Hi everybody
I have some problems with PERL programming.
I have a file with two columns, both with numeric values.
I have to extract the values > 50 from the 2nd columns and sum them among them.
The I have to sum the respective values in the first column on the same line and, at the end, I... (6 Replies)
Hi I have a csv file which is below
A,5
B,6
C,10
D,7
I want the values who's second column is greater than 7
say
C,10
D,7
Help me please...
Thanks,
Maruth (3 Replies)
Can Anyone tell me how to extract the second column of a xls sheet
And compare the content of each row of the column with a .h file.
xls sheet is having only one spreadsheet. (2 Replies)
Hello Gurus
I have a source file which has the first line as header and the rest are the records
I need to extract the first column from the second line to extract a value
I/P
... (7 Replies)
Greetings, salutations.
I have a 3 column csv file with ~13 million rows and I would like to generate a correlation matrix. Interestingly, you all previously provided a solution to the inverse of this problem. Thread title: "awk? adjacency matrix to adjacency list / correlation matrix to list"... (6 Replies)
Hi
I want to grep a column 6 & column 7 from a CSV Format file & then i have to find the difference between these columns as these both columns contains date & time in 7/7/2012 9:20 this format . So kindly help me out ASAP.
But please kindly dis xls has to be converted in csv format as may... (5 Replies)
Hi,
I am trying with the below Perl one-liner using regular expression to extract the first and second column of a text file:
perl -p -e "s/\s*(\w+).*/$1/"
perl -p -e "s/\s*.+\s(.+)\s*/$1\n/"
whereas the text file's data looks like:
Error: terminated 2233
Warning: reboot 3434
Warning:... (3 Replies)
Hi,
I want to extract first column from a file and redirect the output to another file in perl.
I am able to do this from command line by executing below commands.
perl -anle 'print $F' Input.dat > Output.dat
perl -ne '@F = split("\t", $_); print "$F\n";' Input.dat > Output.dat
perl -anE... (7 Replies)
Hi, I am newbie in shell script.
I need your help to solve my problem.
Firstly, I have 2 files of csv and i want to compare of the contents then the output will be written in a new csv file.
File1:
SourceFile,DateTimeOriginal
/home/intannf/foto/IMG_0713.JPG,2015:02:17 11:14:07... (8 Replies)
file1:
Name,Threshold,Curr Samples,Curr Error%,Curr ART
GETHome,100,21601,0.00%,47
GETregistry,100,21592,0.00%,13
GEThomeLayout,100,30466,0.00%,17
file2:
Name,Threshold,Curr Samples,Curr Error%,Curr ART
GETHome,100,21601,0.00%,33
GETregistry,100,21592,0.00%,22... (6 Replies)
Discussion started by: Raghuram717
6 Replies
LEARN ABOUT DEBIAN
bio::index::fastq
Bio::Index::Fastq(3pm) User Contributed Perl Documentation Bio::Index::Fastq(3pm)NAME
Bio::Index::Fastq - Interface for indexing (multiple) fastq files
SYNOPSIS
# Complete code for making an index for several
# fastq files
use Bio::Index::Fastq;
use strict;
my $Index_File_Name = shift;
my $inx = Bio::Index::Fastq->new(
'-filename' => $Index_File_Name,
'-write_flag' => 1);
$inx->make_index(@ARGV);
# Print out several sequences present in the index
# in Fastq format
use Bio::Index::Fastq;
use strict;
my $Index_File_Name = shift;
my $inx = Bio::Index::Fastq->new('-filename' => $Index_File_Name);
my $out = Bio::SeqIO->new('-format' => 'Fastq','-fh' => *STDOUT);
foreach my $id (@ARGV) {
my $seq = $inx->fetch($id); # Returns Bio::Seq::Quality object
$out->write_seq($seq);
}
# or, alternatively
my $id;
my $seq = $inx->get_Seq_by_id($id); #identical to fetch
DESCRIPTION
Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic funtionallity for indexing fastq files, and
retrieving the sequence from them. Note: for best results 'use strict'.
Bio::Index::Fastq supports the Bio::DB::BioSeqI interface, meaning it can be used as a Sequence database for other parts of bioperl
FEED_BACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. 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 the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Tony Cox
Email - avc@sanger.ac.uk
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
_file_format
Title : _file_format
Function: The file format for this package, which is needed
by the SeqIO system when reading the sequence.
Returns : 'Fastq'
_index_file
Title : _index_file
Usage : $index->_index_file( $file_name, $i )
Function: Specialist function to index FASTQ format files.
Is provided with a filename and an integer
by make_index in its SUPER class.
Example :
Returns :
Args :
id_parser
Title : id_parser
Usage : $index->id_parser( CODE )
Function: Stores or returns the code used by record_id to
parse the ID for record from a string. Useful
for (for instance) specifying a different
parser for different flavours of FASTQ file.
Returns &default_id_parser (see below) if not
set. If you supply your own id_parser
subroutine, then it should expect a fastq
description line. An entry will be added to
the index for each string in the list returned.
Example : $index->id_parser( &my_id_parser )
Returns : ref to CODE if called without arguments
Args : CODE
default_id_parser
Title : default_id_parser
Usage : $id = default_id_parser( $header )
Function: The default Fastq ID parser for Fastq.pm
Returns $1 from applying the regexp /^>s*(S+)/
to $header.
Returns : ID string
Args : a fastq header line string
perl v5.14.2 2012-03-02 Bio::Index::Fastq(3pm)