thanks Neo, maybe I did not explain it correctly..
what you suggest will cat all files in the directory...but I need to cat them depending on the number after "An_A" . So, since the name of the file go from An_A1* to An_A900* I finally will have 900 cat results..
---------- Post updated at 05:18 PM ---------- Previous update was at 04:56 PM ----------
Quick question,
File A has one line (10 charachters), File B has one line (10 charachters).
how do a concat these two files together to produce a file (File C) that has the contents of Files A + B together onto one line of 20 Charachters
if I use:
cat FileA FileB > FileC
I get the... (5 Replies)
Hi,
I was a typical Windows guy. Like to do things just by clicking my mouse:cool:. I got a new job now...where they are big on unix.
I am trying to wet my fingures now with unix. Haven't taken the dive yet.
I am trying to find a solution for this problem.
Please help me with some... (4 Replies)
i have data files in different directories like /jadat
/cadat etcc... i have list of this directories in a file files.
content of files:
ja
ca
directories:
/jadat
/cadat
file in each of these directories
natt_trans_like.dat
i need to loop though each directory for a... (1 Reply)
Hi all,
I have a directory with many subdirectories each named like so: KOG0001, KOG0002, ...KOG9999.
Each of these subdirectories contain a variable number two kinds of files (nuc and prot) named like so: Capitella_sp_nuc_hits.fasta (nuc) and Capitella_sp_prot_hits.fasta (prot). The... (2 Replies)
Hi, sometimes one wants to edit files while still seeing output of earlier commands in terminal. I've found out that cat test && cat - >> test does the trick for displaying file content and adding lines but I believe I saw a much cooler command that was also able to erase lines from files. I cannot... (6 Replies)
I am concatenating txt-files using cat:
cat *.txt > file.dat
However, the same directory has the installation instructions included, which is also a txt file: install.txt
I currently have the install.txt file renamed to install._txt, but I prefer a solution using regular expressions.
Is there... (5 Replies)
I want to printing into two files under difference situation.
For example, file 1 name.txt
>gma-miR172a Glyma02g28845
>gma-miR1513a-3p Glyma02g15840
>gma-miR166a-5p Glyma02g15840
>gma-miR1530 Glyma02g15130
>gma-miR1507a Glyma02g01841
File 2 a.gff
Glyma01g07930 ... (4 Replies)
I am trying to cat 3 files. They all have the same name MFExtract.txt. But, they are in 3 seperate file names. Any idea how I could cat the 3 together. It's throwing me off figuring out a way because the names are the same. I was thinking just doing a 3 cat commands with the full path names and... (2 Replies)
I am new to Linux and I am trying to cat only N files in a folder. N is dynamically given number at runtime.
If I give N as 2 then cat only 2 files in the folder
and If I give N as 5 then cat only 5 files in the folder.
Is there any way to do that? (6 Replies)
Discussion started by: KMusunuru
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)