Hi,
I have a program that runs two threads in stead of two processes. I want to use pipe to redirect the output of the first thread to the input of the second thread.
One thread is continuously writing to a pipe, and the other thread will read from the pipe.
How do I do that?
Is there... (2 Replies)
i am new to linux programming. can anyone answer my question?
there is one pipe file "my_pipe"
prw-r--r-- 1 john rnd 32 Aug 17 19:45 my_pipe
how to output string message (char*) to this pipe? which API should I use? (3 Replies)
anybody can help, plz:
I want to pass the output of "ls" to "grep":
ftp -n host <<!
USER user passwd
ls
bye
! | grep file
exit 0
It does not work!!
Any idea??
Sami (7 Replies)
I am using grep and I want the output to go into two files without going to the screen. I used tee to get the output into two files, but it is also putting the output on the screen which i do not want. Can this be fixed. (2 Replies)
Hi,
I am having a list of directories with different login id's. My requirement is that i need to list the directories of my id and need to delete them. So i am using following code
ls -ltr ¦ grep userid ¦ rm -rf
But this is not working. So is there any way of doing it. Please note... (3 Replies)
Hi All. Thanks for your help in advance.
I have a requirement to examine the number of delimiters in each record of a file. If the record has the expected number of delimiters it should be passed into a 'good' file. If it does not, the record should be passed into a 'bad' file. I have been able... (8 Replies)
I can use pipe output to a file. For example
./somescript.sh > output.txt
But for example if the output from ./somescript.sh is slow. like if it prints one line every minute then output.txt is not updated every minute. Lines are written to output.txt in one go, hence have to wait for the whole... (2 Replies)
Hi All,
i have the following command
df|awk '{print $5}'|grep /| egrep -v '^/$|/usr|/opt|/var/log|/home|/tmp'
output looks like:
/filesystem/number1
/filesystem/number2
/filesystem3
/possiblymoreoutput
i want the output to look like the below (either in a file or to output to... (3 Replies)
I'm trying to get an output to echo on the next line in a given color and outputted next to a label.
Sorry if that's a bit vague, see below.
#!/bin/bash
YELLOW=$(tput setaf 3 && tput bold)
echo -n 'plaintext' | openssl md2 || read hash
echo "$YELLOW Hash:$hash"
But I can't seem to get the... (2 Replies)
Hi,
I want to grep multiple patterns from multiple files and save to multiple outputs. As of now its outputting all to the same file when I use this command.
Input : 108 files to check for 390 patterns to check for. output I need to 108 files with the searched patterns.
Xargs -I {} grep... (3 Replies)
Discussion started by: Diya123
3 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)