Hi,
I need to cut values after searching for similar patterns in a file. For example, I have the following pattern in a file:
####<Nov12 2007> <user: Vijay> <user id:123456 college:anna univ> <error code: runtime exception>
I need the values for
date:
User:
User id:
College:... (5 Replies)
I'm trying to parse COBOL code to combine variables into one string. I have two variable names that get literals moved into them and I'd like to use sed, awk, or similar to find these lines and combine the variables into the final component. These variable names are always VAR1 and VAR2. For... (8 Replies)
I need to compile a large amount of data with a common string from individual text files throughout many directories.
An example data file is below. I want to search for the following string, "cc_sectors_1" and combine all the data from each file which contains this string, into one new... (2 Replies)
Hi All,
I have a file in which i have to search for a pattern from the beginning of the file and if the pattern is found , then i have to perform a reverse search from that line to the beginning of the file to get the first occurrence of another pattern.
sample input file
hey
what are you... (8 Replies)
Hello everyone
A few years Ago the user radoulov posted a fancy solution for a problem, which was about finding common lines (gene variation names) between multiple samples (files). The code was:
awk 'END {
for (R in rec) {
n = split(rec, t, "/")
if (n > 1)
dup = dup ?... (5 Replies)
Hi,
I want to grep multiple patterns from multiple files and save to multiple outputs. As of now its outputting all to the same file when I use this command.
Input : 108 files to check for 390 patterns to check for. output I need to 108 files with the searched patterns.
Xargs -I {} grep... (3 Replies)
Hi
I have a file like
1 2
1 2 3
1 5 6
11 12
10 2
7 5
17 12
I would like to have an output as
1 2 3 5 6 10 7
11 12 17
any help would be highly appreciated
Thanks (4 Replies)
Hi,
I need help to find matched patterns in 30 files residing in a folder simultaneously. All these files only contain 1 column. For example,
File1
Gr_1
st-e34ss-11dd
bt-wwd-fewq
pt-wq02-ddpk
pw-xsw17-aqpp
Gr_2
srq-wy09-yyd9
sqq-fdfs-ffs9
Gr_3
etas-qqa-dfw
ddw-ppls-qqw... (10 Replies)
Hi,
I have multiple files in my log folder. e.g:
a_m1.log
b_1.log
c_1.log
d_1.log
b_2.log
c_2.log
d_2.log
e_m1.log
a_m2.log
e_m2.log
I need to keep latest 10 instances of each file.
I can write multiple find commands but looking if it is possible in one line.
m file are monthly... (4 Replies)
Hello.
For a given folder, I want to select any files find $PATH1 -f \( -name "*" but omit any files like pattern name ! -iname "*.jpg" ! -iname "*.xsession*" ..... \) and also omit any subfolder like pattern name -type d \( -name "/etc/gconf/gconf.*" -o -name "*cache*" -o -name "*Cache*" -o... (2 Replies)
Discussion started by: jcdole
2 Replies
LEARN ABOUT DEBIAN
re-pcr
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)