module for more information.
AUTHOR
stevan little, <stevan@iinteractive.com>
COPYRIGHT AND LICENSE
Copyright 2004, 2005 by Infinity Interactive, Inc.
<http://www.iinteractive.com>
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
perl v5.10.1 2005-10-24 Tree::Simple::Visitor::FindByPath(3pm)