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  • How can I save BioPerl sequence nested features in genbank or embl format?

    - by Ryan Thompson
    In BioPerl, a sequence object can have any number of features, and each of these can have subfeatures nested within them. For example, a feature may be a complete coding sequence of a gene, and its subfeatures might be individual exons that are concatenated to form the full coding sequence. However, when I use BioPerl to write a sequence object to a file in genbank or embl format, only the top-level features are written to the file, not the sub-features nested within the top-level features. How can I store my subfeatures in sequence files? Should I just convert all my subfeatures into top-level features, and then reconstruct the tree structure next time I read in the sequence?

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  • How to redirect output away from /dev/null

    - by Gowtham
    I have an application that runs the a command as below: <command> >& /dev/null I have no control on this. All the o/p generated by this command goes to /dev/null. I want the output to be visible on screen or redirected to a log file. I tried to use freopen() and related functions to reopen /dev/null to another file, but could not get it working. Do you have any other ideas? Is this possible at all? Thanks for your time. PS: I am working on Linux. -Gowtham

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  • Parsing line and selecting values corresponding to a key

    - by gagneet
    there is a set of data which is arranged in a specific manner (as a tree), as is given below. basically a key=value pair, with some additional values at the end, which informs how many children does the branch have and some junk value. 11=1 123 2 11=1>1=45 234 1 11=1>1=45>9=16 345 1 11=1>1=45>9=16>2=34 222 1 11=1>1=45>9=16>2=34>7=0 2234 1 11=1>1=45>9=16>2=34>7=0>8=0 22345 1 11=1>1=45>9=16>2=34>7=0>8=0>0=138 22234 1 11=1>1=45>9=16>2=34>7=0>8=0>0=138>5=0 5566 1 11=1>1=45>9=16>2=34>7=0>8=0>0=138>5=0>4=0 664 1 11=1>1=45>9=16>2=34>7=0>8=0>0=138>5=0>4=0>6=10 443 1 11=1>1=45>9=16>2=34>7=0>8=0>0=138>5=0>4=0>6=10>3=11 445 0 11=1>1=47 4453 1 11=1>1=47>9=16 887 1 11=1>1=47>9=16>2=34 67 1 11=1>1=47>9=16>2=340>7=0 98 1 11=1>1=47>9=16>2=34>7=0>8=0 654 1 11=1>1=47>9=16>2=34>7=0>8=0>0=138 5789 1 11=1>1=47>9=16>2=34>7=0>8=0>0=138>5=0 9870 1 11=1>1=47>9=16>2=34>7=0>8=0>0=138>5=0>4=0 3216 1 11=1>1=47>9=16>2=34>7=0>8=0>0=138>5=0>4=0>6=10>3=11 66678 0 my problem is to get the appropriate branch from the above data, which satisfies exactly the values, which i give as the input. suppose, my input value to search in the above data stack are: 5=0 4=0 6=10 3=11 11=1 1=45 0=138 9=16 2=34 7=0 8=0 for the above given list of key-values, the function should return 11=11=459=162=347=08=00=1385=04=06=103=11 as the match. likewise, for another input file, in which another set of keys is given: 5=0 4=0 6=10 3=11 11=1 1=45 9=16 2=34 7=0 8=0 the function should return 11=11=459=162=347=08=0 1 as the match. not the last line; as that would also match all the values given in my input key, but, i want only the exact match. Also, I want to find out how many nodes were selected in the given array. (separated by ). What will be the best way to implement this kind of scenario?

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  • Array comparison

    - by devtech
    I have two arrays A & B. I want to do a compare among the elements of the two arrays. @a = "abc,def,efg,ghy,klm,ghn" @b = "def,ghy,jgk,lom,com,klm" If any element matches then set a flag 0 else 1. Is there any simple way to do this? Please advise.

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  • Parse and display MIME multipart email on website

    - by aidan
    I have a raw email, (MIME multipart), and I want to display this on a website (e.g. in an iframe, with tabs for the HTML part and the plain text part, etc.). Are there any CPAN modules or Template::Toolkit plugins that I can use to help me achieve this? At the moment, it's looking like I'll have to parse the message with Email::MIME, then iterate over all the parts, and write a handler for all the different mime types. It's a long shot, but I'm wondering if anyone has done all this already? It's going to be a long and error prone process writing handlers if I attempt it myself. Thanks for any help.

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  • DateTime::Astro::Sunrise is giving bad values

    - by BozoJoe
    Using the example code included in the man page for DateTime::Astro::Sunrise I'm getting back ~14:00 for the sunrise and ~2:00 for the sunset. my machine's time and timezone are set correctly (AFAIK) Am I reading something wrong? 2am and 2pm are just so brutually wrong.

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  • Is this trivial function silly?

    - by Chas. Owens
    I came across a function today that made me stop and think. I can't think of a good reason to do it: sub replace_string { my $string = shift; my $regex = shift; my $replace = shift; $string =~ s/$regex/$replace/gi; return $string; } The only possible value I can see to this is that it gives you the ability to control the default options used with a substitution, but I don't consider that useful. My first reaction upon seeing this function get called is "what does this do?". Once I learn what it does, I am going to assume it does that from that point on. Which means if it changes, it will break any of my code that needs it to do that. This means the function will likely never change, or changing it will break lots of code. Right now I want to track down the original programmer and beat some sense into him or her. Is this a valid desire, or am I missing some value this function brings to the table?

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  • Escape Single Quotes in Template Toolkit

    - by Zach
    Do you ever escape single quotes in template toolkit for necessary javascript handlers? If so, how do you do it. [% SET s = "A'B'C" %] <a href="/abc.html" onclick="popup('[% s | html_entity %]')">ABC</a> html_entity obviously doesn't work because it only handles the double quote. So how do you do it?

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  • Regex for capturing number in brackets

    - by neversaint
    I have a lines like this NF419andZNF773 (e=10^-92,). ZNF571 (e=2 10^-14,) What's the regex for extracting the results above so that it gives NF419andZNF773 - 10^-92 ZNF571 - 2 10^-14 I tried this but fail. $line =~ /(\w+)\s\(e=\s(.*),\)/; print "$1 - $2\n";

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  • How can I modify a scalar reference passed to a subroutine reference

    - by Mark
    I have a function to convert documents into different formats, which then calls another function based on the type document. It's pretty straight forward for everything aside from HTML documents which require a bit of cleaning up, and that cleaning up is different based on where it's come from. So I had the idea that I could pass a reference to a subroutine to the convert function so the caller has the opportunity to modify the HTML, kinda like so (I'm not at work so this isn't copy-and-pasted): package Converter; ... sub convert { my ($self, $filename, $coderef) = @_; if ($filename =~ /html?$/i) { $self->_convert_html($filename, $coderef); } } sub _convert_html { my ($self, $filename, $coderef) = @_; my $html = $self->slurp($filename); $coderef->(\$html); #this modifies the html $self->save_to_file($filename, $html); } which is then called by: Converter->new->convert("./whatever.html", sub { s/<html>/<xml>/i }); I've tried a couple of different things along these lines but I keep on getting 'Use of uninitialized value in substitution (s///)'. Is there any way of doing what I'm trying to do? Thanks

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  • How do I store and retrieve TimeUUIDType types with Net::Cassandra::Easy?

    - by Holden Robbins
    Doing the following: my $c = Net::Cassandra::Easy->new(server => 'localhost', port => '9160', keyspace => 'Keyspace1'); $c->connect(); my $uuid_bin = Data::UUID->new()->create_bin(); eval { $result = $c->mutate([$key], family => 'StandardByUUID1', insertions => { $uuid_bin => '123' }); }; warn $@ if $@; Result is a: Net::GenCassandra::InvalidRequestException I didn't see anything similar to Net::Cassandra::Easy::pack_decimal for UUIDs.

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  • Could someone please explain this REGEX?

    - by NJTechGuy
    if($title =~ s/(\s|^|,|\/|;|\|)$replace(\s|$|,|\/|;|\|)//ig) $title can be a set of titles ranging from President, MD, COO, CEO,... $replace can be (shareholder), (Owner) or the like. I keep getting this error. I have checked for improperly balanced '(', ')', no dice :( Unmatched ) in regex; marked by <-- HERE in m/(\s|^|,|/|;|\|)Owner) <-- HERE (\s|$|,|/|;|\|)/ If you could tell me what the regex does, that had be awesome. It strips those symbols is it? Sorry long day at work. Thanks guys!

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  • Regex take too long to match the result

    - by Joe Ijam
    Hi all I have this regex pattern <(\d+)>(\d+\.\d+|\d{4}\-\d+\-\d+\s+\d{2}:\d{2}:\d{2})(?:\..*?)*\s+(ALER|NOTI) and this is my input (will not matched at all) <150>2010-12-29 18:11:30.883 -0700 192.168.2.145 80 192.168.2.87 2795 "-" "-" GET HTTP 192.168.2.145 HTTP/1.1 200 36200 0 1038 544 192.168.2.221 80 540 SERVER DEFAULT PASSIVE VALID /joomla/ "-" http://192.168.2.145/joomla/index.php?option=com_content&view=a be4d44e8f3986183a87991398c1c212e=1; be4d44e8f3986183a87991398c1c212e=1 This will return not matched result but it takes too long to output the result. Since i have a thousand of logs/inputs in a second, it should finish very fast for every single log/input. Sometime it reaches CPU 100%. Can anyone help me to solve this regex problem? Thanks

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  • how to find the last instance of a setting in a config file

    - by Glenn Kelley
    I am trying to figure out how to find the last entry of a string in multiple config files across a server. Each of the strings will be in the /home/***usernamewouldbehere/public_html/typo3conf/localconf.php file In short - the last entry in the config files will point to the database server the application is utilizing - and we need to know which accounts point to which db server. While I can run something like this - grep "$_db_host" /home/*/public_html/conf/localconf.php It does not really help much because it gives us way to much information ... and not what we really need. What i really need to know is the last entry of this string $_db_host = 'xx'; and to sort them out in an export file Since the config files may have multiple entries (example below) $_db_host = 'localhost'; $_db_host = '10.0.1.234'; It would be great to list in a file all of those that have the entry for 'localhost' and then list all of those that have the entry for '10.0.1.234' (or whichever server there may be there) but even if I need to do that manually that would be great. I am not sure how to get to it using Awk - ... and really stuck What I am hoping for is something that would be piped as follows db_host = localhost /home/username1/www/conf/localconf.php db_host = localhost / home/username2/public_html/conf/localconf.php db_host= '10.1.2.23' /home/username55/public_html/conf/localconf.php hoping that helps you help me :-)

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  • How can I write a Template.pm filter to generate PNG output from LaTeX source code?

    - by Sinan Ünür
    I am looking for a way of generating PNG images of equations from LATEX source code embedded in templates. For example, given: [% FILTER latex_display ] \begin{eqnarray*} \max && U(x,y) \\ \mathrm{s.t.} && p_x x + p_y y \leq I \\ && x \geq 0, y \geq 0 \end{eqnarray*} [% END %] I would like to get the output: <div class="latex display"><img src="equation.png" width="x" height="y"></div> which should ultimately display as: I am using ttree to generate documents offline. I know about Template::Plugin::Latex but that is geared towards producing actual documents out of LATEX templates. Any suggestions?

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  • How do I set up my own proxy server?

    - by NJTechGuy
    This website (abc.com) slowed access from our original IP address. How do I implement my own proxy server to hide my IP while browsing abc.com? Do I need special hardware/software combo to achieve this? If I can generate about 5 proxies and alternate amongst those 5 while browsing abc.com would be awesome. Please suggest. Thanks guys!

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  • can't create socket using IO::Socket

    - by Haiyuan Zhang
    when I run the following code, the execution is just hanging there, No response at all. does any of you can tell me what's wrong with the sample code? use strict; use warnings; use IO::Select; use IO::Socket; my $s = new IO::Socket ( LocalPort => 8889, Proto => 'tcp', Listen => 16, Reuse => 1 ); die "could not create socket $!\n" unless $s;

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  • Can't modify constant item in scalar assignment

    - by joe
    sub new { my $class = shift; my $ldap_obj = Net::LDAP->new( 'test.company.com' ) or die "$@"; my $self = { _ldap = $ldap_obj, _dn ='dc=users,dc=ldap,dc=company,dc=com', _dn_login = 'dc=login,dc=ldap,dc=company,dc=com', _description ='company', }; # Print all the values just for clarification. bless $self, $class; return $self; } what is wrong on this code : i got this error Can't modify constant item in scalar assignment at Core.pm line 12, near "$ldap_obj,"

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