Hi,
I have a folder that contains many (multiple) files
1.fasta
2.fasta
3.fasta
4.fasta
5.fasta
.
.
100's of files
Each such file have data in the following format
for example:
vi 1.fasta
I would like to edit these files such a way that the data below so that the file will look like
That is remove every thing after >AB_1 ..same with >AB_2....etc
Please let me know the best way to do it using awk or sed as I have to edit hundred's of files.
LA
when we are spooling query o/p to certain txt file,in that file how we can get headers in the query.(through unix shell scripting).
for exmple
q1="slect * from XXXXXX;";
sqlplus XXX/XXXX@XXXXX
spool XXXX.txt
$q1
spool off
in the text file i want the headers of the query.....
... (0 Replies)
Hi,
I'm trying to strip all lines between two headers in a file:
### BEGIN ###
Text to remove, contains all kinds of characters
...
Antispyware-Downloadserver.com (Germany)=http://www.antispyware-downloadserver.c
om/updates/
Antispyware-Downloadserver.com #2... (3 Replies)
Hi ,
I have a typical situation. I have 4 files and with different headers (number of headers is varible ).
I need to make such a merged file which will have headers combined from all files (comman coluns should appear once only).
For example -
File 1
H1|H2|H3|H4
11|12|13|14
21|22|23|23... (1 Reply)
Hi!
Trying to find string and then put the above Headers of corresponding fist line.
After executing a Property command a get this output:
SP/CH-CH Span Name Type TG Idle InUse OffHk OnHk Ring
-------- ------------------------------ ------ ---- ----- ----- -----
02/01-24 CARRIERSS7... (6 Replies)
I have a simple program to create a poker deck, shuffle it and deal cards. Here it is:
#include <stdio.h>
#include <stdlib.h>
#include <time.h>
struct Card {
char *face,
*suit;
};
void fillDeck (Card *deck, char *face, char *suit);
void shuffle (Card *deck);
void... (4 Replies)
Hey Guys,
Absolute neewbie here. I am trying to see if it is possible to edit headers/meta-data of files in Mac OSX. I am basically trying to change an audio file header to read 16bit instead of 24bit.
We have an issue with some of our software and it regularly exports 16bit audio files with... (3 Replies)
Hi,
I have a folder that contains many (multiple) files
1.fasta
2.fasta
3.fasta
4.fasta
5.fasta
.
.
100's of files
Each such file have data in the following format
for example:
vi 1.fasta
58 390
A
GTATACATTATTGATGAAGTCCACATGCTTTCTATGGGTGCCTTCAATGCGCTTTTAAAA (7 Replies)
I'm trying to pick up some Unix SysAdmin skills on my own outside of work through the use of the "Unix and Linux System Administrators Handbook." I've found the exercises to be very beneficial, until I came to this.... "What path did the email take? To Whom was it addressed, and to whom was it... (0 Replies)
Dear Guru's
I'm using Putty and want to edit a file. I know we generally use vi editor to do it. As I'm not good in using vi editor, I want to convert the vi into something like text pad. Is there any option in Putty to do the same ? Thanks for your response.
Srini (6 Replies)
Discussion started by: thummi9090
6 Replies
LEARN ABOUT DEBIAN
bio::seqio::fasta
Bio::SeqIO::fasta(3pm) User Contributed Perl Documentation Bio::SeqIO::fasta(3pm)NAME
Bio::SeqIO::fasta - fasta sequence input/output stream
SYNOPSIS
Do not use this module directly. Use it via the Bio::SeqIO class.
DESCRIPTION
This object can transform Bio::Seq objects to and from fasta flat file databases.
FEEDBACK
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/
AUTHORS - Ewan Birney & Lincoln Stein
Email: birney@ebi.ac.uk
lstein@cshl.org
CONTRIBUTORS
Jason Stajich, jason-at-bioperl.org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
next_seq
Title : next_seq
Usage : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq object, or nothing if no more available
Args : NONE
write_seq
Title : write_seq
Usage : $stream->write_seq(@seq)
Function: Writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Array of 1 or more Bio::PrimarySeqI objects
width
Title : width
Usage : $obj->width($newval)
Function: Get/Set the line width for FASTA output
Returns : value of width
Args : newvalue (optional)
preferred_id_type
Title : preferred_id_type
Usage : $obj->preferred_id_type('accession')
Function: Get/Set the preferred type of identifier to use in the ">ID" position
for FASTA output.
Returns : string, one of values defined in @Bio::SeqIO::fasta::SEQ_ID_TYPES.
Default = $Bio::SeqIO::fasta::DEFAULT_SEQ_ID_TYPE ('display').
Args : string when setting. This must be one of values defined in
@Bio::SeqIO::fasta::SEQ_ID_TYPES. Allowable values:
accession, accession.version, display, primary
Throws : fatal exception if the supplied id type is not in @SEQ_ID_TYPES.
perl v5.14.2 2012-03-02 Bio::SeqIO::fasta(3pm)