Removing rows that contain non-unique column entry
Background:
I have a file of thousands of potential SSR primers from Batch Primer 3.
I can't use primers that will contain the same sequence ID or sequence as another primer.
I have some basic shell scripting skills, but not enough to handle this.
What you need to know:
I need to remove the entire line(row) if its entry in column 3 or 13 is not unique when compared to the rest of its column. Or, I need to cat all lines that have a unique entry in columns 3 and 13 to a new file.
Note: I can't just remove the duplicate value, I have to remove the whole row after checking a value in that row against the rest of its column.
Example data is attached. Red values are duplicates.
Dear people, can you please enlighten:
I need to do a (most probably) very simple thing but couldn't figure how.
I have files with lots of lines starting with a fixed expression:
Query=. (the dot is a space)
followed by different combinations of characters including special ones such... (5 Replies)
Hello,
I have 2 columns (1st column has multiple entries but the corresponding values in the column 2 may be the same or different.) however I want to extract unique values for each entry in column 1 by assigning the max value from column 2
SDF4 -0.211654
SDF4 0.978068
... (1 Reply)
Hi All,
I have a file example.csv which looks like this
GrpID,TargetID,Signal,Avg_Num
CSCH74_1_1,2007,61,256
CSCH74_1_1,212007,647,679
CSCH74_1_1,12007,3,32
CSCH74_1_1,207,299,777
I want the output as
GrpID,TragetID,Signal-CSCH74_1_1,Avg_Num
CSCH74_1_1,2007,61,256... (4 Replies)
Hi all
I have a file which looks like this
1234|1|Jon|some text|some text
1234|2|Jon|some text|some text
3453|5|Jon|some text|some text
6533|2|Kate|some text|some text
4567|3|Chris|some text|some text
4567|4|Maggie|some text|some text
8764|6|Maggie|some text|some text
My third column is my... (9 Replies)
I have 2 files,
file01= 7 columns, row unknown (but few)
file02= 7 columns, row unknown (but many)
now I want to create an output with the first field that is shared in both of them and then subtract the results from the rest of the fields and print there
e.g.
file 01
James|0|50|25|10|50|30... (1 Reply)
Hi all,
I have the following input - the unique row key is 1st column
cat file.txt
A response
C request
C response
D request
C request
C response
E request
The desired output should be
C request (7 Replies)
I do have a tab delimited file of the following format:
431 kat1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
432 kat2 2 NA NA NA NA NA NA NA NA NA NA NA NA NA
433 KATe NA 3 NA NA 6 NA NA NA 10 11 NA NA NA NA
542 Kaed 2 NA NA NA NA NA NA NA NA NA NA NA NA NA
543 hkwuy NA NA NA NA 6 NA NA NA NA 11 NA NA... (11 Replies)
Hello Team,
I need your help on the following:
My input file a.txt is as below:
3330690|373846|108471
3330690|373846|108471
0640829|459725|100001
0640829|459725|100001
3330690|373847|108471
Here row 1 and row 2 of column 1 are identical but corresponding column 2 value are... (4 Replies)
Hi All ,
I am having an input file as stated below
Input file
6 ddk/djhdj/djhdj/Q 10 0.5
dhd/jdjd.djd.nd/QB 01 0.5
hdhd/jd/jd/jdj/Q 10 0.5
512 hd/hdh/gdh/Q 01 0.5
jdjd/jd/ud/j/QB 10 0.5
HD/jsj/djd/Q 01 0.5
71 hdh/jjd/dj/jd/Q 10 0.5
... (5 Replies)
Discussion started by: kshitij
5 Replies
LEARN ABOUT DEBIAN
bio::primerdesigner::epcr
Bio::PrimerDesigner::epcr(3pm) User Contributed Perl Documentation Bio::PrimerDesigner::epcr(3pm)NAME
Bio::PrimerDesigner::epcr - A class for accessing the epcr binary
SYNOPSIS
use Bio::PrimerDesigner::epcr;
DESCRIPTION
A low-level interface to the e-PCR binary. Uses supplied PCR primers, DNA sequence and stringency parameters to predict both expected and
unexpected PCR products.
METHODS
run
Sets up the e-PCR request for a single primer combination and returns an Bio::PrimerDesigner::Result object
If the permute flag is true, all three possible primer combinations will be tested (ie: forward + reverse, forward + forward, reverse +
reverse)
request
Assembles the e-PCR config file and command-line arguments and send the e-PCR request to the local e-PCR binary or remote server.
verify
Check to make that the e-PCR binary is installed and functioning properly. Since e-PCR returns nothing if no PCR product is found in the
sequence, we have to be able to distinguish between a valid, undefined output from a functioning e-PCR and an undefined output for some
other reason. verify uses sham e-PCR data that is known to produce a PCR product.
binary_name
Defines the binary's name on the system.
list_aliases
There are no aliases to list for epcr.
list_params
Returns a list of e-PCR configuration options. Required e-PCR input is a sequence string or file and the left and right primers. Default
values will be used for the remaining options if none are supplied.
AUTHOR
Copyright (C) 2003-2009 Sheldon McKay <mckays@cshl.edu>, Ken Youens-Clark <kclark@cpan.org>.
LICENSE
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by
the Free Software Foundation; version 3 or any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation,
Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
SEE ALSO
Bio::PrimerDesigner::primer3.
perl v5.10.0 2009-08-04 Bio::PrimerDesigner::epcr(3pm)