Hi RudiC,
The standard split utility creates output filenames with sequence "numbers" added to the end of a given output filename prefix where the "numbers" aren't numeric; they are names like fasta.aa, fasta.ab, fasta.ac, ...
Like you said, awk would work well for this.
Hi laura,
To get the requested output, one could use something like:
but that would produce names with varying output lengths that would be inconvenient to process if you wanted to handle them in the same order that they originally appeared in the file named out1. If you do later want to process them in that order, you would probably be happier with something more like:
which would produce all 34900 output files with names that start with 5 decimal digits (with leading zeros on the first 9999 files so normal listings of the produced files are in the order you probably want.
If you intend to try this on a Solaris/SunOS operating system, change awk in both of the above suggestions to /usr/xpg4/bin/awk or nawk.
As RudiC said, next time you need help, plan to tell us what operating system as well as what shell you're using and show us what you have tried to solve the problem on your own. We want to help you learn how to do stuff like this on your own; not to act as your unpaid programming staff.
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
bio::alignio::fasta
Bio::AlignIO::fasta(3pm) User Contributed Perl Documentation Bio::AlignIO::fasta(3pm)NAME
Bio::AlignIO::fasta - fasta MSA Sequence input/output stream
SYNOPSIS
Do not use this module directly. Use it via the Bio::AlignIO class.
DESCRIPTION
This object can transform Bio::SimpleAlign objects to and from fasta flat file databases. This is for the fasta alignment format, not for
the FastA sequence analysis program. To process the alignments from FastA (FastX, FastN, FastP, tFastA, etc) use the Bio::SearchIO module.
FEEDBACK
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/
AUTHORS
Peter Schattner
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
next_aln
Title : next_aln
Usage : $aln = $stream->next_aln
Function: returns the next alignment in the stream.
Returns : Bio::Align::AlignI object - returns 0 on end of file
or on error
Args : -width => optional argument to specify the width sequence
will be written (60 chars by default)
See Bio::Align::AlignI
write_aln
Title : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the $aln object into the stream in fasta format
Returns : 1 for success and 0 for error
Args : L<Bio::Align::AlignI> object
See Bio::Align::AlignI
_get_len
Title : _get_len
Usage :
Function: determine number of alphabetic chars
Returns : integer
Args : sequence string
width
Title : width
Usage : $obj->width($newwidth)
$width = $obj->width;
Function: Get/set width of alignment
Returns : integer value of width
Args : on set, new value (a scalar or undef, optional)
perl v5.14.2 2012-03-02 Bio::AlignIO::fasta(3pm)