06-23-2009
What you want is "Beginning Perl for Bioinformatics" you can purchase on amazon.com. Also look into
BioPerl
10 More Discussions You Might Find Interesting
1. Shell Programming and Scripting
PROJECT: Extracting data from an employee timesheet. The timesheets are done in excel (for user ease) and then converted to .csv files that look like this (see color code key below):
,,,,,,,,,,,,,,,,,,,
9/14/2003,<-- Week Ending,,,,,,,,,,,,,,,,,,
Craig Brennan,,,,,,,,,,,,,,,,,,,... (3 Replies)
Discussion started by: kregh99
3 Replies
2. Shell Programming and Scripting
Hey guys,
I'm doing some Perl scripting for genomic data out of GenBank files...I have to extract the name of the plant, the file name, the number of bases, and all of the genes including their starting and ending positions...for example, with this GenBank file,
LOCUS NC_010093 ... (7 Replies)
Discussion started by: akreibich07
7 Replies
3. Shell Programming and Scripting
Hi ,
I have list of genbank id's and ref number in this format.
gi|9910297|ref|NM_019974.1|
I want to retrive the gene name and fuction for each genbank list. I have around 1300 gi numbers in my excel sheet.
So anybody can help me to retrive the information from NCBI through perl script... (0 Replies)
Discussion started by: shibujohn82
0 Replies
4. UNIX for Advanced & Expert Users
i want to write a perl script that gets/displays all those files having multiple links (in current directory) (4 Replies)
Discussion started by: guptesanket
4 Replies
5. Shell Programming and Scripting
Hello
Kindly help me to find out the first column from first line of a flat file in perl
I/P
9869912|20110830|00000000000013009|130|09|10/15/2010 12:36:22|W860944|N|00
9869912|20110830|00000000000013013|130|13|10/15/2010 12:36:22|W860944|N|00... (5 Replies)
Discussion started by: Pratik4891
5 Replies
6. Shell Programming and Scripting
I am trying to reverse and complement my DNA sequences. The file format is FASTA, something like this:
Now, to reverse the sequence, I should start reading from right to left. At the same should be complemented. Thus, "A" should be read as "T"; "C" should be read as "G"; "T" should be converted... (8 Replies)
Discussion started by: Xterra
8 Replies
7. Shell Programming and Scripting
I have two files containing hundreds of different sequences with the same Identifiers (ID-001, ID-002, etc.,), something like this:
Infile1:
ID-001 ATGGGAGCGGGGGCGTCTGCCTTGAGGGGAGAGAAGCTAGATACA
ID-002 ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACA
ID-003... (18 Replies)
Discussion started by: Xterra
18 Replies
8. Shell Programming and Scripting
Hi,
I am having a file of dna sequences in fasta format which look like this:
>admin_1_45
atatagcaga
>admin_1_46
atatagcagaatatatat
with many such thousands of sequences in a single file. I want to the replace the accession Id "admin_1_45" similarly in following sequences to... (5 Replies)
Discussion started by: margarita
5 Replies
9. Shell Programming and Scripting
hey!!! I have 2 files file1 is as ids.txt and is
>gi|546473186|gb|AWWX01630222.1|
>gi|546473233|gb|AWWX01630175.1|
>gi|546473323|gb|AWWX01630097.1|
>gi|546474044|gb|AWWX01629456.1|
>gi|546474165|gb|AWWX01629352.1|
file2 is sequences.fasta and is like
>gi|546473233|gb|AWWX01630175.1|... (9 Replies)
Discussion started by: harpreetmanku04
9 Replies
10. Shell Programming and Scripting
I am trying to write a bash script that would be able to read DNA sequences (each line in the file is a sequence) from a file, where sequences are separated by an empty line. I am then to find the amino acid that these DNA sequences encode per codon (each group of three literals.) For example, if I... (3 Replies)
Discussion started by: faizlo
3 Replies
LEARN ABOUT SUSE
map_slippy_fetcher
map::slippy::fetcher(n) Mapping utilities map::slippy::fetcher(n)
__________________________________________________________________________________________________________________________________________________
NAME
map::slippy::fetcher - Accessing a server providing tiles for slippy-based maps
SYNOPSIS
package require Tcl 8.4
package require Tk 8.4
package require img::png
package require map::slippy
package require map::slippy::fetcher ?0.2?
::map::slippy::fetcher fetcherName levels url
fetcherName levels
fetcherName tileheight
fetcherName tilewidth
fetcherName get tile donecmd
_________________________________________________________________
DESCRIPTION
This package provides a class for accessing http servers providing tiles for slippy-based maps.
API
::map::slippy::fetcher fetcherName levels url
Creates the fetcher fetcherName and configures it with the number of zoom levels supported by the tile server, and the url it is
listening on for tile requests.
The result of the command is fetcherName.
METHODS
fetcherName levels
This method returns the number of zoom levels supported by the fetcher object, and the tile server it is accessing.
fetcherName tileheight
This method returns the height of tiles served, in pixels.
fetcherName tilewidth
This method returns the width of tiles served, in pixels.
fetcherName get tile donecmd
This is the main method of the fetcher, retrieving the image for the specified tile. The tile identifier is a list containing three
elements, the zoom level, row, and column number of the tile, in this order.
The command refix donecmd will be invoked when the fetcher either knows the image for the tile or that no image will forthcoming.
It will be invoked with either 2 or 3 arguments, i.e.
[1] The string set, the tile, and the image.
[2] The string unset, and the tile.
These two possibilities are used to either signal the image for the tile, or that the tile has no image defined for it.
REFERENCES
[1] http://wiki.openstreetmap.org/wiki/Main_Page
KEYWORDS
http, location, map, server, slippy, tile, url, zoom
map 0.2 map::slippy::fetcher(n)