I had a comment on the non-fitting file names similar to what you said but removed it when I tested the split installed on my linux (split (GNU coreutils) 8.28):
Code:
$ split -dl2 --additional-suffix=.fasta file ""
$ ls -la
-rw-rw-r-- 1 user group 379 Feb 16 19:39 00.fasta
-rw-rw-r-- 1 user group 349 Feb 16 19:39 01.fasta
-rw-rw-r-- 1 user group 175 Feb 16 19:39 02.fasta
Had the requestor told us what system s/he has, a more specific answer had resulted.
hi, first congratulations on the nice forum!
Can anybody write script, which can make copy of some or all files of the current directory in new directory (called "backups", which must be made in the current directory, if it's not already exist). And bring out a massage (report) with the count... (7 Replies)
Hi,
root@server] df -h
121G 14G 101G 12% /home
147G 126G 14G 91% /backup
We having our site files and images are storing in
/backup/home/user/files/ through symbolic link created in /home directory pointing in /backup directory as following.
root@server] cd /home... (1 Reply)
I am very new to Linux/Unix. Kindly assist the following:
I wish to write a bash shell script called how_many_to_go that calculates and prints the number of days, hours, minutes and/or seconds until the end of the current month (based on the output of the date command).
Do ... (2 Replies)
I am newbie to UNIX. I came across this exercise in one the books.Can anyone help me with this question??????
Write a short Bash script that, given the name of a file as an argument,
reads the file name and creates a new file containing only lines which consist
of one word. Here is an example... (4 Replies)
Hi all,
This is my sample code in /etc/httpd/conf.d/applications.conf file currently we are creating subdomain mannually for every new subdomain. I want to automate this process througs bash script , how its possible.
<VirtualHost *:80>
ServerName google.com
ServerAlias google.com... (5 Replies)
Hi All,
I am unable to write the script for the below requirement.
Requirement:
Main table dir_ancillary table contain three column "dir_ancillary.table_name"," dir_ancillary.text_file_name ", "dir_ancillary.Include" .
This dir_ancillary contain undefined tables in the column... (2 Replies)
Hi Team
I am trying to put together a nice small script to mount my lvm snapshot
Here are my objectives
1 Check whether snapshot is currently mounted. If so echo umount snapshot and exit from the script.
2 If it's not mounting, check whether the mount point exist, If so, create lvm... (0 Replies)
Hello everyone.
I'm a Linux novice trying out a lot of bash scripting lately, as it is so very addictive.
Lately I have been setting up one of my boxes remotely and have been hardening it as much as possible. Please allow me to explain the scenario, as it does tend to become a little... (1 Reply)
#!/bin/bash -i
SAVEIFS=$IFS
IFS=$"\n\b"
picc=$*
if ; then
echo $TDATE
if ; then
touch dummy
touch -t "tdate" dummy
touch -r "dummy" "$picc"
else
echo -e "No mod date value to apply. If there is one in your shell,\ninvoke \eStarted asking advice on this (on Linuxquestions.org).... (9 Replies)
How would I write a value to a physical memory address?
I was able to read a physical memory address (for example, 0x400) using this line:
dd if=/dev/mem count=4 bs=1 skip=$(( 0x400 ))
But I get an error:
dd: 'standard input': cannot skip to specified offset
when I try to write using... (1 Reply)
Discussion started by: rabrandt
1 Replies
LEARN ABOUT DEBIAN
bp_load_gff
BP_LOAD_GFF(1p) User Contributed Perl Documentation BP_LOAD_GFF(1p)NAME
bp_load_gff.pl - Load a Bio::DB::GFF database from GFF files.
SYNOPSIS
% bp_load_gff.pl -d testdb -u user -p pw
--dsn 'dbi:mysql:database=dmel_r5_1;host=myhost;port=myport'
dna1.fa dna2.fa features1.gff features2.gff ...
DESCRIPTION
This script loads a Bio::DB::GFF database with the features contained in a list of GFF files and/or FASTA sequence files. You must use the
exact variant of GFF described in Bio::DB::GFF. Various command-line options allow you to control which database to load and whether to
allow an existing database to be overwritten.
This script uses the Bio::DB::GFF interface, and so works with all database adaptors currently supported by that module (MySQL, Oracle,
PostgreSQL soon). However, it is slow. For faster loading, see the MySQL-specific bp_bulk_load_gff.pl and bp_fast_load_gff.pl scripts.
NOTES
If the filename is given as "-" then the input is taken from standard input. Compressed files (.gz, .Z, .bz2) are automatically
uncompressed.
FASTA format files are distinguished from GFF files by their filename extensions. Files ending in .fa, .fasta, .fast, .seq, .dna and their
uppercase variants are treated as FASTA files. Everything else is treated as a GFF file. If you wish to load -fasta files from STDIN,
then use the -f command-line swith with an argument of '-', as in
gunzip my_data.fa.gz | bp_fast_load_gff.pl -d test -f -
On the first load of a database, you will see a number of "unknown table" errors. This is normal.
About maxfeature: the default value is 100,000,000 bases. If you have features that are close to or greater that 100Mb in length, then the
value of maxfeature should be increased to 1,000,000,000, or another power of 10.
COMMAND-LINE OPTIONS
Command-line options can be abbreviated to single-letter options. e.g. -d instead of --database.
--dsn <dsn> Data source (default dbi:mysql:test)
--adaptor <adaptor> Schema adaptor (default dbi::mysqlopt)
--user <user> Username for mysql authentication
--pass <password> Password for mysql authentication
--fasta <path> Fasta file or directory containing fasta files for the DNA
--create Force creation and initialization of database
--maxfeature Set the value of the maximum feature size (default 100 Mb; must be a power of 10)
--group A list of one or more tag names (comma or space separated)
to be used for grouping in the 9th column.
--upgrade Upgrade existing database to current schema
--gff3_munge Activate GFF3 name munging (see Bio::DB::GFF)
--quiet No progress reports
--summary Generate summary statistics for drawing coverage histograms.
This can be run on a previously loaded database or during
the load.
SEE ALSO
Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl
AUTHOR
Lincoln Stein, lstein@cshl.org
Copyright (c) 2002 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
perl v5.14.2 2012-03-02 BP_LOAD_GFF(1p)