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 DEBIAN
bio::treeio::newickparser
Bio::TreeIO::NewickParser(3pm) User Contributed Perl Documentation Bio::TreeIO::NewickParser(3pm)
NAME
Module which implements a newick string parser as a finite state machine which enables it to parse the full Newick specification.
Taken largely from the Ensembl Compara file with the same name (Bio::EnsEMBL::Compara::Graph::NewickParser), this module adapts the parser
to work with BioPerl's event handler-based parsing scheme.
This module is used by nhx.pm and newick.pm, and is NOT called directly. Instead, both of those parsing modules extend this module in order
to gain access to the main parsing method.
SYNOPSIS
# From newick.pm
use base qw(Bio::TreeIO Bio::TreeIO::NewickParser);
# in the next_tree method...
$self->parse_newick($_);
DESCRIPTION
This module correctly parses the Newick and NHX formats, sending calls to the BioPerl TreeEventHandler when appropriate in order to build
and populate the node objects.
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 - Jessica Severin (EnsEMBL implementation), Greg Jordan (BioPerl adaptation)
perl v5.14.2 2012-03-02 Bio::TreeIO::NewickParser(3pm)