I have two questions which I would massively appreciate help with.
1.
I am trying to insert a field into a file similar to the vlookup function in excel. In column 2 is a gene id for which i would like to insert the full name in the adjacent column. I have a map file (map.file) which has two columns - in column 1 is the gene ID and column 2 is the full gene name
The second query I have is that i want to be able to filter the file so that the output only contains those fields where for example column 7 <0.5 and column 8 <0.3 and column 9 <0.2 (sometimes there is just a blank in the field which effectively equals 0)
Is there a way to do this so that the filtering is done based on the column header rather than the column number as I have different files which have a different arrangement of columns but with the same headers.
Write a quick shell snippet to find all of the IPV4 IP addresses
in any and all of the files under /var/lib/output/*, ignoring
whatever else may be in those files. Perform a reverse lookup on
each, and format the output neatly, like "IP=192.168.0.1,
... (0 Replies)
Hello Guys,
I want to write a script which will search for all the *.c,*.h,*.txt in the file.
The result will be again search in a .csv file.
If that .c file or .h or .txt is existing in the .csv,then put a * mark corresponding to the row in .csv file.
---------- Post updated at 05:19 AM... (2 Replies)
Hi all
I had a mail issue earlier today where I was not receiving any emails from the servers of one of our clients.
The mail queue just showed this:
-----Q-ID----- --Size-- -----Q-Time----- ------------Sender/Recipient-----------
o8S7eSpp020274* 5858 Tue Sep 28 10:42... (0 Replies)
Hi,
I've internally searched through forums for about 2+ hours. Unfortunately, with no luck. Although I've found some cases close to mine below, but didn't help so much.
Actually, I'm in short with time. So I had to post my case. Hoping that you can help.
I have 2 files,
FILE1
... (0 Replies)
Hi,
I've internally searched through forums for about 2+ hours. Unfortunately, with no luck. Although I've found some cases close to mine below, but didn't help so much.
Actually, I'm in short with time. So I had to post my case. Hoping that you can help.
I have 2 files,
FILE1
... (1 Reply)
Hi, all:
My writed network device driver works fine when the transmitted file is under several MegaBytes, but above this size, especially dozens of or hundreds of MegaBytes, the kernel panic ocurres! I check the kern.log and find this error :
522 Nov 14 19:35:32 liklstar-server kerneNov 14... (2 Replies)
I have the below 2 files:
1) Third field from file1.txt should be compared to the first field of lookup.txt.
2) If match found then third field, file1.txt should be substituted with the second field from lookup.txt.
3)Else just print the line from file1.txt.
File1.txt:... (4 Replies)
Hi All,
I don't know how to fast do this field replace that need lookup from another file to form the update result:confused:
I want to do it by general shell script
Can anyone help to solve it ? Thanks for your kindly reply in advance.
CK (0 Replies)
I have 2 fixed length files input#1 & input#2. I want to match the rows based on the value in position 37-50 in both files (pos 37-50 will have same value in both files).
If any matching record is found then cut the value against company code & Invoice number from input file #1 (position 99 until... (3 Replies)
The below awk uses $3 and $4 in search as the min and max, then takes each $2 value in lookup and compares it. If the value in lookupfalls within the range in searchthen it prints the entire line in lookup/ICODE]. What I can't seem to figure out is how to print the matching $5 from search on that... (4 Replies)
Discussion started by: cmccabe
4 Replies
LEARN ABOUT DEBIAN
bio::map::generelative
Bio::Map::GeneRelative(3pm) User Contributed Perl Documentation Bio::Map::GeneRelative(3pm)NAME
Bio::Map::GeneRelative - Represents being relative to named sub-regions of a
gene.
SYNOPSIS
use Bio::Map::GeneRelative;
# say that a somthing will have a position relative to the start of the
# gene on map
my $rel = Bio::Map::GeneRelative->new(-gene => 0);
# or that something will be relative to the third transcript of a gene
# on a map
$rel = Bio::Map::GeneRelative->new(-transcript => 3);
# or to the 5th intron of the default transcript
$rel = Bio::Map::GeneRelative->new(-intron => [0, 5]);
# use the $rel as normal; see L<Bio::Map::Relative>
DESCRIPTION
Be able to say that a given position is relative to some standard part of a gene.
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 the
Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Sendu Bala
Email bix@sendu.me.uk
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : my $relative = Bio::Map::Relative->new();
Function: Build a new Bio::Map::Relative object.
Returns : Bio::Map::Relative object
Args : -gene => int : coordinates are relative to the int'th base
downstream of the Position's map's gene
[default is gene => 0, ie. relative to the
start of the gene],
-transcript => int : or relative to the start of the int'th
transcript of the Position's map's gene,
-exon => [i, n] : or relative to the start of the n'th
transcript's i'th exon,
-intron => [i, n] : or intron,
-coding => int : or the start of the int'th transcript's coding
region.
-description => string : Free text description of what this relative
describes
(To say a Position is relative to something and upstream of it,
the Position's start() co-ordinate should be set negative)
In all cases, a transcript number of 0 means the active transcript.
absolute_conversion
Title : absolute_conversion
Usage : my $absolute_coord = $relative->absolute_conversion($pos);
Function: Convert the start co-ordinate of the supplied position into a number
relative to the start of its map.
Returns : scalar number
Args : Bio::Map::PositionI object
type
Title : type
Usage : my $type = $relative->type();
Function: Get the type of thing we are relative to. The types correspond
to a method name, so the value of what we are relative to can
subsequently be found by $value = $relative->$type;
Note that type is set by the last method that was set, or during
new().
Returns : 'gene', 'transcript', 'exon', 'intron' or 'coding'
Args : none
gene
Title : gene
Usage : my $int = $relative->gene();
$relative->gene($int);
Function: Get/set the distance from the start of the gene that the Position's
co-ordiantes are relative to.
Returns : int
Args : none to get, OR
int to set; a value of 0 means relative to the start of the gene.
transcript
Title : transcript
Usage : my $int = $relative->transcript();
$relative->transcript($int);
Function: Get/set which transcript of the Position's map's gene the Position's
co-ordinates are relative to.
Returns : int
Args : none to get, OR
int to set; a value of 0 means the active (default) transcript.
exon
Title : exon
Usage : my ($exon_number, $transcript_number) = @{$relative->exon()};
$relative->exon($exon_number, $transcript_number);
Function: Get/set which exon of which transcript of the Position's map's gene
the Position's co-ordinates are relative to.
Returns : reference to list with two ints, exon number and transcript number
Args : none to get, OR
int (exon number) AND int (transcript number) to set. The second int
is optional and defaults to 0 (meaning default/active transcript).
intron
Title : intron
Usage : my ($intron_number, $transcript_number) = @{$relative->intron()};
$relative->intron($intron_number, $transcript_number);
Function: Get/set which intron of which transcript of the Position's map's gene
the Position's co-ordinates are relative to.
Returns : reference to list with two ints, intron number and transcript number
Args : none to get, OR
int (intron number) AND int (transcript number) to set. The second
int is optional and defaults to 0 (meaning default/active
transcript).
coding
Title : coding
Usage : my $transcript_number = $relative->coding;
$relative->coding($transcript_number);
Function: Get/set which transcript's coding region of the Position's map's gene
the Position's co-ordinates are relative to.
Returns : int
Args : none to get, OR
int to set (the transcript number, see transcript())
perl v5.14.2 2012-03-02 Bio::Map::GeneRelative(3pm)