For 3 and 4, you start with 3 lines and end with 1 line. Is this intended? I've assumed it's not, that you want 3 lines out for 3 lines in.
Hi Corona,
Thanks for your time.
For 3 and 4, usually the output file has thousands of records. But, I want to consider the maximum value of fourth column and print the filename as another column.
So, the three records will go out and only one record will remain, as in the example.
How can I run a program ('prog') through perl (in unix) and feed her required parameters?
system ("prog \n"); ?????????
now 'prog' ask for parameters and I want the perl script to give them automaticly without humen intervention? (2 Replies)
Hi,
I can't find how to achive such thing, please help.
I have try with uniq and comm but those command can't compare columns just whole lines,
I think awk will be the best but awk is magic for me as of now.
file a
a1~a2~a3~a4~a6~a7~a8
file b
b1~b2~b3~b4~b6~b7~b8
output 1:
compare... (2 Replies)
Hello,
I have a 1.6 GB file that I would like to modify by matching some ids in col1 with the ids in col 1 of file2.txt and save the results into a 3rd file.
For example:
File 1 has 1411 rows, I ignore how many columns it has (thousands)
File 2 has 311 rows, 1 column
Would like to... (7 Replies)
Hello everyone,
I am writing a script to process data from the ATP world tour.
I have a file which contains:
t=540 y=2011 r=1 p=N409
t=540 y=2011 r=2 p=N409
t=540 y=2011 r=3 p=N409
t=540 y=2011 r=4 p=N409
t=520 y=2011 r=1 p=N409
t=520 y=2011 r=2 p=N409
t=520 y=2011 r=3 p=N409
The... (4 Replies)
Hi,
I am facing issue while reading data from a file in UNIX. my requirement is to compare two files and for the text pattern matching in the 1st file, replace the contents in second file by the contents of first file from start to the end and write the contents to thrid file.
i am able to... (2 Replies)
Hi All,
I have around 900 Select Sql's which I would like to run in an awk script and print the output of those sql's in an txt file.
Can you anyone pls let me know how do I do it and execute the awk script? Thanks. (4 Replies)
Hi Folks,
Below is an extract from a VME Print file which gets handed over to a print house. The problem I have is not that tricky rther looking for a way to handle it in a simple and clean way.
Is to first select all lines with "0058" which have four spaces so "0058 " as the selcetion... (3 Replies)
hello,
i have a undelimited file which contains 229 byte records. i want to change column 23 - 26 with a new value and also change the sign of the data in colulmn 30 - 70. i've tried SED for the first change, but nothing happens:
sed 's/\(^.\{22\}\).\{4\}\(.*\)/\0603\2/' inputfile
heres an... (8 Replies)
Shell script logic
Hi
I have 2 input files like with file 1 content as (file1)
"BRGTEST-242" a.txt "BRGTEST-240" a.txt "BRGTEST-219" e.txt
File 2 contents as fle(2)
"BRGTEST-244" a.txt "BRGTEST-244" b.txt "BRGTEST-231" c.txt "BRGTEST-231" d.txt "BRGTEST-221" e.txt
I want to get... (22 Replies)
I am trying to consolidate multiple information files (<hostname>.Linux.nfslist) into one file so that I can import it into Excel. I can get the file contents with cat *Linux.nfslist >> nfslist.txt. I need each line prefaced with the hostname. I am unsure how to do this.
--- Post updated at... (5 Replies)
Discussion started by: Kentlee65
5 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)