Hi,
I would like to batch concatenate files by pairs. I have quite a few of them so I would not like to do that pair by pair separately.
the names of the file is of the type:
I would like to concatenate file1 and newfile1 together etc...
Any idea how I could script that in shell commands?
Thanks a lot for your help!!
Last edited by Scrutinizer; 06-11-2015 at 07:41 AM..
Reason: code tags
Hi,
I have a text file with the following contents
/C=IT/O=INFN/OU=Personal Certificate/L=Napoli/CN=Some guy
/C=IT/O=INFN/CN=INFN CA
/O=Grid/O=NorduGrid/OU=uninett.no/CN=Another guy
/O=Grid/O=NorduGrid/CN=NorduGrid Certification Authority
/C=TW/O=AP/OU=GRID/CN=Someone else... (5 Replies)
I have directory structure sales_only under which i have multiple directories for each dealer
example:
../../../Sales_Only/xxx_Dealer
../../../Sales_Only/yyy_Dealer
../../../Sales_Only/zzz_Dealer
Every day i have one file produce under each directory when the process runs.
The requirement... (3 Replies)
Hi, I want to create a batch(bash) file to combine 23 files together. These files have the same extension. I want the final file is save to a given folder. Once it is done it will delete the 23 files.
Thanks for help. Need script. (6 Replies)
I have a number of files in a directory named like this:
fooP1, fooN1, fooP2, fooN2 ... fooP(i), fooN(i).
I'd like to know how to combine each P and N pair into a single file, foo(i)
TIA
John Balwit (1 Reply)
I have a file named "file1" which has the following data
10000
20000
30000
And I have a file named "file2" which has the following data
ABC
DEF
XYZ
My output should be
10000ABC
20000DEF (3 Replies)
Hi All,
Need your help.
I will need to concatenate around 100 files but each end of the file I will need to insert my name DIRT1228 on each of the file and before the next file is added and arrived with just one file for all the 100files.
Appreciate your time.
Dirt (6 Replies)
Hi
I am trying to learn linux step by step an i am wondering
can i use cat command for concatenate files but i want to place context of file1 to a specific position in file2 place of file 2 and not at the end as it dose on default?
Thank you. (3 Replies)
- Concatenate files and delete source files. Also have to add a comment.
- I need to concatenate 3 files which have the same characters in the beginning and have to remove those files and add a comment and the end.
Example:
cat REJ_FILE_ABC.txt REJ_FILE_XYZ.txt REJ_FILE_PQR.txt >... (0 Replies)
Hi all,
please help me construct the command. i want to loop through all files named bam* and bed*. My awk works for a particular pair but there are too many pairs to do manually.
I have generated multiple files in a folder in a given pattern. The files are named like
bam_fixed1.bam... (2 Replies)
Hi all,
Please guide. It has to do with parsing the input file names.
I have a fairly large number of files, I want to do some operations on them in a pairwise fashion (every file has a pair).
The names are in the following pattern, with the pairs of files named with _1 and _2 , the... (4 Replies)
Discussion started by: newbie83
4 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)