sorry this was my first post, so I didn't have much idea.
Regarding problem:
It is a particular gene position in the whole genome, now this gene is madeup of CDS, mRNA, Introns etc..the information is right below it like:
etc..until the information of next gene comes..
like: (say gene2)
So I have file with these 'gene' location, now I need to extract its sub-location, like whether its in CDS, mRNA or Intron(in case no match found).
The location of gene(that we need to find) is in separate file:
I have to read it line by line, extract gene position, then search it in the main gene info. (gff) file. like:
note: '..' denotes FROM postion 52698648 TO 52707224.
Last edited by reena2305; 06-28-2011 at 01:32 AM..
Good evening All,
I have a perl script to pull out all occurrences of a files beginning with xx and ending in .p. I will then loop through all 1K files in a directory. I can grep for xx*.p files but it gives me the entire line. I wish to output to a single colum with only the hits found. ... (3 Replies)
Create a script that copies files from one specified directory to another specified directory, in the order they were created in the original directory between specified times. Copy the files at a specified interval. (2 Replies)
Hi,
I am logging to a linux server through a user "user1" in /home directory.
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When the script is added to crontab, on... (1 Reply)
Hey,
I've been trying to break a massive fasta formatted file into files containing each gene separately. Could anyone help me? I've tried to use the following code but i've recieved errors every time:
for i in *.rtf.out
do
awk '/^>/{f=++d".fasta"} {print > $i.out}' $i
done (1 Reply)
I have a file with
<suit:run date="Trump Tue 06/19/2012 11:41 AM EDT" machine="garg-ln" build="19921" level="beta" release="6.1.5" os="Linux">
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I have hundreds of files to process. In each file
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extract value(s) from next line and then
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HEADER ELECTRON TRANSPORT 18-MAR-98 1A7V
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Hi
This is my third past and very impressed with previous post replies
Hoping the same for below query
How to find a existing file location and directory location in solaris box (1 Reply)
Hi,
I have a log file which is the output from a xml script :
<?xml version="1.0" ?>
<!DOCTYPE svc_result SYSTEM "MLP_SVC_RESULT_320.DTD">
<svc_result ver="3.2.0">
<slia ver="3.0.0">
<pos>
<msid type="MSISDN" enc="ASC">8093078040</msid>
<poserr>
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I have the following data set about the snps ID txt file
POS ID
78599583 rs987435
33395779 rs345783
189807684 rs955894
33907909 rs6088791
75664046 rs11180435
218890658 rs17571465
127630276 rs17011450
90919465 rs6919430
and a gene... (7 Replies)
I want to search a small string in a large string and find the locations of the string. For this I used grep "string" -ob <file name where the large string is stored>. Now this gives me the locations of that string. Now how do I store these locations in a text file.
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Discussion started by: ANKIT ROY
7 Replies
LEARN ABOUT DEBIAN
bio::graphics::glyph::gene
Bio::Graphics::Glyph::gene(3pm) User Contributed Perl Documentation Bio::Graphics::Glyph::gene(3pm)NAME
Bio::Graphics::Glyph::gene - A GFF3-compatible gene glyph
SYNOPSIS
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
DESCRIPTION
This glyph is used for drawing genes that may have alternatively-spliced transcripts. The various isoforms are stacked on top of each other
and given a single label and description that apply to the entire stack. Each individual transcript's name is optionally printed to the
left of the transcript glyph.
Transcripts (splice isoforms) are drawn using the processed_transcript glyph. CDS features are drawn in the background color, and the UTRs
are drawn in an alternate color selected by the utr_color option. In addition, you can make the UTRs thinner than the CDS by setting the
"thin_utr" option.
This glyph is designed to work properly with GFF3-style three-tier genes, in which the top level feature has the Sequence Ontology type of
"gene", the second level feature(s) have the SO type "mRNA", and the third level feature(s) have the SO type "CDS", "five_prime_utr" and
"three_prime_utr." Subparts named "UTR" are also honored. The feature can contain other subparts as well (e.g. exon, intron,
translation), but they are currently ignored unless the option sub_part is supplied. If the sub_part option is used that feature type will
be used and CDS and UTR features will be excluded. This could be used for specifying that exons be used instead, for example.
This glyph is a subclass of processed_transcript, and recognizes the same options.
OPTIONS
The following options are standard among all Glyphs. See Bio::Graphics::Glyph for a full explanation.
Option Description Default
------------------------
-fgcolor Foreground color black
-outlinecolor Synonym for -fgcolor
-bgcolor Background color turquoise
-fillcolor Synonym for -bgcolor
-linewidth Line width 1
-height Height of glyph 10
-font Glyph font gdSmallFont
-connector Connector type undef (false)
-connector_color
Connector color black
-label Whether to draw a label undef (false)
-description Whether to draw a description undef (false)
-strand_arrow Whether to indicate undef (false)
strandedness
-hilite Highlight color undef (no color)
In addition, the gene glyph recognizes the following glyph-specific options:
Option Description Default
------------------------
-label_transcripts undef (false)
Flag. If true, then the
display name of each
transcript will be drawn
to the left of the transcript
glyph.
-thin_utr Flag. If true, UTRs will undef (false)
be drawn at 2/3 of the
height of CDS segments.
-utr_color Color of UTR segments. Gray #D0D0D0
-decorate_introns
Draw strand with little arrows undef (false)
on the intron.
The -adjust_exons and -implied_utrs options are inherited from processed_transcript, but are quietly ignored. Please use the
processed_transcript glyph for this type of processing.
BUGS
The SO terms are hard-coded. They should be more flexible and should recognize ISA relationships.
SEE ALSO
Bio::Graphics::Panel, Bio::Graphics::Glyph, Bio::Graphics::Glyph::arrow, Bio::Graphics::Glyph::cds, Bio::Graphics::Glyph::crossbox,
Bio::Graphics::Glyph::diamond, Bio::Graphics::Glyph::dna, Bio::Graphics::Glyph::dot, Bio::Graphics::Glyph::ellipse,
Bio::Graphics::Glyph::extending_arrow, Bio::Graphics::Glyph::generic, Bio::Graphics::Glyph::graded_segments,
Bio::Graphics::Glyph::heterogeneous_segments, Bio::Graphics::Glyph::line, Bio::Graphics::Glyph::pinsertion, Bio::Graphics::Glyph::primers,
Bio::Graphics::Glyph::rndrect, Bio::Graphics::Glyph::segments, Bio::Graphics::Glyph::ruler_arrow, Bio::Graphics::Glyph::toomany,
Bio::Graphics::Glyph::transcript, Bio::Graphics::Glyph::transcript2, Bio::Graphics::Glyph::translation, Bio::Graphics::Glyph::triangle,
Bio::DB::GFF, Bio::SeqI, Bio::SeqFeatureI, Bio::Das, GD
AUTHOR
Lincoln Stein <lstein@cshl.org>
Copyright (c) 2001 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
perl v5.14.2 2012-02-20 Bio::Graphics::Glyph::gene(3pm)