Dear all,
How can i unset arrays. I mean all the subscripts including the array after using them.
Could you direct me to some links of array memory handling in the korn shell.
Thanks (2 Replies)
PHP question...
I have an SQL query that's pulled back user IDs as a set of columns. Rather than IDs, I want to use their names.
So I have an array of columns $col with values 1,7,3,12 etc and I've got an array $person with values "Fred", "Bert", "Tom" etc
So what I want to do is display the... (3 Replies)
Hello,
I am some what of a newbie to awk scripting and I seem to be struggling with this problem.
I know I need to use arrays but I can't figure out how to use them.
I have an input file that looks like this;
Name,Team,First Test, Second Test, Third Test
Crystal,Red,5,17,22... (1 Reply)
Hi
I am having text file like this
001|ramu|hno221|><
sheshadripuram|delhi|560061><
002|krishna|hno225|><
newdelhimain|delhi|560061><
i want to combine every two lines as single...line...
i.e
001|ramu|hno221|sheshadripuram|delhi|560061
can u pls help me (3 Replies)
Hi all.
I'm trying to finish a bash script with the following elements:
ARRAY="blah $ITEM blah blah"
ARRAY="blah blah $ITEM blah bluh"
#ARRAY="...."
# ...the ARRAY elements represent a variable but defined
# syntax and they're all hard-coded in the script.
#(...)
ITEMS='1.0 2.3... (2 Replies)
if i declare both but don't input any variables what values will the int array and file pointer array have on default, and if i want to reset any of the elements of both arrays to default, should i just set it to 0 or NULL or what? (1 Reply)
Hi all,
I have a file test1.txt with the below contents
abc
def
ghj
xyz
I tried printing these values using arrays.
Script tried :
===========
set -A array1 `cat test1.txt`
count=${#array1
}
i=0
while
do
echo "element of array $array1"
done (1 Reply)
I've noticed something interesting in C++ programming. I've always done tricky stuff with pointers and references to have functions deal with arrays. Doing exercises again out of a C++ book has shown me an easier way, I didn't even know was there. It's weird to me.
When dealing with arrays, it... (4 Replies)
I have never used arrays before but I have a script like this:
var1=$(for i in $(cat /tmp/jobs.021013);do $LIST -job $i -all |
perl -ne 'print /.*(\bInfo.bptm\(pid=\d{3,5}).*/' | tr -d "(Info=regpid" | tr -d ')'; $LIST -job $i -all |
cut -f7 -d','| sed -e "s/^\(*\)\(*\)\(*\)\(.*\)/\1... (2 Replies)
Am using bash
For eg:
Suppose i have a array
arr=(1 2 3 4 5 6 7 8 9 10 11 12)
suppose i give input 5 to a script and script should able to print values greater than or equal to 5 like below:
Input:
5
output:
5,6,7,8,9,10,11,12 (7 Replies)
Discussion started by: manid
7 Replies
LEARN ABOUT DEBIAN
cdhit-2d
CD-HIT-2D(1) User Commands CD-HIT-2D(1)NAME
cdhit-2d - quickly group sequences in db1 or db2 format
SYNOPSIS
cdhit-2d [Options]
DESCRIPTION
====== CD-HIT version 4.6 (built on Apr 26 2012) ======
Options
-i input filename for db1 in fasta format, required
-i2 input filename for db2 in fasta format, required
-o output filename, required
-c sequence identity threshold, default 0.9 this is the default cd-hit's "global sequence identity" calculated as: number of identical
amino acids in alignment divided by the full length of the shorter sequence
-G use global sequence identity, default 1 if set to 0, then use local sequence identity, calculated as : number of identical amino
acids in alignment divided by the length of the alignment NOTE!!! don't use -G 0 unless you use alignment coverage controls see
options -aL, -AL, -aS, -AS
-b band_width of alignment, default 20
-M memory limit (in MB) for the program, default 800; 0 for unlimitted;
-T number of threads, default 1; with 0, all CPUs will be used
-n word_length, default 5, see user's guide for choosing it
-l length of throw_away_sequences, default 10
-t tolerance for redundance, default 2
-d length of description in .clstr file, default 20 if set to 0, it takes the fasta defline and stops at first space
-s length difference cutoff, default 0.0 if set to 0.9, the shorter sequences need to be at least 90% length of the representative of
the cluster
-S length difference cutoff in amino acid, default 999999 if set to 60, the length difference between the shorter sequences and the
representative of the cluster can not be bigger than 60
-s2 length difference cutoff for db1, default 1.0 by default, seqs in db1 >= seqs in db2 in a same cluster if set to 0.9, seqs in db1
may just >= 90% seqs in db2
-S2 length difference cutoff, default 0 by default, seqs in db1 >= seqs in db2 in a same cluster if set to 60, seqs in db2 may 60aa
longer than seqs in db1
-aL alignment coverage for the longer sequence, default 0.0 if set to 0.9, the alignment must covers 90% of the sequence
-AL alignment coverage control for the longer sequence, default 99999999 if set to 60, and the length of the sequence is 400, then the
alignment must be >= 340 (400-60) residues
-aS alignment coverage for the shorter sequence, default 0.0 if set to 0.9, the alignment must covers 90% of the sequence
-AS alignment coverage control for the shorter sequence, default 99999999 if set to 60, and the length of the sequence is 400, then the
alignment must be >= 340 (400-60) residues
-A minimal alignment coverage control for the both sequences, default 0 alignment must cover >= this value for both sequences
-uL maximum unmatched percentage for the longer sequence, default 1.0 if set to 0.1, the unmatched region (excluding leading and tailing
gaps) must not be more than 10% of the sequence
-uS maximum unmatched percentage for the shorter sequence, default 1.0 if set to 0.1, the unmatched region (excluding leading and tail-
ing gaps) must not be more than 10% of the sequence
-U maximum unmatched length, default 99999999 if set to 10, the unmatched region (excluding leading and tailing gaps) must not be more
than 10 bases
-B 1 or 0, default 0, by default, sequences are stored in RAM if set to 1, sequence are stored on hard drive it is recommended to use
-B 1 for huge databases
-p 1 or 0, default 0 if set to 1, print alignment overlap in .clstr file
-g 1 or 0, default 0 by cd-hit's default algorithm, a sequence is clustered to the first cluster that meet the threshold (fast clus-
ter). If set to 1, the program will cluster it into the most similar cluster that meet the threshold (accurate but slow mode) but
either 1 or 0 won't change the representatives of final clusters
-bak write backup cluster file (1 or 0, default 0)
-h print this help
Questions, bugs, contact Weizhong Li at 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
Godzik. Bioinformatics, (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
cd-hit-2d 4.6-2012-04-25 April 2012 CD-HIT-2D(1)