10 More Discussions You Might Find Interesting
1. Shell Programming and Scripting
Example:
I have files in below format
file 1:
zxc,133,joe@example.com
cst,222,xyz@example1.com
File 2 Contains:
hxd
hcd
jws
zxc
cst
File 1 has 50000 lines and file 2 has around 30000 lines :
Expected Output has to be :
hxd
hcd
jws (5 Replies)
Discussion started by: TestPractice
5 Replies
2. Shell Programming and Scripting
The bash bash below extracts the oldest folder from a directory and stores it in filename
That result will match a line in bold in input. In the matching line there is an_xxx digit in italics that
(once the leading zero is removed) will match a line in link. That is the lint to print in output.... (2 Replies)
Discussion started by: cmccabe
2 Replies
3. Shell Programming and Scripting
The below awk uses $3 and $4 in search as the min and max, then takes each $2 value in lookup and compares it. If the value in lookupfalls within the range in searchthen it prints the entire line in lookup/ICODE]. What I can't seem to figure out is how to print the matching $5 from search on that... (4 Replies)
Discussion started by: cmccabe
4 Replies
4. Shell Programming and Scripting
Hi,
I have the following input in a file & need output as mentioned below(need counter of every occurance of field which is to be increased by 1).
Input:
919143110065
919143110065
919143110052
918648846132
919143110012
918648873782
919143110152
919143110152
919143110152... (2 Replies)
Discussion started by: siramitsharma
2 Replies
5. Shell Programming and Scripting
Hi all,
I am new to using awk and am quickly discovering what a powerful pattern-recognition tool it is. However, I have what seems like a fairly basic task that I just can't figure out how to perform in one line. I want awk to find and print all the lines in which one of multiple patterns (e.g.... (8 Replies)
Discussion started by: elgo4
8 Replies
6. Shell Programming and Scripting
Hi,
My input files is like this
axis1 0 1 10
axis2 0 1 5
axis1 1 2 -4
axis2 2 3 -3
axis1 3 4 5
axis2 3 4 -1
axis1 4 5 -6
axis2 4 5 1
Now, these are my following tasks
1. Print a first column for every two rows that has the same value followed by a string.
2. Match on the... (3 Replies)
Discussion started by: jacobs.smith
3 Replies
7. Shell Programming and Scripting
Dear All,
I have a data file input.csv like below. (Only five column shown here for example.)
Data1,StepNo,Data2,Data3,Data4
2,1,3,4,5
3,1,5,6,7
3,2,4,5,6
5,3,5,5,6
From this I want the below output
Data1,StepNo,Data2,Data3,Data4
2,1,3,4,5
3,1,5,6,7
where the second column... (4 Replies)
Discussion started by: ks_reddy
4 Replies
8. Shell Programming and Scripting
Hi. How do I find an expression with awk in only one column, and if it fits, then print that whole column.
1 apple oranges
2 bannanas pears
3 cats dogs
4 hesaid shesaid
echo "which number:"
read NUMBER (user inputs number 2 for this example)
awk " /$NUMBER/ {field to search is field... (2 Replies)
Discussion started by: glev2005
2 Replies
9. Shell Programming and Scripting
I want to lookup filea with fileb,filec and filed.
If entry in filea exist in fileb and filec mark Y and then if entry in filea exist in filed mark as Y.
Final output should have all the entries from filea.
This prints only matching entries from file a in fileb i want all entries from... (9 Replies)
Discussion started by: pinnacle
9 Replies
10. Shell Programming and Scripting
As I know:
FNR: The ordinal number of the current record in the current file.
NR: The ordinal number of the current record from the start of input.
I don't understand really differency between NR and FNR. Who can explain it for me? And give me an example.
Thanks (1 Reply)
Discussion started by: anhtt
1 Replies
RE-PCR(1) General Commands Manual RE-PCR(1)
NAME
re-PCR -- Find sequence tagged sites (STS) in DNA sequences
SYNOPSIS
re-PCR [-hV] -p hash-file [-g gaps] [-n mism] [-lq] [primer ...]
re-PCR [-hV] -P hash-file [-g gaps] [-n mism] [-l] [-m margin] [-O+|-] [-C batchcnt] [-o outfile] [-r+|-] [primers-file ...]
re-PCR [-hV] -s hash-file [-g gaps] [-n mism] [-lq] [-m margin] [-o outfile] [-r+|-] [left right lo[-hi] [...]]
re-PCR [-hV] -S hash-file [-g gaps] [-n mism] [-lq] [-m margin] [-O+|-] [-C batchcnt] [-o outfile] [-r+|-] [stsfile ...]
DESCRIPTION
Implements reverse searching (called Reverse e-PCR) to make it feasible to search the human genome sequence and other large genomes by per-
forming STS and primer searches.
OPTIONS
-p=hash-file
Perform primer lookup using hash-file
-P=hash-file
Perform primer lookup using hash-file
-s=hash-file
Perform STS lookup using hash-file
-S=hash-file
Perform STS lookup using hash-file
-n=mism Set max allowed mismatches per primer for lookup
-g=gaps Set max allowed indels per primer for lookup
-m=margin Set variability for STS size for lookup
-l Use presize alignments (only if gaps>0)
-G Print alignments in comments
-d=min-max
Set default STS size
-r=+|- Enable/disable reverse STS lookup
-O=+|- Enable/disable syscall optimisation
-C=batchcnt
Set number of STSes per batch
-o=outfile
Set output file name
-q Quiet (no progress indicator)
EXAMPLE
famap -tN -b genome.famap org/chr_*.fa
fahash -b genome.hash -w 12 -f3 ${PWD}/genome.famap
re-PCR -s genome.hash -n1 -g1 ACTATTGATGATGA AGGTAGATGTTTTT 120-200
See famap(1) and fahash(1)
SEE ALSO
/usr/share/doc/ncbi-epcr/README.txt
bioperl(1), e-pcr(1), famap(1) and fahash(1)
AUTHORS
This manual page was written by Andreas Tille <tille@debian.org> for the Debian system (but may be used by others). Permission is granted
to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by
the Free Software Foundation.
On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.
April 2008 RE-PCR(1)
