Format of one input file:
Desired output result:
I wanna to replace all the column 1 content (exclude the content start with "#") with the info in # but remove the ">"
Command I try:
The command I try is also able to generate my desired output result.
Thanks for any advice to improve it.
Hi,
variable1="This is a car"
Now I want to replace the content of variable1, "car" to "dog". Is there any simple command I can use.
Thanks.
Joseph (4 Replies)
Hi Experts,
I have binary files contain an ID Line as:
:
:
$Header: FNDSCMON.fmb 115.6 2000/01/11 10:26:10 pkm ship$
:
:
where the ID Line format is:
$Header: <File_Name> <Version> <Last_update_date_time> pkm ship$
In this Example:
File_Name = FNDSCMON.fmb
Version = 115.6... (13 Replies)
Hi All,sorry for inconvience....please find the attachement for my question i am unable to paste the question here....please help me in slving thisthanksk.k (4 Replies)
My input:
Data name: ABC001
Data length: 1000
Detail info
Data Direction Start_time End_time Length
1 forward 10 100 90
1 forward 15 200 185
2 reverse 50 500 450
Data name: XFG110
Data length: 100
Detail info
Data Direction Start_time End_time Length
1 forward 50 100 50 ... (11 Replies)
Hi All,
I have two files one of which having some mobile numbers and corresponding value whose sample content as follows:
9058629605,8.0
9122828964,30.0
And in second file complete details of all mobile numbers and sample content as follows and delimeter used is comma(,):
... (8 Replies)
Hi,
I am having trouble while using 'sed' with reading files. Please help. I have 3 files. File A, file B and file C. I want to find content of file B in file A and replace it by content in file C.
Thanks a lot!!
Here is a sample of my question.
e.g. (file A: a.txt; file B: b.txt; file... (3 Replies)
I have a wordpress site. I need add "post_title" to all my "post_content" mysql field. Thanks.
my content: Free <b>Online Tips</b> output:Free post_title <b>Online Tips</b>:
This code does not work:
UPDATE wp_posts SET post_content = REPLACE ( post_content, 'Free <b>Online... (0 Replies)
Hello all ; )
I'got a file1 with a lot of emails like :
fistname.lastname@domaine1.comAnd another file2 with emails like
fistname.lastname@domaine2.ct.netI need a shell script that will read each line from the file1 and try to find if in file2 the fistname.lastname exist.
If yes, the... (1 Reply)
Discussion started by: Aswex
1 Replies
LEARN ABOUT DEBIAN
bio::seqio::kegg
Bio::SeqIO::kegg(3pm) User Contributed Perl Documentation Bio::SeqIO::kegg(3pm)NAME
Bio::SeqIO::kegg - KEGG sequence input/output stream
SYNOPSIS
# It is probably best not to use this object directly, but
# rather go through the SeqIO handler system. Go:
use Bio::SeqIO;
$stream = Bio::SeqIO->new(-file => $filename, -format => 'KEGG');
while ( my $seq = $stream->next_seq() ) {
# do something with $seq
}
DESCRIPTION
This class transforms KEGG gene records into Bio::Seq objects.
Mapping of record properties to object properties
This section is supposed to document which sections and properties of a KEGG databank record end up where in the Bioperl object model. It
is far from complete and presently focuses only on those mappings which may be non-obvious. $seq in the text refers to the
Bio::Seq::RichSeqI implementing object returned by the parser for each record.
'ENTRY'
$seq->primary_id
'NAME'
$seq->display_id
'DEFINITION'
$seq->annotation->get_Annotations('description');
'ORTHOLOG'
grep {$_->database eq 'KO'} $seq->annotation->get_Annotations('dblink')
'CLASS'
grep {$_->database eq 'PATH'}
$seq->annotation->get_Annotations('dblink')
'POSITION'
FIXME, NOT IMPLEMENTED
'PATHWAY'
for my $pathway ( $seq->annotation->get_Annotations('pathway') ) {
#
}
'DBLINKS'
$seq->annotation->get_Annotations('dblink')
'CODON_USAGE'
FIXME, NOT IMPLEMENTED
'AASEQ'
$seq->translate->seq
'NTSEQ'
$seq-E<gt>seq
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/
AUTHOR - Allen Day
Email allenday@ucla.edu
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::RichSeq object
Args :
write_seq
Title : write_seq
Note : write_seq() is not implemented for KEGG format output.
perl v5.14.2 2012-03-02 Bio::SeqIO::kegg(3pm)