Hi I have a file which contains data (list of data) and I want to put a number with bracket 1) 2) 3) etc at the beginning of every successive line
I can do it with SED and I can also do it using the nl route but am looking for a different method.
I'm guessing I would need some sort of loop... (3 Replies)
Hi Everybody,
I am trying to write a script that will get some perticuler data from a file and redirect to a file.
My Question is,
I have a Very huge file,In that file I have my required data is started from 25th line and it will ends in 100th line.
I know the line numbers, I need to get all... (9 Replies)
Hi,
I am trying to count the number of occurance of a specific value in a column and increment the variable in the second column accordingly. I have very little information about Unix. As an example,
21 1
32 1
32 2
45 1
56 1
56 2
56 3
73 1
82 1
Thanks,
Natasha (2 Replies)
Hello everybody!
I am quit new here and hope you can help me.
Using an awk script I am trying to extract data from several files. The structure of the input files is as follows:
TimeStep parameter1 parameter2 parameter3 parameter4
e.g.
1 X Y Z L
1 D H Z I
1 H Y E W
2 D H G F
2 R... (2 Replies)
Hi !
How to increment a varibale in ksh.
#!/bin/ksh
set -x
RELEASE_NUM=5.2.103
VAL=0.0.1
RELEASE_NUM=`echo $RELEASE_NUM + $VAL | bc`
echo $RELEASE_NUM
The above code is throwing this error.
+ RELEASE_NUM=5.2.103 (2 Replies)
Hi Forum.
I was trying to search the following scenario on the forum but was not able to.
Let's say that I have a very large file that has some bad data in it (for ex: 0.0015 in the 12th column) and I would like to find the line number and remove that particular line.
What's the easiest... (3 Replies)
Hi
I have the file called "file.txt" which contains the following output
$cat file.txt
sandy
<version>1</version>
karen
<version>2</version>
Rob
<version>3</version>
peter
<version>4</version>
i want to write a command which will add the value 1 to the digits and show the output... (2 Replies)
Hello,
I have a few thousand .pdf files in various folders each have a naming scheme like this:
006_-_Titled_Document_#34_-_September-25-2011-side-1.pdf
In each folder, the number system starts at 001 (as you see on the far left of the file name), and then ends at 999 (maximum .pdf files).... (4 Replies)
Hy!
I need to post-process some data files which have variable (and periodic) number of fields. For example, I need to square (data -> data*data) the folowing data file: -5.34281E-28 -3.69822E-29 8.19128E-29 9.55444E-29 8.16494E-29 6.23125E-29
4.42106E-29 2.94592E-29 1.84841E-29 ... (5 Replies)
Hi All,
I am looking for a perl/awk/sed command to auto-increment the numbers line in file, P1.tcl:
run_build_model sparc_ifu_dec
run_drc
set_faults -model path_delay -atpg_effectiveness -fault_coverage
add_delay_paths P1
set_atpg -abort_limit 1000
run_atpg -ndetects 1000
I would like... (6 Replies)
Discussion started by: jypark22
6 Replies
LEARN ABOUT DEBIAN
bio::popgen::utilities
Bio::PopGen::Utilities(3pm) User Contributed Perl Documentation Bio::PopGen::Utilities(3pm)NAME
Bio::PopGen::Utilities - Utilities for working with PopGen data and objects
SYNOPSIS
use Bio::PopGen::Utilities;
use Bio::AlignIO;
my $in = Bio::AlignIO->new(-file => 't/data/t7.aln',
-format => 'clustalw');
my $aln = $in->next_aln;
# get a population, each sequence is an individual and
# for the default case, every site which is not monomorphic
# is a 'marker'. Each individual will have a 'genotype' for the
# site which will be the specific base in the alignment at that
# site
my $pop = Bio::PopGen::Utilities->aln_to_population(-alignment => $aln);
# get the synonymous sites from the alignemt only as the 'genotypes'
# for the population
my $synpop = Bio::PopGen::Utilities->aln_to_population(-site_model => 'cod',
-alignment => $aln);
DESCRIPTION
This object provides some convience function to turn sequence alignments into usable objects for the Population genetics modules
(Bio::PopGen).
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 - Jason Stajich
Email jason-at-bioperl-dot-org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
aln_to_population
Title : aln_to_population
Usage : my $pop = Bio::PopGen::Utilities->aln_to_population($aln);
Function: Turn and alignment into a set of L<Bio::PopGen::Individual>
objects grouped in a L<Bio::PopGen::Population> object
Sites are treated as 'Markers' in the Bioperl PopGen object
model in the sense that a site is a unique location for which
an individual will have a genotype (a set of alleles).
In this implementation we are assuming that each individual
has a single entry in the alignment file.
Specify a site model as one of those listed
'all' -- every base in the alignment is considered a site
'cod' -- codons
The option -site_model
for All sites : 'all'
Codon sites : 'cod' or 'codon'
To see all sites, including those which are fixed in the population
add -include_monomorphic => 1
to the arguments
Returns :
Args : -include_monomorphic => 1 to specify all sites,
even those which are monomorphic
in the population
(useful for HKA test mostly)
[default is false]
-phase => specify a phase for the data, this is only
used if the site_mode is codon
[default is 0]
-site_model => one-of 'all', 'codon'
to specify a site model for the data extraction
from the alignment
[default is all]
-alignment => provide a L<Bio::SimpleAlign> object [required]
perl v5.14.2 2012-03-02 Bio::PopGen::Utilities(3pm)