03-03-2009
I found the unix command to be useful.
cat filename | sort | uniq -c | sort -nr
What if I am using a tab-delimited text file with multiple columns?
Example:
S100A16 hsa-miR-125a-3p S100A16 0.0011959 0.768059
PBXIP1 hsa-miR-125a-3p PBXIP1 0.0199898 0.700326
CYB5R3 hsa-miR-125a-3p CYB5R3 0.0081174 0.748953
BEST3 hsa-miR-125a-3p BEST3 0.00148927 0.756234
FAM101A hsa-miR-125a-3p FAM101A 0.0196212 0.783555
KIAA0195 hsa-miR-125a-3p KIAA0195 0.0019755 0.747427
LLGL2 hsa-miR-125a-3p LLGL2 0.0248212 0.876563
FBLN5 hsa-miR-125a-3p FBLN5 0.0162988 0.776446
IFITM3 hsa-miR-125a-3p IFITM3 0.00896808 0.478704
SSH3 hsa-miR-125a-3p SSH3 0.0301693 0.836054
EXTERNAL_NAME SEQ EXTERNAL_NAME p-value(1 vs. 2) Ratio(1 vs. 2)
EMILIN1 hsa-miR-369-5p EMILIN1 0.0254294 0.720094
ADD3 hsa-miR-369-5p ADD3 0.0184075 0.742096
AIFM2 hsa-miR-369-5p AIFM2 0.00646348 0.829228
GPT2 hsa-miR-369-5p GPT2 0.00473291 0.706895
and I want the output to read
10 hsa-miR-125a-3p
4 hsa-miR-369-5p
1 SEQ
Initially, I made a new file, composing only the column of interest, using perl (column 1 here), named it filenam_list; then applied the
cat filenam_list | sort | uniq -c | sort -nr > filename_counts
rm filenam_list
Is there a more efficient way of doing this? I'm sure there has to be. I repeated the procedure on 7 files and I have to it again.
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LEARN ABOUT MOJAVE
xml::xpath::nodeset5.18
XPath::NodeSet(3) User Contributed Perl Documentation XPath::NodeSet(3)
NAME
XML::XPath::NodeSet - a list of XML document nodes
DESCRIPTION
An XML::XPath::NodeSet object contains an ordered list of nodes. The nodes each take the same format as described in XML::XPath::XMLParser.
SYNOPSIS
my $results = $xp->find('//someelement');
if (!$results->isa('XML::XPath::NodeSet')) {
print "Found $results
";
exit;
}
foreach my $context ($results->get_nodelist) {
my $newresults = $xp->find('./other/element', $context);
...
}
API
new()
You will almost never have to create a new NodeSet object, as it is all done for you by XPath.
get_nodelist()
Returns a list of nodes. See XML::XPath::XMLParser for the format of the nodes.
string_value()
Returns the string-value of the first node in the list. See the XPath specification for what "string-value" means.
to_literal()
Returns the concatenation of all the string-values of all the nodes in the list.
get_node($pos)
Returns the node at $pos. The node position in XPath is based at 1, not 0.
size()
Returns the number of nodes in the NodeSet.
pop()
Equivalent to perl's pop function.
push(@nodes)
Equivalent to perl's push function.
append($nodeset)
Given a nodeset, appends the list of nodes in $nodeset to the end of the current list.
shift()
Equivalent to perl's shift function.
unshift(@nodes)
Equivalent to perl's unshift function.
prepend($nodeset)
Given a nodeset, prepends the list of nodes in $nodeset to the front of the current list.
perl v5.18.2 2002-09-02 XPath::NodeSet(3)