I am trying to add a static value to a field in perl. Basically, what happens is a file is created and "null" results in the fields then after some manipulation a field (AB) is split and the text from that is parsed into the desired fields. All that works great what doesn't is the line in bold where I am trying to add a static value of "VUS" to field 46. As of now it is still "Null". Thank you .
Code:
my @colsleft = map "Null",(1..$#left);
my @colsright = map "Null",(0..$#right);
while(<FH>) { # puts row of input file into $_
chomp;
my @vals = split/\t/; # this splits the line at tabs
my @mutations=split/,/,$vals[9]; # splits on comma to create an array of mutations
my ($gene,$transcript,$exon,$coding,$aa);
for (@mutations)
{
($gene,$transcript,$exon,$coding,$aa) = split/\:/; # this takes col AB and splits it at colons
grep {$transcript eq $_} keys %nms or next;
}
# warn join ("\t",$gene,$transcript,$exon,$coding,$aa);
my @out=($.,@colsleft,$_,@colsright);
$out[2]=$gene;
$out[3]=$nms{$transcript};
$out[4]=$transcript;
$out[15]=$coding;
$out[17]=$aa;
$out[45]="VUS";
I have a machine with an interface that has two different addresses on CentOS 5
eth0: 10.20.21.77
eth0:1 141.218.1.221
If I issue this command I get the result I'm looking for.
/sbin/route add -net 141.218.1.0 netmask 255.255.255.0 gw 10.20.21.77
ip route show dev eth0
141.218.1.0/24... (1 Reply)
I've got a simple log file that looks something like this:
And I need to append it to look like this:
So I just want to add a timestamp and a static (non-variable) word to each line in the file. Is there an easy scripted way to cat the file and append that data to each line....?? (4 Replies)
hello, i need help on setting my coyote linux, i've working on this for last 5 days, can't get it to work. I've been posting this message to coyote forum, and other linux forum, but haven't get any answer yet. Hope someone here can help me...... please see my attached picture first.
... (0 Replies)
Hi everyone,
I need to replace the text between two strings (html tags) and I'm having trouble figuring out how to do so. I can display the text with sed but I'm not having any luck deleting the text between the two strings.
My file looks like this:
<oths>test</oths><div class="text">1928... (2 Replies)
As an addition to our ongoing investigation into static code analysis tools for a Perl programming we are maintaining, can anyone recommend a certain tool that he/she is experienced with?
We are already actively using perl::critic (Perl::Critic) and rats... (2 Replies)
I'm writing a program which uses curl to be run on Linux PCs which will be used by a number of different users. I cannot make the users all install curl on their individual machines, so I have tried to link curl in statically, rather than using libcurl.so. I downloaded the source and created a... (8 Replies)
Hi All
I need to add a line to a file but after a certain block of text is found
The block of text looks like this
<RDF:Description RDF:about="urn:mimetype:video/quicktime"
NC:value="video/quicktime"
and i need to add this in the next line down ( note there is... (4 Replies)
I am trying to use awk skip each line with a ## or # and check each line after for STB= and if that value in greater than or = to 0.8, then at the end of line the text "STRAND BIAS" is written in else "GOOD".
So in the file of 4 entries attached.
awk tried:
awk NR > "##"' "#" -F"STB="... (6 Replies)
Below code extracts multiple field values from XML into array and prints all in one line.
perl -nle '@r=/(?: jndiName| authDataAlias| value| minConnections| maxConnections| connectionTimeout| name)="(+)/g and print join ",",$ENV{tIPnSCOPE},$ENV{pr
ovider},$ENV{impClassName},@r' server.xml
... (4 Replies)
Discussion started by: kchinnam
4 Replies
LEARN ABOUT DEBIAN
bio::seqfeature::gene::transcripti
Bio::SeqFeature::Gene::TranscriptI(3pm) User Contributed Perl Documentation Bio::SeqFeature::Gene::TranscriptI(3pm)NAME
Bio::SeqFeature::Gene::TranscriptI - Interface for a feature representing a
transcript of exons, promoter(s), UTR, and a poly-adenylation site.
SYNOPSIS
#documentation needed
DESCRIPTION
A feature representing a transcript.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably
to one of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Hilmar Lapp
Email hlapp@gmx.net
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
promoters
Title : promoters()
Usage : @proms = $transcript->promoters();
Function: Get the promoter features of this transcript.
Note that OO-modeling of regulatory elements is not stable yet.
This means that this method might change or even disappear in a
future release. Be aware of this if you use it.
Returns : An array of Bio::SeqFeatureI implementing objects representing the
promoter regions or sites.
Args :
exons
Title : exons()
Usage : @exons = $transcript->exons();
@inital = $transcript->exons('Initial');
Function: Get the individual exons this transcript comprises of, or all exons
of a specified type.
Refer to the documentation of the class that produced this
transcript object for information about the possible types.
See Bio::SeqFeature::Gene::ExonI for properties of the
returned objects.
Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
Args : An optional string specifying the type of the exon.
introns
Title : introns()
Usage : @introns = $transcript->introns();
Function: Get all introns this transcript comprises of.
Returns : An array of Bio::SeqFeatureI implementing objects representing the
introns.
Args :
poly_A_site
Title : poly_A_site()
Usage : $polyAsite = $transcript->poly_A_site();
Function: Get the poly-adenylation site of this transcript.
Returns : A Bio::SeqFeatureI implementing object.
Args :
utrs
Title : utrs()
Usage : @utr_sites = $transcript->utrs();
Function: Get the UTR regions this transcript comprises of.
See Bio::SeqFeature::Gene::ExonI for properties of the
returned objects.
Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
Args :
mrna
Title : mrna()
Usage : $mrna = $transcript->mrna();
Function: Get the mRNA of the transcript as a sequence object.
Returns : A Bio::PrimarySeqI implementing object.
Args :
cds
Title : cds()
Usage : $cds = $transcript->cds();
Function: Get the CDS (coding sequence) of the transcript as a sequence
object.
Returns : A Bio::PrimarySeqI implementing object.
Args :
protein
Title : protein()
Usage : $protein = $transcript->protein();
Function: Get the protein encoded by the transcript as a sequence object.
Returns : A Bio::PrimarySeqI implementing object.
Args :
parent
Title : parent
Usage : $obj->parent($newval)
Function: get the parent gene of the transcript
Returns : value of parent - a Bio::SeqFeature::Gene::GeneStructureI-compliant object
Args : a Bio::SeqFeature::Gene::GeneStructureI-compliant object (optional)
perl v5.14.2 2012-03-02 Bio::SeqFeature::Gene::TranscriptI(3pm)
02-03-2016
.