Hi,
I did not understand why the following did not work out as I expected:
find . -name "pqp.txt" | grep -v "Permission"
I thought I would be able to catch whichever paths containing my pqp.txt file without receiving the display of messages such as "find: cannot access... Permisson... (1 Reply)
Howdy folks,
I am fairly new to scripting but have lost of expirience in c++, pascal, and a few other. I am trying to complete a file search script that is sent a file name containing data to search that is arranged like this
"id","name","rating"
"1","bob","7"
etc
and an argument to... (1 Reply)
Hi all.
I have a problem at work which I have managed to break down into a simple test scenario:
I have written a monitoring script that outputs every second the status of various processes, but for now, lets just print the date
input.sh:
while true
do
date
sleep 1
done
This... (9 Replies)
Hi,
I need to use a double grep so to speak. I need to grep for a particular item say BOB and then for each successful result I need to grep for another item say SMITH.
I tried grep "BOB" filename | grep "SMITH"
but it does not seem to work.
I can achieve my desired result using an... (12 Replies)
$>cat file.txt
123 d3
234 abc 3
zyf 23
124 def 8
ghi kz0
...
...
I have the following output on the screen through <some command>.
$> <some command>
abc
def
ghi
...
...
I have to search for each of these patterns in the file.txt and print the lines in file.txt matching the... (4 Replies)
Hi everybody,
I have a big file with blast results (if you know what this means, otherwise look at it just as a text file with a specific form).
I am trying to extract some ids from within this file, which have certain parameters.
For example, some Of my IDs have the term 'No hit results'... (1 Reply)
I am trying to extract the file names alone, for example "TVLI_STATS_NRT_XLSTWS03_20120215_132629.csv", from below output
which was given by the grep.
sam:/data/log: grep "C10_Subscribe.000|subscribe|newfile|" PDEWG511_TVLI_JOB_STATS.ksh.201202*
Output:
... (6 Replies)
Hi,
I have a number of files containing the information below.
"""""
Fundallinfo
6.3950 14.9715 14.0482
"""""
I would like to grep for Fundallinfo and use it to read the next line? I ideally would like to read the three numbers that follow in the next line and... (2 Replies)
So, this is weird... I'm running this command:
iotop -o -P -k -bt -d 5
I'd like to save the output relelvant to rsyslogd to a file, so I do this:
iotop -o -P -k -bt -d 5 | grep rsyslogd >> /var/log/rsyslogd
Nothing is written to the file! I can write the full output to the file:
... (2 Replies)
cat file
1 aaa
2 bbb
3 ccc
4 ddd
In TextEdit, I then copy the characters “ccc” to the clipboard. The problem is that the following command gives no output:
bash-3.2$ pbpaste | grep - file
Desired output:
3 ccc
What should the syntax be for that command? I am using MacOS El... (3 Replies)
Discussion started by: palex
3 Replies
LEARN ABOUT DEBIAN
psi-cd-hit
PSI-CD-HIT.PL(1) User Commands PSI-CD-HIT.PL(1)NAME
psi-cd-hit.pl - runs similar algorithm like CD-HIT but using BLAST to calculate similarities
DESCRIPTION
Usage psi-cd-hit [Options]
Options
-i in_dbname, required
-o out_dbname, required
-c clustering threshold (sequence identity), default 0.3
-ce clustering threshold (blast expect), default -1,
it means by default it doesn't use expect threshold, but with positive value, the program cluster seqs if similarities meet either
identity threshold or expect threshold
-L coverage of shorter sequence ( aligned / full), default 0.0
-M coverage of longer sequence ( aligned / full), default 0.0
-R (1/0) use psi-blast profile? default 0 perform psi-blast / pdb-blast type search
-G (1/0) use global identity? default 1 sequence identity calculated as
total identical residues of local alignments / length of shorter seq
if you prefer to use -G 0, it is suggested that you also use -L, such as -L 0.8, to prevent very short matches.
-d length of description line in the .clstr file, default 30 if set to 0, it takes the fasta defline and stops at first space
-l length_of_throw_away_sequences, default 10
-p profile search para, default
"-a 2 -d nr80 -j 3 -F F -e 0.001 -b 500 -v 500"
-bfdb profile database, default nr80
-s blast search para, default
"-F F -e 0.000001 -b 100000 -v 100000"
-be blast expect cutoff, default 0.000001
-b filename of list of hosts to run this program in parallel with ssh calls, you need provide a list of hosts
-pbs No of jobs to send each time by PBS querying system
you can not use both ssh and pbs at same time
-k (1/0) keep blast raw output file, default 1
-rs steps of save restart file and clustering output, default 5000
everytime after process 5000 sequences, program write a restart file and current clustering information
-restart restart file, readin a restart file
if program crash, stoped, termitated, you can restart it by add a option "-restart sth.restart"
-rf steps of re format blast database, default 200,000
if program clustered 200,000 seqs, it remove them from seq pool, and re format blast db to save time
-local dir of local blast db,
when run in parallel with ssh (not pbs), I can copy blast dbs to local drives on each node to save blast db reading time BUT, IT MAY
NOT FASTER
-J job, job_file, exe specific jobs like parse blast outonly DON'T use it, it is only used by this program itself
-single files of ids those you known that they are singletons
so I won't run them as queries
============================== by Weizhong Li, liwz@sdsc.edu ==============================
If you find cd-hit useful, please kindly cite:
"Clustering of highly homologous sequences to reduce thesize of large protein database", Weizhong Li, Lukasz Jaroszewski & Adam
GodzikBioinformatics, (2001) 17:282-283 "Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide
sequences", Weizhong Li & Adam Godzik Bioinformatics, (2006) 22:1658-1659
psi-cd-hit.pl 4.6-2012-04-25 April 2012 PSI-CD-HIT.PL(1)
06-09-2011
