I've got to step out, so can't actually finish this, but I got the bulk of if basically done, just needs some adaptation and to be thrown in a shell script that takes parameters to be done cleaner.
More organized...
That hard coded in a few files will give you what you'd want, just change "[21].txt" to the proper regex or hardcoded names (and this should support 2 or 3 file comparisons as written, just change hardcoded lines). If that isn't enough to get you going I'll try to check back in later this afternoon for anything else.
Edit: What I see running the above with the same text files you gave:
Last edited by Vryali; 07-16-2012 at 02:34 PM..
Reason: Clarity
Can someone point me to a good book for drawing a process diagram for 50+ unix scripts? The scripts run at different frequencies, and do everything from putting and getting data via FTP, to database I/O, to checking disk space ... etc. (0 Replies)
Hey, I'm trying to use awk for some simple file manipulations but i'm getting soem wierd results.
So i want to open up a file which looks like this:
@relation 'autoMpg'
@attribute a numeric
@attribute b numeric
@attribute c numeric
@data
-1.170815,0.257522,0.016416... (2 Replies)
Hi there all,
I am using a line to get some replys from my PS
I do
ps -ef |awk '{printf $9}'
But my result is 1 big line.
No spaces between the lines or someting
for example:... (2 Replies)
In the following line The AWK statement parses through a listing for files and outputs the results using the {print} command to the screen. Is there a way to (a) send the output to a file and (b) actually perform a cp cmd to copy the listed files to another directory?
ls | awk -va=$a -vb=$b... (1 Reply)
I have files structured in stanzas, whose title is '', and the rest couples of 'id: value'. I need to find text within the title and return the whole stanzas that match the title.
The following works:
awk 'BEGIN{RS="";IGNORECASE=1}/^\/' myfileI would need to count all of the occurences, though,... (7 Replies)
Hi - we are looking for a (hopefully free/opensource) solution for diagramming our rack/hardware configuration. the rack solution seems easier to find than the hardware piece. i.e. on our IBM 770 with two CEC's, a method of noting what hardware points to what... for example, on the primary CEC,... (0 Replies)
Hi,
The following awk command :
asmcmd lsdg | awk '{print $13;}' | grep -i ${SID}
return the following output . An Empty line + two lines contain "/" at the end of the line
INDEVDATA/
INDEVFRA/
I need to remove the "/" as well as the empty line.
Please advise
Thanks (3 Replies)
Hi,
My input is like this
head input.txt
Set1,Set2,Set3
g1,g2,g3
g2,g1,g3,
g4,g5,g5
g1,g1,g1,
g2,g1,g1,
g6,g7,g8
,g7,g8
,,g8
My output file should be
Name,Set1,Set2,Set3
g1,1,1,1 (18 Replies)
Discussion started by: jacobs.smith
18 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)