I have a list of files that I need to loop through, parse, and run a command against. Here's my selected approach.
Code:
for i in FIELD1.FIELD2.FIELD3.FIELD4.index
do
j=${i%.index}
loadutility -flag1 FIELD1 -flag2 FIELD2 -flag3 FIELD3 $j(without.index extension)
done < filelist.del
I figure a loop like this is my best approach but I might have to throw some awk into the equation, which unfortunately I haven't touched really!
Any suggestions on a good approach is appreciated!
Hi Friends,
I have a file in the format shown (Name followed by address:)
I need only the address part please see the output.
I have tried using nawk but I am not getting the desired output.
SAM
ADDRS 64874 FRANKLYN DR
IRVINE TX - 74394;
538 FRED ASSOCIATES
PETER
ADDRS 84734... (5 Replies)
I have one file say CM.txt which contains values like below.Its just a flat file
1000,A,X
1001,B,Y
1002,B,Z
...
..
total around 4 million lines of entries will be in that file.
Now i need to write another file CM1.txt which should have
1000,1
1001,2
1002,3
....
...
..
Here i... (6 Replies)
Hi all,
I've got 2 files.
File 1 has a list say
a
b
c
d
e
f
File 2 got
start=
What I want is to create File 3 which look like this
start=a,b,c,d,e,f
So is it possible to loop throught File1 to echo it into File3 in one line? (3 Replies)
Hi
I need to parse the file of same name which exist on different servers and calculate the count of string existed in both files.
Say a file abc.log exist on 2 servers.
I want to search for string "test" on both files and calculate the total count of search string's existence.
For... (6 Replies)
I have an xml file with the structure:
<tag1>
<value1>xyx</value1>
<value2>123</value2>
</tag1>
<tag1>
<value1>568</value1>
<value2>zzzzz</value2>
</tag1>
where I want to parse each data pair in the this single file, so something like:
find first tag1 data pair... (1 Reply)
Greetings,
I recently built a replicated DRBD, Heartbeat, & iSCSI Target Initiator storage server on Ubuntu 10.04 to offer shared storage to server Vmware ESX and Microsoft Clusters. Everything works flawlessly, however I wanted to make a script to create, remove, grow volumes to offer ESX... (6 Replies)
I have a record.txt it will update weekly, and it could be 2 lines or more ...
it just echo each line to the script
san jose,23.34%
tampa,2.15%
dallas,30.20%
seattle,44.29%
Unknown,16.72%
How do i write a shell script to give me a test.pl or bash file which contain
#!/home/perl... (8 Replies)
Hi,
I want to read file multiple times. Right now i am using while loop but that is not working.
ex.
While read line
do
while read line2
do
echo stmt1
#processing some data based on data.,
done < file2.txt
done < file1.txt # This will have 10... (4 Replies)
Discussion started by: tmalik79
4 Replies
LEARN ABOUT DEBIAN
bio::index::swissprot
Bio::Index::Swissprot(3pm) User Contributed Perl Documentation Bio::Index::Swissprot(3pm)NAME
Bio::Index::Swissprot - Interface for indexing one or more Swissprot files.
SYNOPSIS
# Make an index for one or more Swissprot files:
use Bio::Index::Swissprot;
use strict;
my $index_file_name = shift;
my $inx = Bio::Index::Swissprot->new(
-filename => $index_file_name,
-write_flag => 1);
$inx->make_index(@ARGV);
# Print out several sequences present in the index in Genbank
# format:
use Bio::Index::Swissprot;
use Bio::SeqIO;
use strict;
my $out = Bio::SeqIO->new( -format => 'genbank',
-fh => *STDOUT );
my $index_file_name = shift;
my $inx = Bio::Index::Swissprot->new(-filename => $index_file_name);
foreach my $id (@ARGV) {
my $seq = $inx->fetch($id); # Returns a Bio::Seq object
$out->write_seq($seq);
}
# alternatively
my ($id, $acc);
my $seq1 = $inx->get_Seq_by_id($id);
my $seq2 = $inx->get_Seq_by_acc($acc);
DESCRIPTION
By default the index that is created uses the AC and ID identifiers as keys. This module inherits functions for managing dbm files from
Bio::Index::Abstract.pm, and provides the basic functionality for indexing Swissprot files and retrieving Sequence objects from them. For
best results 'use strict'.
You can also set or customize the unique key used to retrieve by writing your own function and calling the id_parser() method. For
example:
$inx->id_parser(&get_id);
# make the index
$inx->make_index($index_file_name);
# here is where the retrieval key is specified
sub get_id {
my $line = shift;
$line =~ /^KWs+([A-Z]+)/i;
$1;
}
FEED_BACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Ewan Birney
Also lorenz@ist.org, bosborne at alum.mit.edu
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
_index_file
Title : _index_file
Usage : $index->_index_file( $file_name, $i )
Function: Specialist function to index Swissprot format files.
Is provided with a filename and an integer
by make_index in its SUPER class.
Example :
Returns :
Args :
id_parser
Title : id_parser
Usage : $index->id_parser( CODE )
Function: Stores or returns the code used by record_id to
parse the ID for record from a string.
Returns &default_id_parser (see below) if not
set. An entry will be added to
the index for each string in the list returned.
Example : $index->id_parser( &my_id_parser )
Returns : ref to CODE if called without arguments
Args : CODE
default_id_parser
Title : default_id_parser
Usage : $id = default_id_parser( $line )
Function: The default parser for Swissprot.pm
Returns $1 from applying the regexp /^IDs*(S+)/
or /^ACs+([A-Z0-9]+)/ to the current line.
Returns : ID string
Args : a line string
_file_format
Title : _file_format
Usage : Internal function for indexing system
Function: Provides file format for this database
Example :
Returns :
Args :
perl v5.14.2 2012-03-02 Bio::Index::Swissprot(3pm)