Hi, I have a file that looks like this
dasdjasdjoasjdoasjdoa SYN dakspodkapsdka
asdasdasdasdasdasdasd SYN sdfsdfsdfsdfdf
shfishifhsdifhsidhfif fsdfsdfsdfsdfs
sdfsdfsdfsdsdfsdfsdff cercercercerce
sdasdajsdoajsodasodoo FIN dasdaskdpasdda... (4 Replies)
Hi,
Is there any way of using grep (this may be done in awk, not sure?) that I can stop grep'n a file once I have found the first occurrence of my search string. Looking through grep man pages
-q will exit without printing the lines after the first match, but I need the output.
I have... (5 Replies)
Hi All,
is there a way to extract the line number of an occurrence using grep?
I know that with the -n option it prints out the line number as well.
I would like to assign the line number to a variable.
Thanks,
Sarah (5 Replies)
Hi,
Is there a command to print one character x amont of times?
I need for example 10 comma's (,,,,,,,,,,). Instead of creating a loop, I was wondering if there is a way to do this with sed or awk?
Thanks! (3 Replies)
I have 1300 files (SearchFiles0001.txt, SearchFiles0002.txt, etc.) , each with 650,000 lines, tab-delimited data.
I have a pattern file, with about 1000 lines with a single word. Each single word is found in the 1300 files once.
If I grep -f PatternFile.txt SearchFiles*.txt >OutputFile.txt... (2 Replies)
I have a file similar to the following
filler filler filler
car 6 mazda
filler filler filler filler
car civic honda
car rav 4 toyota
filler filler
If i do a "grep -i car file.txt" the output would be
car 6 mazda
car civic honda
car rav 4 toyota
however, i want to have the... (4 Replies)
Hi,
I want to add a text to the end of the specific line in a file. Now my file looks like this:
999
111
222
333
111
444
I want to add the string " 555" to the end of the first line contaning 111. Moreover, I want to insert a newline after this line containg the "000" string. The... (8 Replies)
Hi,
I have been trying to do a small fun project for myself.
I want to run a command for 45 seconds.
And to get the final output of this command, the script requires I push the "q" key on my keyboard and then the final output file becomes available.
I tried the following script. But it... (12 Replies)
I have file contents
/tmp/x/abc.txt
/home/bin/backup/sys/a.log
I need this output:
/tmp/x/
/home/bin/backup/sys/
Can somebody please help me out
Please use CODE tags as required by forum rules! (3 Replies)
Discussion started by: jhonnyrip
3 Replies
LEARN ABOUT DEBIAN
clonalframe
ClonalFrame(1) General Commands Manual ClonalFrame(1)NAME
ClonalFrame - inference of bacterial microevolution using multilocus sequence data
SYNOPSIS
ClonalFrame [OPTIONS] inputfile outputfile
DESCRIPTION
ClonalFrame identifies the clonal relationships between the members of a sample, while also estimating the chromosomal position of homolo-
gous recombination events that have disrupted the clonal inheritance.
Options:
-x NUM Sets the number of iterations after burn-in (default is 50000)
-y NUM Sets the number of burn-in iterations (default is 50000)
-z NUM Sets the number of iterations between samples (default is 100)
-e NUM Sets the number of branch-swapping moves per iterations (default is so that half of the time is spent branch-swapping)
-m NUM Sets the initial value of theta to NUM (default is Watterson estimate)
-d NUM Sets the initial value of delta to NUM (default is 0.001)
-n NUM Sets the initial value of nu to NUM (default is 0.01)
-r NUM Sets the initial value of R to NUM (default is initial theta/10)
-M Do update the value of theta
-D Do not update the value of delta
-N Do not update the value of nu
-R Do not update the value of R
-T Do not update the topology
-A Do not update the ages of the nodes
-G Remove all gaps
-H Remove all gaps at non-polymorphic positions
-t NUM Indicate which initial tree to use: 0 for a null tree, 1 for a uniformly chosen coalescent tree and 2 for UPGMA tree (default)
-w FILE
Use Newick file for initial tree
-a NUM Sets the first parameter of the beta prior distribution of nu
-b NUM Sets the second parameter of the beta prior distribution of nu
-U Use uniform priors for rho, theta and delta
-B Run in BURST mode
-C Run in UPGMA mode with a site-by-site bootstrap procedure
-c Run in UPGMA mode with a fragment-by-fragment bootstrap procedure
-S NUM Sets the seed for the random number generator to NUM
-E NUM Sets the rate of exponential growth (default is 0)
-I Ignores first block in the alignment
-L Clean-up the alignment before running ClonalFrame
-l Minimum distance between two reference sites (default is 50)
-v Verbose mode
AUTHOR
ClonalFrame was written by Xavier Didelot.
This manual page was written by Andreas Tille <tille@debian.org>, for the Debian project (but may be used by others).
February 2011 1.2 ClonalFrame(1)