Utility msort allows fields to be described as hybrid, mixed characters and numeric:
producing:
See link listed in script if msort is not your repository ... cheers, drl
Hi All,
I am having a pipe delimited file .In this file the 3rd column is having date values.I need to get the min date and max date from that file.
I have used
cut -d '|' test.dat -f 3|sort -u
But it is not sorting the date .How to sort the date column using unix commands
Thanks ... (4 Replies)
I want to sort alphabetically on the first field and sort in descending numerical order on the 2nd field. With a normal "sort -r -n" it does this:
abc ||| 5e-05 ||| bla
abc ||| 3 ||| ble
def ||| 1 ||| abc
def ||| 0.2 ||| def
As you can see it ignores the fact that 5e-05 is actually 0.00005... (1 Reply)
Can some one provide me a shell script.
I have file with many columns and many rows. need to sort the first column and then remove the duplicates records if exists.. finally print the full data with first coulm as unique.
Sort BASED ON FIRST FIELD and remove the duplicates if exists... (2 Replies)
I have a csv flatfile with a few million rows. I need to replace a field (field number is 85) in the file with a sequential number.
As an example, let's assume there are only 4 fields in the file:
A,A,,32
A,A,,27
A,B,,43
C,C,,354
If I wanted to amend the 3rd field in this way my... (2 Replies)
Experts
I have a list of files in the directory
mysample1
mysample2
mysample3
mysample4
mysample5
mysample6
mysample7
mysample8
mysample9
mysample10
mysample11
mysample12
mysample13
mysample14
mysample15 (4 Replies)
I have a file (input) I want to sort the file based on the number of times a pattern in the first column occurs for example grapes occurs 4 times in combination with other patterns so i want it to be first like shown in the output file. then apple ocuurs thrice so it occupies second position and so... (7 Replies)
I am working on a script to convert bank data to a csv file. I have the format done - columns etc. The final piece of the puzzle is to change the second field (after the R) of every line to reflect its' line number in the file. I am stumped. I can use awk on each line but need help looping through... (9 Replies)
Hi,
Need to sort file based on the number of delimeters in the lines.
cat testfile
/home/oracle/testdb
/home
/home/oracle/testdb/newdb
/home/oracle
Here delimeter is "/"
expected Output:
/home/oracle/testdb/newdb
/home/oracle/testdb
/home/oracle
/home (3 Replies)
Hello Friends
I have a data file which is comma seperate (,) where i am expecting 2 column but there are number of time when file comes with data having more than 2 column.
I want to check which line has more columns
20141115,15/11/2014
20141129,29/11/2014
20141003,03/10/2014... (4 Replies)
Discussion started by: guddu_12
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)