10 More Discussions You Might Find Interesting
1. Programming
Hi All,
I would like get the minimum value in the certain column with respect to other column.
For example, I have a text file like this.
ATOM 1 QSS SPH S 0 -2.790 -1.180 -2.282 2.28 2.28
ATOM 1 QSS SPH S 1 -2.915 -1.024 -2.032 2.31 2.31
ATOM 1 ... (4 Replies)
Discussion started by: bala06
4 Replies
2. Shell Programming and Scripting
Need your support for below. Please help to get required output
If column 5 is INV then only consider column1 and take out duplicates/identical rows/values from column1 and then put minimum value of column6 in column7 and put maximum value in column 8 and then need to do subtract values of... (7 Replies)
Discussion started by: as7951
7 Replies
3. Shell Programming and Scripting
Hello,
I need to find out the minimum and maximum values based on specific column, and then print out the entire row with the max value.
Infile.txt:
scf6 290173 290416 . + X_047241 T_00113118-1
scf6 290491 290957 . + X_047241 T_00113118-2
scf6 290898 290957 . + X_047241 T_00113119-3
scf6... (2 Replies)
Discussion started by: yifangt
2 Replies
4. Shell Programming and Scripting
input
1 2 3 4 5 2 8
2 1 1 1 4 2 1
5 4 4 4 2 1 3
2 2 6 7 4 5 4
5 5 5 4 3 3 5
I woud like to print a min of each row such that my output would look like
1
1
1
2
3 (5 Replies)
Discussion started by: johnkim0806
5 Replies
5. Shell Programming and Scripting
Hi Friends,
I have an input file like this
chr1 100 200 1 2 3 4
chr1 150 200 4 5 6 7
chr2 300 400 9 6 7 1
chr2 300 410 -10 21 -11 13
chr3 700 900 -21 -22 130 165
Now, my output file is
chr1 100 200 1
chr1 150 200 4
chr2 300 400 1
chr2 300 410 10
chr3 700 900 21
Remove... (5 Replies)
Discussion started by: jacobs.smith
5 Replies
6. Shell Programming and Scripting
Hello,
I have this file file1.csv
Element1;23-10-2012;1,450;1,564;1,428
Element2;23-10-2012;1,448;1,565;1,427
Element3;23-10-2012;1,453;1,570;1,424
Element4;23-10-2012;1,428;1,542;1,405
Element5;23-10-2012;1,461;;1,453
Element6;23-10-2012;1,438;1,555;1,417... (6 Replies)
Discussion started by: saba01
6 Replies
7. Shell Programming and Scripting
Hi all,
I am having multiple files with the pattern given below:
I need to find the minimum value of 5th column if column 1 is x and 2nd column is awh or vbn or ... (20 different strings).
the output must be like:
Kindly help me to figure out this prob....
Thanks in... (4 Replies)
Discussion started by: CAch
4 Replies
8. Shell Programming and Scripting
Hi there
I have generated a column containing 100.000 values. Sample:
94.971
101.468
73.120
100.601
102.329
I need to find the minimum value in this file and I must know which row it is in (no sorting).
I hope you can help!
Thanks! (16 Replies)
Discussion started by: cno
16 Replies
9. Shell Programming and Scripting
Input
10 8 20 8 10 9 20 9
10 12 20 19 10 10 20 40
Output1
10 8 2 20 8 12 10 9 1 20 9 11
10 12 -2 20 19 1 10 10 0 20 40 -20
Output2
10 9 ... (0 Replies)
Discussion started by: repinementer
0 Replies
10. Shell Programming and Scripting
Hi,
Suppose I have a space delimited file like this:
Serial# 1970 1971 1972 1973 1974
193532 21 2 X X X
200201 20 30 X X 40
200201 X X 13 15 X
393666 66 3 X X 5 ... (2 Replies)
Discussion started by: grossgermany
2 Replies
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)