Outputting characters after a given string and reporting the characters in the row below --sed
I have this fastq file:
And I am using this script to output the three characters after this sting GCATGAAAACATACA:
This is my current output:
However, I would like to output the three characters in the same position two rows below from each sequence, something like this:
Is there a way to accomplish this with sed? operative system W10; shell cygwin
Hi all,
if for example I had a variable containing the string 'hello', is the any way I can output, for example, the e and the 2nd l based on their position in the string not their character (in this case 2 and 4)?
any general pointers in the right direction will be much appreciated, at... (3 Replies)
Hi Please help me to refine my syntax. I want to delete the excess characters from the out put below.
-bash-3.00$ top -b -n2 -d 00.20 |grep Cpu|tail -1 | awk -F ":" '{ print $2 }' | cut -d, -f1
4.4% us
now i want to delete the % and us. How wil i do that to make it just 4.4.
Thanks (7 Replies)
Hi,
I've a csv file seperated by '|' from which I'm trying to remove the excess '|' characters more than the existing fields. My CSV looks like as below.
HRLOAD|Service|AddChange|EN
PERSONID|STATUS|LASTNAME|FIRSTNAME|ITDCLIENTUSERID|ADDRESSLINE1
10000001|ACTIVE|Testazar1|Testore1|20041|||... (24 Replies)
sed -e "s// /g" old.txt > new.txt
While I do know some control characters need to be escaped, can normal characters also be escaped and still work the same way? Basically I do not know all control characters that have a special meaning, for example, ?, ., % have a meaning and have to be escaped... (11 Replies)
helloo
I wonder if there's a way to cut characters out of a string and keep only
the last 2 by using sed.
For example if there's the todays' date:
2012-05-06
and we only want to keep the last 2 characters which are the day.
Is there a quick way to do it with sed? (2 Replies)
Hey guys,
I know that title is a mouthful - I'll try to better explain my struggles a little better...
What I'm trying to do is:
1. Query a db and output to a file, a list of column data.
2. Then, for each line in this file, repeat these values but wrap them with:
ITEM{
... (3 Replies)
Hi,
I have a xml file (Config.xml)
<Header name="" TDate="" PDate="">
<Config>
{"config" { "Nation" "Pri:|Sec:"}}
</Config>
</Header>
Now I wanted to printed all the strings between "". I tried the following
cat Config.xml | sed -n 's/.*\.*//p'
... (8 Replies)
Hi,
I hope you can help me out please?
I need to replace from character 8-16 with AAAAAAAA and the rest should stay the same after character 16
gtwrhtrd11111111rjytwyejtyjejetjyetgeaEHT
wrehrhw22222222hytekutkyukrylryilruilrGEQTH
hrwjyety33333333gtrhwrjrgkreglqeriugn;RUGNEURGU
... (4 Replies)
I have a file that looks like this:
>ID 1
AATAATTCCGGATCGTGC
>ID 2
TTTGACAGTAGAC
>ID 3
AGACGATGACGAT
I am using the following script to report if AATTCCGGATCG is present in any sequence:
awk 'FNR==1{n=substr(FILENAME,1,index(FILENAME,".")-1)} { print n "\t"... (10 Replies)
Discussion started by: Xterra
10 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)