I can not figure out why there are 56,548 unique entries in test.bed. However, perl and awk see only 56,543 and that # is what my analysis see's as well. What happened to the 5 missing? Thank you .
Hello experts,
I do -
$ ls -lhtr logs2007*
Is it possible that i can get the results of-
totals size in MB/KB for ALL "logs2007*"
note: in the same directory I have "logs2006*" & "logs2007*" files. (4 Replies)
To start I have a table that has ticketholders. Each ticket holder has a unique number and each ticket holder is associated to a so called household number. You can have multiple guests w/i a household.
I would like to create 3 flags (form a, for a household that has 1-4 gst) form b 5-8 gsts... (3 Replies)
I am working on this script, but hit a bump. Looking for a little help figuring out the last part:
open(MY_FILE, $ARGV) or die
$COUNTER = 1;
$LINE = <FILE>;
while ($LINE, <FILE>) {
# Adds leading zeros for numbers 1 digit long
if ($COUNTER<10){
print "000";
}
# Adds... (2 Replies)
If i have a file sample.txt with more than 10 columns and 11th column as following data. would it be possible to get the distinct counts of values in single shot,Thank you.
Y
Y
N
N
N
P
P
o
Expected Result:
Value count
Y 2
N 3
P 2 (2 Replies)
HI ,
I am having a huge comma delimiter file, I have to append the following four lines before the starting of the file through a shell script.
FILE NAME = TEST_LOAD
DATETIME = CURRENT DATE TIME
LOAD DATE = CURRENT DATE
RECORD COUNT = TOTAL RECORDS IN FILE
Source data
1,2,3,4,5,6,7... (7 Replies)
I have any XML ouput file(file name TABLE.xml), where the data is loaded in A SINGLE LINE, I need help in writting a ksh shell script which gives me the word counts of word <TABLE-ROW>
This is my input file.
<?xml version="1.0" encoding="UTF-8"?><!--Generated by Ascential Software... (4 Replies)
Hi,
I need help regarding below concern.
There is a script and it has 7 existing files(in a path say,. usr/appl/temp/file1.txt) and I need to create one new blank file say “file_count.txt” in the same script itself.
Then the new file <file_count.txt> should store all the 7 filenames and... (1 Reply)
The awk below is supposed to count all the matching $5 strings and count how many $7 values is less than 20. I don't think I need the portion in bold as I do not need any decimal point or format, but can not seem to get the correct counts. Thank you :).
file
chr5 77316500 77316628 ... (6 Replies)
Discussion started by: cmccabe
6 Replies
LEARN ABOUT DEBIAN
bio::featureio::bed
Bio::FeatureIO::bed(3pm) User Contributed Perl Documentation Bio::FeatureIO::bed(3pm)NAME
Bio::FeatureIO::bed - read/write features from UCSC BED format
SYNOPSIS
my $in = Bio::FeatureIO(-format => 'bed', -file => 'file.bed');
for my $feat ($in->next_feature) {
# do something with $feat (a Bio::SeqFeature::Annotated object)
}
my $out = Bio::FeatureIO(-format=>'bed');
for my $feat ($seq->get_seqFeatures) {
$out->write_feature($feat);
}
DESCRIPTION
See <http://www.genome.ucsc.edu/goldenPath/help/customTrack.html#BED>.
Currently for read and write only the first 6 fields (chr, start, end, name, score, strand) are supported.
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 - Allen Day
Email allenday@ucla.edu
CONTRIBUTORS
Sendu Bala, bix@sendu.me.uk
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
_initialize
Title : _initialize
Function: initializes BED for reading/writing
Args : all optional:
name description
----------------------------------------------------------
-name the name for the BED track, stored in header
name defaults to localtime()
-description the description for the BED track, stored in
header. defaults to localtime().
-use_score whether or not the score attribute of
features should be used when rendering them.
the higher the score the darker the color.
defaults to 0 (false)
use_score
Title : use_score
Usage : $obj->use_score($newval)
Function: should score be used to adjust feature color when rendering? set to true if so.
Example :
Returns : value of use_score (a scalar)
Args : on set, new value (a scalar or undef, optional)
name
Title : name
Usage : $obj->name($newval)
Function: name of BED track
Example :
Returns : value of name (a scalar)
Args : on set, new value (a scalar or undef, optional)
description
Title : description
Usage : $obj->description($newval)
Function: description of BED track
Example :
Returns : value of description (a scalar)
Args : on set, new value (a scalar or undef, optional)
perl v5.14.2 2012-03-02 Bio::FeatureIO::bed(3pm)