01-18-2008
If you provide an example of the output you expect, somebody may be able to help you.
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1. Solaris
My input file looks like
"
@$SCRIPT/atp_asrmt_adj.sql
$SCRIPT/dba2000.scr -s / @$SCRIPT/cim1005w.pls
$SCRIPT/dba2000.scr -s / @$SCRIPT/cim1006w.pls
start $SCRIPT/cim1020d.sql;^M
spool $DATA/cim1021m.sql
@$DATA/cim1021m.sql
! rm $DATA/cim1021m.sql
spool $DATA/cim1021m.sql... (1 Reply)
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2. Shell Programming and Scripting
Hi,
Please help me to extrat values b/w two delimiters.
$ echo $abc
i want to extract the value 12345 b/w %. (5 Replies)
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3. Programming
needa c program to extract text between two delimiters from some text file.
and then storing them in to diffrent variables ?
text file like 0:
abc.txt
=========
aaaaaa|11111111|sssssssssss|333333|ddddddddd|34343454564|asass
aaaaaa|11111111|sssssssssss|333333|ddddddddd|34343454564|asass... (7 Replies)
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4. Shell Programming and Scripting
I need to extract certain pieces from a string, wher delimiters may vary. For example
A0 B0 C0 12345677 X0 Y0 Z0
A1-B1 C1 12345678 X1 Y0 Z0
A1/B2 C77 12345679 X2 Y0 Z0
I need to get
C0 12345677 X0
C1 12345678 X1
C77 12345679 X2
I tried sed, see example below:
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5. AIX
Hi,
Can somebody help me with the below situation,
Input File,
========
2007_08_07_IA-0100-014_(MONTHLY).PDF
2007_08_07_IA-0100-031_(QUARTERLY)(RERUN).PDF
2008-02-28_KR-1022-003_(MONTH)(RERUN)(REC1).CSV
Required output,
============
MONTHLY
QUARTERLY
MONTH
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I try order the content from file by delimiters.
This is the text:
interface Loopback0
description !!!RID RR_SLT
ip address 172.31.128.19 255.255.255.255
interface GigabitEthernet0
description !!!P_SLT GI0/0/9
ip address 172.31.130.246 255.255.255.252
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Good afternoon!
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Hi All,
i have file name like below
ABC_065224_123456_123456_your_130413_163005.txt
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ABC_065224_123456_123456_MAIN_130413_163005.txt
ABC_065224_123456_123456_434567_MAIN_130413_163005.txt
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10. Shell Programming and Scripting
Hi All,
I'm stuck-up in finding a way to skip the delimiter which come within double quotes using awk or any other better option. can someone please help me out.
Below are the details:
Delimited: |
Sample data: 742433154|"SYN|THESIS MED CHEM PTY.... (2 Replies)
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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)