I have a file with userIDs, one per line no spaces. I have a script that accepts userIDs as a parameter and outputs information about them. What I have had to do in the past was to modify each line of the file with userIDs to call the script with the userID and pipe the output to a data file.
... (2 Replies)
Hi All,
I want to connect two tables in DB2 using shell script and then compare the contents of two tables field by field. Could any one please help me in connecting database tables using Unix and retriving data from the same.
Thanks,
Durwas (0 Replies)
Hi....can you guys help me out in this script??
Below is a portion text file and it contains these:
GEF001 000093625 MKL002510 000001 000000 000000 000000 000000 000000 000001
GEF001 000093625 MKL003604 000001 000000 000000 000000 000000 000000 000001
GEF001 000093625 MKL005675 000001... (1 Reply)
I need to pass a variable as a parameter from shell script into a DB2 database.
var=bhuk_1123_Q_11/22/09
select * from tbl1 where serial_id='$var';
I have tried executing it using
db2 -tvf scriptname
Somebody please help me out with this. It is throwing an error. Please tell me how... (2 Replies)
Can anyone please help me with an unix shell script to connect a DB2 database. My requirement is just to display the no of records present in a table of a DB2 database through Unix Shell script. Thx - Ram (1 Reply)
Hi All,
I have written a shell script to compile an oracle R12 form and also a procedure is called from it. The procedure registers the form, function and creates a menu entry.
I took directory as a parameter. Code is as below:
#!/bin/ksh
echo... (3 Replies)
Hi All,
I need urgent Help from all of you here.
Below is my code-
==================================================
#!/usr/bin/sh
cd $1
cat $2 | tr -ds "$" "" > parameter_file.param
export `parameter_file.param`
chmod 777 parameter_file.param
echo $1
echo $2
cd $prmDirInput... (5 Replies)
Hi,
I want to replace a chain of if-else statement in an old AWK file with values from Db2 table or CSV file. The part of code is below...
if (start_new_rec=="true"){
exclude_user="false";
user=toupper($6);
match(user, "XXXXX.");
if (RSTART ==2 ) {
... (9 Replies)
Team
I have files in different directories . How can i take the count of latest file and insert into Db2 table .
I am using
awk 'END{print NR+1-ARGC}' (File name)
to get the counts.
How can i take
1.The count of latest file
2.Insert into Db2 table( File Name and Counts) .
cd... (4 Replies)
HI Team,
I am working on reading hive table and send email in email body using shell script, can you please help on fixing the errors: I have 6 columns in my hive table and trying to send the email in the mail body.
below script:
#!/bin/bash
hive -e 'SELECT count(*) from db.table' >... (4 Replies)
Discussion started by: Mi4304
4 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)