10 More Discussions You Might Find Interesting
1. UNIX for Beginners Questions & Answers
I have a variation table (variation.txt) which is a very big file. The first column in the chromosome number and the second column is the position of the variation. I have a second file annotation.txt which has a list of 37,000 genes (1st column), their chromosome number(2nd column), their start... (1 Reply)
Discussion started by: Sanchari
1 Replies
2. UNIX for Dummies Questions & Answers
Hi,
I would like to know how can I get the ID of a feature if its genomic coordinates overlap the coordinates of another file. Example:
Get the 4th column (ID) of this file1:
chr1 10 100 gene1
chr2 3000 5000 gene2
chr3 200 1500 gene3
if it overlaps with a feature in this file2:
chr2... (1 Reply)
Discussion started by: fadista
1 Replies
3. UNIX for Dummies Questions & Answers
Hi,
I would like to have the length of a segment based on coordinates of its parts.
Example input file:
chr11 genes_good3.gtf aggregate_gene 1 100 gene1
chr11 genes_good3.gtf exonic_part 1 60
chr11 genes_good3.gtf exonic_part 70 100
chr11 genes_good3.gtf aggregate_gene 200 1000 gene2... (2 Replies)
Discussion started by: fadista
2 Replies
4. Shell Programming and Scripting
Hello all, this might be better suited for a bioinformatics forum, but I thought I'd try my luck here as well.
I have several tabular text files of DNA sequence reads that appear as such:
File_1.txt
>H01BA45XW GATTACAGATTCGACATCCAACTGAGGCATT
>H02BG78WR CCTTACAGACTGGGCATGAATATTGCATACC... (3 Replies)
Discussion started by: vectorborne5
3 Replies
5. Shell Programming and Scripting
Hi guys. Can anyone tell me how to determine points between two coardinates. For example: Which type of command line gives me
50 points between (8, -5, 7) and (2, 6, 9) points
Thanks (5 Replies)
Discussion started by: rpf
5 Replies
6. Shell Programming and Scripting
Hi,
I have this problem on how to place the cursor in a text editor (for example: pico).
I made this script that would attach comments to a script file then open the script file,
I would like to know how to place the cursor in a specific place,
for example at the end of the comments,
... (1 Reply)
Discussion started by: lechelle
1 Replies
7. Shell Programming and Scripting
Hi
I have a file whose sample contents are shown here,
1.2.3.4->2.4.2.4 a(10) b(20) c(30)
1.2.3.4->2.9.2.4 a(10) c(20)
2.3.4.3->3.6.3.2 b(40) d(50) c(20)
2.3.4.3->3.9.0.2 a(40) e(50) c(20)
1.2.3.4->3.4.2.4 a(10) c(30)
6.2.3.4->2.4.2.5 c(10)
.
.
.
.
Here I need to search... (5 Replies)
Discussion started by: AKD
5 Replies
8. Shell Programming and Scripting
hi,
i have a pair of latitude and longitude and i want to calculate the distance between these two points. In vbscript i achieved in the following way...Now i want to implement this in unix shell scripting....
<%
Dim lat1, lon1, lat2, lon2
const pi = 3.14159265358979323846
... (8 Replies)
Discussion started by: aemunathan
8 Replies
9. Shell Programming and Scripting
Hello,
I am starting up an Xnest window and trying to place a program inside of it. I have the window inside of it now but it always spawns with the top left corner at (0, 0). I need to find a way to set the x and y coordinates to something other than (0, 0). I tried using the -geometry option... (1 Reply)
Discussion started by: lesnaubr
1 Replies
10. Shell Programming and Scripting
I have duplicates records in a file, but they are not consecutive. I want to remove the duplicates , using script.
Can some one help me in writing a ksh script to implement this task.
Ex file is like below.
1234
5689
4556
1234
4444 (7 Replies)
Discussion started by: Srini75
7 Replies
Geography::NationalGrid::TW(3pm) User Contributed Perl Documentation Geography::NationalGrid::TW(3pm)
NAME
Geography::NationalGrid::TW - Module to convert Taiwan Datum (TWD67/TM2, TWD97/TM2) to/from Latitude and Longitude
SYNOPSIS
You should _create_ the object using the Geography::NationalGrid factory class, but you still need to know the object interface, given
below.
use Geography::NationalGrid;
use Geography::NationalGrid::TW;
# default TWD97
my $point1 = new Geography::NationalGrid::TW(
'Easting' => 302721.36,
'Northing' => 2768851.3995,
);
printf("Point 1 is %f X and %f Y
", $point1->easting, $point1->northing);
printf("Point 1 is %f N and %f E
", $point1->latitude, $point1->longitude);
# transform to TWD67
$point1->transform('TWD67');
DESCRIPTION
Once created, the object allows you to retrieve information about the point that the object represents. For example you can create an
object using easting / northing and the retrieve the latitude / longitude.
OPTIONS
These are the options accepted in the constructor. You MUST provide either Latitude and Longitude, or Easting and Northing.
Projection
Default is 'TWD97', the "TAIWAN DATUM 97". Another projection recognized is 'TWD67', but only 'TWD97' is tested.
GridReference
There is no grid reference in Taiwan datum. Grid related functions are disabled.
Latitude
The latitude of the point. Actually should be the latitude using the spheroid related to the grid projection but for most purposes the
difference is not too great. Specify the amount in any of these ways: as a decimal number of degrees, a reference to an array of three
values (i.e. [ $degrees, $minutes, $seconds ]), or as a string of the form '52d 13m 12s'. North is positive degrees, south is negative
degrees.
Longitude
As for latitude, except that east is positive degrees, west is negative degrees.
Easting
The number of metres east of the grid origin, using grid east.
Northing
The number of metres north of the grid origin, using grid north.
Userdata
The value of this option is a hash-reference, which you can fill with whatever you want - typical usage might be to specify "Userdata
=" { Name => 'Dublin Observatory' }> but add whatever you want. Access using the data() method.
METHODS
Most of these methods take no arguments. Some are inherited from Geography::NationalGrid
latitude
Returns the latitude of the point in a floating point number of degrees, north being positive.
longitude
As latitude, but east is positive degrees.
easting
How many metres east of the origin the point is. The precision of this value depends on how it was derived, but is truncated to an
integer number of metres.
northing
How many metres north of the origin the point is. The precision of this value depends on how it was derived, but is truncated to an
integer number of metres.
deg2string( DEGREES )
Given a floating point number of degrees, returns a string of the form '51d 38m 34.34s'. Intended for formatting, like:
$self->deg2string( $self->latitude );
data( PARAMETER_NAME )
Returns the item from the Userdata hash whose key is the PARAMETER_NAME.
transform( PROJECTION )
Transform the point to the new projection, i.e. TWD67 to TWD97 or reverse. Return the point after transformation and keep original
point intact. Uses the formula proposed by John Hsieh which is supposed to provide 2 meter accuracy conversions.
ACCURACY AND PRECISION
The routines used in this code may not give you completely accurate results for various mathematical and theoretical reasons. In tests the
results appeared to be correct, but it may be that under certain conditions the output could be highly inaccurate. It is likely that output
accuracy decreases further from the datum, and behaviour is probably divergent outside the intended area of the grid.
This module has been coded in good faith but it may still get things wrong. Hence, it is recommended that this module is used for
preliminary calculations only, and that it is NOT used under any circumstance where its lack of accuracy could cause any harm, loss or
other problems of any kind. Beware!
REFERENCES
http://wiki.osgeo.org/wiki/Taiwan_datums
John Hsieh - http://gis.thl.ncku.edu.tw/coordtrans/coordtrans.aspx
AUTHOR AND COPYRIGHT
Copyright (c) 2006 Yen-Ming Lee "<leeym@leeym.com>". All rights reserved. This program is free software; you can redistribute it and/or
modify it under the same terms as Perl itself.
perl v5.10.0 2009-09-06 Geography::NationalGrid::TW(3pm)