It expects input via stdin or a file provided, so call it as either of these:
Besides, it isn't meant to do anything, but to demonstrate how you can replace your system call to cat and cut with pure Perl, shaving off quite some time and resources off a run.
I need to split a long varible which is a whole line read from a file into fields and store them in an array, the fields are delimited by pipe and a field may contain white spaces.
I tried the following concept test and it has problem with field 5 which contain a space, appearently so because... (3 Replies)
I want to read $3,$4,$5,$6,$7 of fileA in array and when
fileb $1 = fileA $4
the i want to print array and few fields from fileB.
This should work but has some syntax error.
nawk -F, 'FNR==NR{a=;next} a{print a}' fileB fileA
Appreciate if someone can correct this. (2 Replies)
I was wondering if ksh supported arrays. I have a script that may work with several hosts. I'd like a means of knowing how many hosts I'm working with and an easy way to access them (as variables) in a loop. I'm assuming there's some kind of foreach in shell scripting. (1 Reply)
consider this is a line A#B#C#D#E#F#G#H
note the delimeter is #
i want to cut or spilt in to fields using the delimeter # and to store in an array.
like this
array=A
array=B
array=C
array=D
array=E
and the array content should be displayed.
echo "${array}"
echo "${array}"... (5 Replies)
Hi experts,
I have been trying for a while to accomplish the following task using awk, and I just don't seem find find a way. I am not particular about using awk, it just seemed like the logical choice at first.
I have a file that contains 5 fields that are delimited by a space character.... (1 Reply)
I want to compare these files while putting $1 and $2 into an array and getting rid of the punctuation. What am i doing wrong?
File1.txt
Apple # 223
Peach # 84;
Banana # 1605.
Banana # 1605;
Orange # 6;
Peach # 84
Peach # 84;
Apple # 229;
Banana # 1605.
Peach # 84
Apple, # 229;... (3 Replies)
Hello
Just edited the entry to make it easier to understand what i want
How can i achieve this: GOAL:
read 2 field from a table with PSQL
result of this PSQL command is this
INSTALLEDLANG=$(su - postgres -c "psql -A -t -q -c -d ${DBNAME} -t -c 'SELECT code, iso_code from res_lang'")
... (0 Replies)
Discussion started by: winston6071
0 Replies
LEARN ABOUT DEBIAN
bp_biofetch_genbank_proxy
BP_BIOFETCH_GENBANK_PROXY(1p) User Contributed Perl Documentation BP_BIOFETCH_GENBANK_PROXY(1p)NAME
biofetch_genbank_proxy.pl - Caching BioFetch-compatible web proxy for GenBank
SYNOPSIS
Install in cgi-bin directory of a Web server. Stand back.
DESCRIPTION
This CGI script acts as the server side of the BioFetch protocol as described in http://obda.open-bio.org/Specs/. It provides two database
access services, one for data source "genbank" (nucleotide entries) and the other for data source "genpep" (protein entries).
This script works by forwarding its requests to NCBI's eutils script, which lives at http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi.
It then reformats the output according to the BioFetch format so the sequences can be processed and returned by the Bio::DB::BioFetch
module. Returned entries are temporarily cached on the Web server's file system, allowing frequently-accessed entries to be retrieved
without another round trip to NCBI.
INSTALLATION
You must have the following installed in order to run this script:
1) perl
2) the perl modules LWP and Cache::FileCache
3) a web server (Apache recommended)
To install this script, copy it into the web server's cgi-bin directory. You might want to shorten its name; "dbfetch" is recommended.
There are several constants located at the top of the script that you may want to adjust. These are:
CACHE_LOCATION
This is the location on the filesystem where the cached files will be located. The default is /usr/tmp/dbfetch_cache.
MAX_SIZE
This is the maximum size that the cache can grow to. When the cache exceeds this size older entries will be deleted automatically. The
default setting is 100,000,000 bytes (100 MB).
EXPIRATION
Entries that haven't been accessed in this length of time will be removed from the cache. The default is 1 week.
PURGE
This constant specifies how often the cache will be purged for older entries. The default is 1 hour.
TESTING
To see if this script is performing as expected, you may test it with this script:
use Bio::DB::BioFetch;
my $db = Bio::DB::BioFetch->new(-baseaddress=>'http://localhost/cgi-bin/dbfetch',
-format =>'genbank',
-db =>'genbank');
my $seq = $db->get_Seq_by_id('DDU63596');
print $seq->seq,"
";
This should print out a DNA sequence.
SEE ALSO
Bio::DB::BioFetch, Bio::DB::Registry
AUTHOR
Lincoln Stein, <lstein-at-cshl.org>
Copyright (c) 2003 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
perl v5.14.2 2012-03-02 BP_BIOFETCH_GENBANK_PROXY(1p)