Hello Everyone!
I am new on this forum and this is my first post. I wish to apologize for my, not canonical, English.
I would like to solve this problem but I have no clue of how do it!I will be grateful if someone could help me!
I have a table like this:
Each row is a gene and each column a transcription factor.The number in the intersection means if the TF there is, there is not, is upregulated, is downregulated.
Now what I would like to obtain is something like that:
Adding at each gene the TF and the relative number!I get crazy!
I really hope that someone could help me!
Thanks a lot
Giuliano
Last edited by joeyg; 11-29-2012 at 02:29 PM..
Reason: corrected spelling
I have a text file in unix with a layout like this
Column 1 - 1-12
Column 2 - 13-39
Column 3 - 40-58
Column 4 - 59-85
Column 5 - 86-120
Columbn 6 - 121-131
The file also has a header on the first 6 lines of each page. Each page is 51 lines long. So I want to remove the header from each... (30 Replies)
Hi All,
I am new to UNIX can you please help me to sort a file with different columns
my file looks like this
$ cat gaut.txt
UID PID PPID PGID SID C STIME TTY TIME CMD
liveuser 3008 2892 3008 3008 0 11:58 ? 00:00:00 gnome-session
liveuser 3019 1 ... (8 Replies)
Hi,
I found the following awk script to transpose multiple (3) columns to multiple rows:
#===
BEGIN {FS=","}
{
for (i=1;i<=NF;i++)
{
arr=$i;
if(nf<= NF)
nf=NF;
}
nr=NR
}
END {
for(i=1;i<=nf;i++)
{ (8 Replies)
Looking to join three files and then transpose some columns from multiple rows into a single row.
File Info:
FIELD TERMINATED BY '^'
ENCLOSED BY '~'
LINE TERMINATED BY '\r\n'
FIRST FILE (FOOD_DES.txt)
~01001~^~0100~^~Butter, salted~^~BUTTER,WITH... (2 Replies)
Hi All,
I'm looking for a script which can transpose field names from column headers to values in one column.
for example, the input is:
IDa;IDb;IDc;PARAM1;PARAM2;PARAM3;
a;b;c;p1val;p2val;p3val;
d;e;f;p4val;p5val;p6val;
g;h;i;p7val;p8val;p9val;
into the output like this:
... (6 Replies)
Hi
I have 5 columns like this
a b c d e
f g h i j
k l m n o
From 2nd column till the 5th column of every record, I would like to transpose them as rows, so my output file contains only one row
a
b
c
d
e
f
g
h
i
j (9 Replies)
hello gurus,
Somebody must have done this before, I couldn't find anything. Please redirect me if this was solved before, and if not please help.
To the problem now, I have multiple csv files (about 1000) which I need to concatenate by column header. The final file should have a superset... (4 Replies)
Gents,
Transpose from row to column, taking in consideration the first column, which contends the date.
Input file
72918,111000009,111000009,111000009,111000009,111000009,111000009,111000009,111000009,111000009
72918,2356,2357,2358,2359,2360,2361,2362,2363,2364
72918,0,0,0,0,0,0,0,0,0... (12 Replies)
Discussion started by: jiam912
12 Replies
LEARN ABOUT DEBIAN
bio::tools::grail
Bio::Tools::Grail(3pm) User Contributed Perl Documentation Bio::Tools::Grail(3pm)NAME
Bio::Tools::Grail - Results of one Grail run
SYNOPSIS
$grail = Bio::Tools::Grail->new(-file => 'result.grail');
# filehandle:
$grail = Bio::Tools::Grail->new( -fh => *INPUT );
# parse the results
while($gene = $grail->next_prediction()) {
# $gene is an instance of Bio::Tools::Prediction::Gene
# $gene->exons() returns an array of
# Bio::Tools::Prediction::Exon objects
# all exons:
@exon_arr = $gene->exons();
# initial exons only
@init_exons = $gene->exons('Initial');
# internal exons only
@intrl_exons = $gene->exons('Internal');
# terminal exons only
@term_exons = $gene->exons('Terminal');
# singleton exons only -- should be same as $gene->exons() because
# there are no other exons supposed to exist in this structure
@single_exons = $gene->exons('Single');
}
# essential if you gave a filename at initialization (otherwise the file
# will stay open)
$genscan->close();
DESCRIPTION
The Grail module provides a parser for Grail gene structure prediction output.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason Stajich
Email jason-at-bioperl.org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
next_prediction
Title : next_prediction
Usage : while($gene = $grail->next_prediction()) {
# do something
}
Function: Returns the next gene structure prediction of the Grail result
file. Call this method repeatedly until FALSE is returned.
Example :
Returns : A Bio::Tools::Prediction::Gene object.
Args :
_parse_predictions
Title : _parse_predictions()
Usage : $obj->_parse_predictions()
Function: Parses the prediction section. Automatically called by
next_prediction() if not yet done.
Example :
Returns :
_prediction
Title : _prediction()
Usage : $gene = $obj->_prediction()
Function: internal
Example :
Returns :
_add_prediction
Title : _add_prediction()
Usage : $obj->_add_prediction($gene)
Function: internal
Example :
Returns :
_predictions_parsed
Title : _predictions_parsed
Usage : $obj->_predictions_parsed
Function: internal
Example :
Returns : TRUE or FALSE
_has_cds
Title : _has_cds()
Usage : $obj->_has_cds()
Function: Whether or not the result contains the predicted CDSs, too.
Example :
Returns : TRUE or FALSE
perl v5.14.2 2012-03-02 Bio::Tools::Grail(3pm)