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 REDHAT
uri::url
URI::URL(3) User Contributed Perl Documentation URI::URL(3)
NAME
URI::URL - Uniform Resource Locators
SYNOPSIS
$u1 = URI::URL->new($str, $base);
$u2 = $u1->abs;
DESCRIPTION
This module is provided for backwards compatibility with modules that depend on the interface provided by the "URI::URL" class that used to
be distributed with the libwww-perl library.
The following differences compared to the "URI" class interface exist:
o The URI::URL module exports the url() function as an alternate constructor interface.
o The constructor takes an optional $base argument. The "URI::URL" class is a subclasses of "URI::WithBase".
o The URI::URL->newlocal class method is the same as URI::file->new_abs
o URI::URL::strict(1)
o $url->print_on method
o $url->crack method
o $url->full_path; same as ($uri->abs_path || "/")
o $url->netloc; same as $uri->authority
o $url->epath, $url->equery; same as $uri->path, $uri->query
o $url->path and $url->query pass unescaped strings.
o $url->path_components; same as $uri->path_segments (if you don't consider path segment parameters).
o $url->params and $url->eparams methods.
o $url->base method. See URI::WithBase.
o $url->abs and $url->rel have an optional $base argument. See URI::WithBase.
o $url->frag; same as $uri->fragment
o $url->keywords; same as $uri->query_keywords;
o $url->localpath with friends map to $uri->file
o $url->address and $url->encoded822addr; same as $uri->to for mailto URI.
o $url->groupart method for news URI.
o $url->article; same as $uri->message
SEE ALSO
URI, URI::WithBase
COPYRIGHT
Copyright 1998-2000 Gisle Aas.
perl v5.8.0 2002-05-09 URI::URL(3)