SBATCH trinity for multiple files and rename/move the output files
Hey guys,
I have wrote the following script to apply a module named "trinity" on my files. (it takes two input files and spit a trinity.fasta as output)
Now I cannot figure out how to modify this to take multiple files (2 inputs in each iteration) and then rename the output file (which is "trinity.fasta") and move it to another folder so it won't be overwritten every time.
all my files are like this:
and obviously the desired outputs:
Thanks in advance!
1. If I have a file-yyyymmdd.dat in a directory DATA1, then how do I move this file to directory DATA2 and the file name change to file-yyyymmdd.dat.currenttime
I can manual do this
$mv fileA-yyyymmdd.dat ./DATA2/fileA-yyyymmdd.dat.`date +%Y%m%d%H%M%S`
but how do I move all of the files in... (1 Reply)
Using a bash script, I need to find all files in a folder "except" the newest file. Then I need to insert the contents of one text file into all the files found. This text needs to be placed at the beginning of each file and needs a blank line between it and the current contents of the file. Then I... (5 Replies)
I am connecting to a remote server (Unix) and doing a ftp dowmload of files. The script (VB script) works fine except for not being able to move the downloaded files on the remote server to another folder.
I need to move all files with an .asc extesnion from folder "tovecellio_edi" to folder... (1 Reply)
Variations of multiple renames seems to come up a lot but i can't find the answer to this situation.
Tidying up a directory where people rename files to .working, .bob, .attempt1 & so on.
what i am trying to do is: list the file type, & rename from ".whatever" to .fixed.
As the ".whatever" is... (5 Replies)
Hello,
I'm new in the forum and in UNIX scripting, what I need is to write a simple batch script that renames or move the files back & forth from one directory to another, and then schedule the script to run on the server when the scheduled down time is, which is on Thursdays at 8pm and during... (5 Replies)
Hi,
I need to do something easy but I can't seem to figure out how to do this.
Let's say I have 6 files in the directory below:
/ebsbeta_f/flash/EBSUATQB/onlinelog
o1_mf_6_55klt7nr_.log
o1_mf_3_55klskj4_.log
o1_mf_4_55klsrl1_.log
o1_mf_5_55klt09p_.log
o1_mf_2_55klv1ts_.log... (10 Replies)
I have a directory e2e_ms_xfer/cent01
this contains the multiple files some of which will be named below with unique date time stamps
e2e_ms_edd_nom_CCYYMMDD_HHMM.csv
What I want to do is in a loop
1) Get the oldest file
2) Rename
3) Move it up one level from e2e_ms_xfer/cent01 to... (1 Reply)
Hi all,
I have a many folders with zipped files in them. The zipped files are txt files from different folders. The txt files have the same names. If i try to
find . -type f -name "*.zip" -exec cp -R {} /myhome/ZIP \; it fails since the ZIP files from different folders have the same names and... (2 Replies)
I'm using cygwin32 on Windows.
DN is an environment variable pointed at my download directory.
This command works to move the single most recent file in my download directory to my current directory:
mv "`perl -e '$p = $ARGV; opendir $h, $p or die "cannot opendir $p: $!"; @f = sort { -M $a... (2 Replies)
I want to rename (move) multiple files on remote server. I tried the following command to move all TXT files from my_dir directory to /new_dir. But it does not work. Any help?
#!/bin/ksh
sftp -dev3 << ABC
cd my_dir
$(for i in TXT; do echo "ls *.$i" ; rename $x /new_dir/$x;... (1 Reply)
Discussion started by: Soham
1 Replies
LEARN ABOUT DEBIAN
bio::index::fasta
Bio::Index::Fasta(3pm) User Contributed Perl Documentation Bio::Index::Fasta(3pm)NAME
Bio::Index::Fasta - Interface for indexing (multiple) fasta files
SYNOPSIS
# Make an index for one or more fasta files
use Bio::Index::Fasta;
use strict;
my $Index_File_Name = shift;
my $inx = Bio::Index::Fasta->new(-filename => $Index_File_Name,
-write_flag => 1);
$inx->make_index(@ARGV);
# Once the index is made it can accessed, either in the
# same script or a different one
use Bio::Index::Fasta;
use strict;
my $Index_File_Name = shift;
my $inx = Bio::Index::Fasta->new(-filename => $Index_File_Name);
my $out = Bio::SeqIO->new(-format => 'Fasta',
-fh => *STDOUT);
foreach my $id (@ARGV) {
my $seq = $inx->fetch($id); # Returns Bio::Seq 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 fasta files, and
retrieving the sequence from them. For best results 'use strict'.
Bio::Index::Fasta supports the Bio::DB::BioSeqI interface, meaning it can be used as a Sequence database for other parts of bioperl
Additional example code is available in scripts/index/*PLS and in the Bioperl Tutorial (<http://www.bioperl.org/wiki/Bptutorial.pl>)
Note that by default the key for the sequence will be the first continuous string after the '>' in the fasta header. If you want to use a
specific substring of the fasta header you must use the id_parser() method.
You can also set or customize the unique key used to retrieve by writing your own function and calling the id_parser() method. For
example:
$inx->id_parser(&get_id);
# make the index
$inx->make_index($file_name);
# here is where the retrieval key is specified
sub get_id {
my $line = shift;
$line =~ /^>.+gi|(d+)/;
$1;
}
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 - James Gilbert
Email - jgrg@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 : 'Fasta'
_index_file
Title : _index_file
Usage : $index->_index_file( $file_name, $i )
Function: Specialist function to index FASTA 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 FASTA file.
Returns &default_id_parser (see below) if not
set. If you supply your own id_parser
subroutine, then it should expect a fasta
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 Fasta ID parser for Fasta.pm
Returns $1 from applying the regexp /^>s*(S+)/
to $header.
Returns : ID string
Args : a fasta header line string
perl v5.14.2 2012-03-02 Bio::Index::Fasta(3pm)