01-10-2010
10 More Discussions You Might Find Interesting
1. Shell Programming and Scripting
If I had a list of numbers in two different files, what would be the fastest and easiest way to find out which numbers in list B are not in list A without reading each number in list B one at a time and using grep thousands of times against list A?
I have two very long lists of numbers and the... (4 Replies)
Discussion started by: keelba
4 Replies
2. UNIX for Dummies Questions & Answers
Hi ,
I have a peculiar case, where my sed command is working on a file which contains lines of small length.
sed "s/XYZ:1/XYZ:3/g" abc.txt > xyz.txt
when abc.txt contains lines of small length(currently around 80 chars) , this sed command is working fine.
when abc.txt contains lines of... (3 Replies)
Discussion started by: thanuman
3 Replies
3. UNIX for Dummies Questions & Answers
hello all,
I wonder if anybody might be able to help with this.
I have file 1 and file2.
Both files may contain thousands of lines that have variable contents.
file1
234GH
5234BTW
89er
678tfg
234
234YT
tfg456
wert
78gt
gh23444 (7 Replies)
Discussion started by: Garrred
7 Replies
4. Shell Programming and Scripting
The following bash script does not work because the java/groovy code always thinks there are four arguments even if there are only 1 or 2. As you can see from my hideous backslashes, I am using cygwin bash on windows.
export... (1 Reply)
Discussion started by: siegfried
1 Replies
5. Programming
Hi.
I am trying to write a Python programme that compares two different text files which both contain a list of words. Each word has its own line
worda
wordb
wordc
I want to compare textfile 2 with textfile 1, and if there's a word in textfile 2 that is NOT in textfile 1, I want to... (6 Replies)
Discussion started by: Bloomy
6 Replies
6. Shell Programming and Scripting
hi,
I have 2 large lists:
LIST A: containes 6 fields of many entries (VARIABLE number), like:
2011-07-10 | 18:19:47 | 38037300 | 9647808003122 | 2 | success
LIST B: containes 3 fields & 183 entries (FIXED number), like:
9647805651885 9647805651885 SCP_10
What I want is a... (8 Replies)
Discussion started by: amurib
8 Replies
7. Shell Programming and Scripting
Hi,
I do little bash scripting so sorry for my ignorance.
How do I compare if the two variable not match and if they do not match run a command.
I was thinking a for loop but then I need another for loop for the 2nd list and I do not think that would work as in the real world there could... (2 Replies)
Discussion started by: GermanJulian
2 Replies
8. Shell Programming and Scripting
Hi everybody!
I'm trying to delete some elements from a list with two elements on each row agreeing with the elements in another list. Pratically I want a perl script able to take each element of the second list (that is a single column list), compare it with both elements of each row from the... (3 Replies)
Discussion started by: gabrysfe
3 Replies
9. Shell Programming and Scripting
I have two files A and B listing ip addresses
and all the ip addresses in B are in A, and A includes other ip addresses
now I want to get the list of the ip addresses that are in A but not in B
how to achieve this? thanks (1 Reply)
Discussion started by: esolvepolito
1 Replies
10. Homework & Coursework Questions
Hello,
I'm new to the python programming, and I have a question.
I have to write a program that prints a receipt for a restaurant. The input is a list which looks like:
product1
product3
product8
....
In the other input file there is a list which looks like:
product1 coffee 5,00... (1 Reply)
Discussion started by: dagendy
1 Replies
LEARN ABOUT DEBIAN
bio::mapio::fpc
Bio::MapIO::fpc(3pm) User Contributed Perl Documentation Bio::MapIO::fpc(3pm)
NAME
Bio::MapIO::fpc - A FPC Map reader
SYNOPSIS
# do not use this object directly it is accessed through the Bio::MapIO system
use Bio::MapIO;
-format : specifies the format of the file format is "fpc",
-file : specifies the name of the .fpc file
-readcor : boolean argument, indicating if .cor is to be read
or not. It looks for the .cor file in the same path
as .fpc file.
0 : doesn't read .cor file
1 : reads the .cor file
[default 0]
-verbose : indicates the process of loading of fpc file
my $mapio = Bio::MapIO->new(-format => "fpc",
-file => "rice.fpc",
-readcor => 0,
-verbose => 0);
my $map = $mapio->next_map();
foreach my $marker ( $map->each_markerid() ) {
# loop through the markers associated with the map
# likewise for contigs, clones, etc.
}
DESCRIPTION
This object contains code for parsing and processing FPC files and creating Bio::Map::Physical object from it.
For faster access and better optimization, the data is stored internally in hashes. The corresponding objects are created on request.
We handle reading of the FPC ourselves, since MapIO module of Bioperl adds too much overhead.
Initializer
_initialize
Title : _initialize
Usage : called implicitly
Function: calls the SUPER::_initialize
Returns : nothing
Args : species, readcor
Access Methods
These methods let you get and set the member variables
next_map
Title : next_map
Usage : my $fpcmap = $mapio->next_map();
Function: gets the fpcmap from MapIO
Returns : object of type L<Bio::Map::MapI>
Args : none
write_map
Title : write_map
Usage : $mapio->write_map($map);
Function: Write a map out
Returns : none
Args : Bio::Map::MapI
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 - Gaurav Gupta
Email gaurav@genome.arizona.edu
PROJECT LEADERS
Jamie Hatfield jamie@genome.arizona.edu
Dr. Cari Soderlund cari@genome.arizona.edu
PROJECT DESCRIPTION
The project was done in Arizona Genomics Computational Laboratory (AGCoL) at University of Arizona.
This work was funded by USDA-IFAFS grant #11180 titled "Web Resources for the Computation and Display of Physical Mapping Data".
For more information on this project, please refer:
http://www.genome.arizona.edu
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
perl v5.14.2 2012-03-02 Bio::MapIO::fpc(3pm)