So the two rows have 2nd cols as At1g14590 and Hs20533698.
At1g14590 is not found in the lookup file but Hs20533698 is classified under
[U] KOG0811 SNARE protein PEP12/VAM3/Syntaxin 7/Syntaxin 17 in
the lookup file.
Is there a way to collect data from top command to a file at regular intervals. I need this on HP-UX. I need to gather resident memory usage. I know that sar will give %cpu usage. There is a pmap command which gives memory usage in solaris. Is there a similar command in HP-UX
Thanks (5 Replies)
Hi All,
Since i am very new to shell scripting, i need help from you guys.
Suppose there is a file containing:
Log message:
Ashish
"asasasa"
asasa
asasa
asasas.info1
Log message:
Kapil
"asasasa"
asasa
asasa
asasas..info1 (2 Replies)
say i have these many file in a directory named exam.
1)/exam/newfolder/link.txt.
2)/exam/newfolder1/
and i create a tar say exam.tar
well the problem is,
when i read the tar file i dont find any metadata about the directories,as you cannot create a tar containig empty directories.
on the... (2 Replies)
I have a file which contains data like
a
b
x
col1:data1
formula:data3
this is for 2
a
c
col1:@bkw
formula:dontad ad
asd
as per
a
\
i want the data from col1 and formula to keep the col1 data in left side of excel and col2 data in right side of it (1 Reply)
Hi all,
I am having lots of oracle servers. I want to collect some health check details from all the server and report to one single centralized server. What would be best solution for this?
OS: AIX
Thanks
Gopal (1 Reply)
Hi Experts,
In our project we have requirement where in we have to compare header of one file with header in the parameter file.
There are 20 files which we ftp from one site. All this files have different header.
We are comapring this file with our parameter file(which is having the header... (2 Replies)
Friends,
I need help with the following in UNIX.
Merge all csv files in one folder considering only 1 header row and ignoring header of all other files.
FYI - All files are in same format and contains same headers.
Thank you (4 Replies)
Hello There...
I have a sample input file ..
number:department:amount
125:Market:125.23
126:Hardware store:434.95
127:Video store:7.45
128:Book store:14.32
129:Gasolline:16.10
I will be doing some manipulations on all the records except the header, but the header should always be... (2 Replies)
I've been struggling with this one for quite a while and cannot seem to find a solution for this find/replace scenario. Perhaps I'm getting rusty.
I have a file that contains a number of metrics (exactly 3 fields per line) from a few appliances that are collected in parallel. To identify the... (3 Replies)
Discussion started by: verdepollo
3 Replies
LEARN ABOUT DEBIAN
bio::featureio::ptt
Bio::FeatureIO::ptt(3pm) User Contributed Perl Documentation Bio::FeatureIO::ptt(3pm)NAME
Bio::FeatureIO::ptt - read/write features in PTT format
SYNOPSIS
# read features
my $fin = Bio::FeatureIO->new(-file=>'genes.ptt', -format=>'ptt');
my @cds;
while (my $f = $fin->next_feature) {
push @cds, $f if $f->strand > 0;
}
# write features (NOT IMPLEMENTED)
my $fout = Bio::FeatureIO->new(-fh=>*STDOUT, -format=>'ptt');
for my $f (@cds) {
$fout->write_feature($f);
}
DESCRIPTION
The PTT file format is a table of protein features. It is used mainly by NCBI who produce PTT files for all their published genomes found
in <ftp://ftp.ncbi.nih.gov/genomes/>. It has the following format:
Line 1
Description of sequence to which the features belong
eg. "Leptospira interrogans chromosome II, complete sequence - 0..358943"
It is usually equivalent to the DEFINITION line of a Genbank file, with the length of the sequence appended. It is unclear why "0" is
used as a starting range, it should be "1".
Line 2
Number of feature lines in the table
eg. "367 proteins"
Line 3
Column headers, tab separated
eg. "Location Strand Length PID Gene Synonym Code COG Product"
Location : "begin..end" span of feature
Strand : "+" or "-"
Length : number of amino acids excluding the stop codon
PID : analogous to Genbank /db_xref="GI:xxxxxxxxx"
Gene : analogous to Genbank /gene="xxxx"
Synonym : analogous to Genbank /locus_tag="xxxx"
Synonym : analogous to Genbank /locus_tag="xxxx"
COG : CDD COG code with COG letter categories appended
Product : analogous to Genbank /product="xxxx"
Line 4 onwards
Feature lines, nine columns, tab separated, "-" used for empty fields
eg. "2491..3423 + 310 24217063 metF LB002 - COG0685E 5,10-methylenetetrahydrofolate reductase"
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 the
Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Torsten Seemann
Email torsten.seemann AT infotech.monash.edu.au
CONTRIBUTORS
Based on bed.pm and gff.pm by Allen Day.
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
_initialize
Title : _initialize
Function: Reading? parses the header of the input
Writing?
next_feature
Title : next_feature
Usage : $io->next_feature()
Function: read the next feature from the PTT file
Example :
Args :
Returns : Bio::SeqFeatureI object
write_feature (NOT IMPLEMENTED)
Title : write_feature
Usage : $io->write_feature($feature)
Function: write a Bio::SeqFeatureI object in PTT format
Example :
Args : Bio::SeqFeatureI object
Returns :
description
Title : description
Usage : $obj->description($newval)
Function: set/get the PTT file description for/from line one
Example :
Returns : value of description (a scalar)
Args : on set, new value (a scalar or undef, optional)
protein_count
Title : protein_count
Usage : $obj->protein_count($newval)
Function: set/get the PTT protein count for/from line two
Example :
Args : on set, new value (a scalar or undef, optional)
Returns : value of protein_count (a scalar)
perl v5.14.2 2012-03-02 Bio::FeatureIO::ptt(3pm)