Hi Experts,
I hav a question for you..
Can we open a new window(SunOS 5.10,Putty) by a unix_command from the one we're on? Is it possible?
Thanks. (2 Replies)
Can 'spawn' script be used more than once in a given expect script ??
What I'm trying to do is, first log-into a remote server through one 'ssh' spawn com and then from there log-into another server using a secod 'ssh' spawn command. But this approach is not working... the second ssh attempt... (1 Reply)
Hi,
I require need help in two aspects actually:
1) Fatal error that gets generated as %F% from a log file say ABClog.dat to trigger a mail. At present I manually grep the log file as <grep %F% ABClog.dat| cut-d "%" -f1>. The idea is to use this same logic to grep the log file which is... (1 Reply)
Hi all,
I have a script that runs sftp with expect so I can login and send a file in a cronjob. I've installed this on a couple other servers and it has been fine. However, this time on this machine, it seems to be giving me an issue. It won't move past the spawn sftp command and return a... (3 Replies)
Hello,
I am working on an Urdu to Hindi dictionary which has the following structure:
a=b
a=c
n=d
n=q
and so on.
i.e. Headword separated from gloss by a =
I am giving below a live sample
بتا=बता
بتا=बित्ता
بتا=बुत्ता
بتان=बतान
بتان=बितान
بتانا=बिताना
I need the following... (3 Replies)
Hi all,
I want to run the following command from my main prompt :
# spawn bash
but I get the following error:
spawn: Command not found.
For this to work , I first have to go into expect.
#expect
expect1.1>spawn bash
spawn bash
564
expect1.2>
Is there any way I can skip the... (2 Replies)
Hi,
I am writing a script to automate installation of java in shell script.
#!/bin/sh
#!/usr/bin/expect
ls -la | grep jdk* | rpm -ivh ./jdk*.rpm
alternatives --install /usr/bin/java java /usr/java/jdk1.7.0_71/bin/java 2
spawn alternatives --config java
expect "Enter to keep the current... (5 Replies)
Today, I noticed some errors in our SSL cert renewal log files, mostly related to domains where the IP address had changed. Concerned about this, rebuilt out SSL cert, which normally goes well without a hiccup.
However, for today, for some reason which I cannot explain, there was a PHP error... (0 Replies)
Discussion started by: Neo
0 Replies
LEARN ABOUT DEBIAN
psi-cd-hit-2d-g1
PSI-CD-HIT-2D-G1.PL(1) User Commands PSI-CD-HIT-2D-G1.PL(1)NAME
psi-cd-hit-2d-g1.pl - runs similar algorithm like CD-HIT but using BLAST to calculate similarities in db1 or db2 format
DESCRIPTION
Usage psi-cd-hit-2d [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
-i2 second input database
-blastn run blastn, default 0
-lo how long can seq in db2 > db1 in a cluster, default 0
means, that seq in db2 should <= seqs in db1 in a cluster
============================== 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-2d-g1.pl 4.6-2012-04-25 April 2012 PSI-CD-HIT-2D-G1.PL(1)