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Top Forums Shell Programming and Scripting find strings at the start of a particular column Post 302479114 by kylle345 on Thursday 9th of December 2010 10:55:01 PM
Old 12-09-2010
find strings at the start of a particular column

Hey,

I have not posted here in a while. I have a biological data file that has 4 columns and I am interested in column 2. Column 5 contains a series of letters AGCT.

Basically the file looks something like this

Code:
Name   AGGTTTTCCCCCCC  L  Q
Name1  AGGTTTTAAAAAACC  L  Q
Name2  ATTGGGGGGGGGGG  L  Q

The file is tab delimited and if it column 2 begins with AGG then I want it to go into another file.

Thanks
Kylle
 

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Alzabo::Create::Column(3pm)				User Contributed Perl Documentation			       Alzabo::Create::Column(3pm)

NAME
Alzabo::Create::Column - Column objects for use in schema creation SYNOPSIS
use Alzabo::Create::Column; DESCRIPTION
This object represents a column. It holds data specific to a column. Additional data is held in a "Alzabo::Create::ColumnDefinition" object, which is used to allow two columns to share a type (which is good when two columns in different tables are related as it means that if the type of one is changed, the other is also.) INHERITS FROM
"Alzabo::Column" Note: all relevant documentation from the superclass has been merged into this document. METHODS
new The constructor accepts the following parameters: * table => "Alzabo::Create::Table" object * name => $name * nullable => 0 or 1 (optional) Defaults to false. * sequenced => 0 or 1 (optional) Defaults to false. * default => $default (optional) * default_is_raw => $boolean (optional) If "default_is_raw" is true, then it will not be quoted when passed to the DBMS in SQL statements. This should be used to allow a default which is a function, like "NOW()". * attributes => @attributes (optional) * length => $length (optional) * precision => $precision (optional) One of either ... * type => $type ... or ... * definition => "Alzabo::Create::ColumnDefinition" object * comment => $comment An optional comment. It returns a new "Alzabo::Create::Column" object. Throws: "Alzabo::Exception::Params" type Returns the column's type as a string. alter This method allows you to change a column's type, length, and precision as a single operation. It should be instead of calling "set_type()" followed by "set_length()". It takes the following parameters: * type => $type * length => $length (optional) * precision => $precision (optional) Throws: "Alzabo::Exception::Params", "Alzabo::Exception::RDBMSRules" set_type ($type) Sets the column's type. Throws: "Alzabo::Exception::Params", "Alzabo::Exception::RDBMSRules" set_table ("Alzabo::Create::Table" object) Sets the "Alzabo::Create::Table" object in which this column is located. Throws: "Alzabo::Exception::Params" name Returns the column's name as a string. set_name ($name) Sets the column's name (a string). Throws: "Alzabo::Exception::Params", "Alzabo::Exception::RDBMSRules" nullable Returns a boolean value indicating whether or not NULLs are allowed in this column. set_nullable (0 or 1) Sets the nullability of the column (this determines whether nulls are allowed in the column or not). Must be 0 or 1. Throws: "Alzabo::Exception::Params" attributes A column's attributes are strings describing the column (for example, valid attributes in MySQL are 'UNSIGNED' or 'ZEROFILL'. This method returns a list of strings of such strings. has_attribute This method can be used to test whether or not a column has a particular attribute. By default, the check is case-insensitive. It takes the following parameters: * attribute => $attribute * case_sensitive => 0 or 1 (defaults to 0) It returns a boolean value indicating whether or not the column has this particular attribute. set_attributes (@attributes) Sets the column's attributes. These are strings describing the column (for example, valid attributes in MySQL are "PRIMARY KEY" or "AUTO_INCREMENT"). Throws: "Alzabo::Exception::RDBMSRules" add_attribute ($attribute) Add an attribute to the column's list of attributes. Throws: "Alzabo::Exception::RDBMSRules" delete_attribute ($attribute) Delete the given attribute from the column's list of attributes. Throws: Throws: "Alzabo::Exception::Params", "Alzabo::Exception::RDBMSRules" default Returns the default value of the column as a string, or undef if there is no default. set_default ($default) Sets the column's default value. length Returns the length attribute of the column, or undef if there is none. precision Returns the precision attribute of the column, or undef if there is none. set_length This method takes the following parameters: * length => $length * precision => $precision (optional) This method sets the column's length and precision. The precision parameter is optional (though some column types may require it if the length is set). Throws: "Alzabo::Exception::RDBMSRules" sequenced The meaning of a sequenced column varies from one RDBMS to another. In those with sequences, it means that a sequence is created and that values for this column will be drawn from it for inserts into this table. In databases without sequences, the nearest analog for a sequence is used (in MySQL the column is given the AUTO_INCREMENT attribute, in Sybase the identity attribute). In general, this only has meaning for the primary key column of a table with a single column primary key. Setting the column as sequenced means its value never has to be provided to when calling "Alzabo::Runtime::Table->insert". Returns a boolean value indicating whether or not this column is sequenced. set_sequenced (0 or 1) Sets the value of the column's sequenced attribute. Throws: "Alzabo::Exception::Params", "Alzabo::Exception::RDBMSRules" is_primary_key Returns a boolean value indicating whether or not this column is part of its table's primary key. is_numeric Returns a boolean value indicating whether the column is a numeric type column. is_character Returns a boolean value indicating whether the column is a character type column. This is true only for any columns which are defined to hold text data, regardless of size. is_blob Returns a boolean value indicating whether the column is a blob column. This is true for any columns defined to hold binary data, regardless of size. definition The definition object is very rarely of interest. Use the "type()" method if you are only interested in the column's type. This methods returns the "Alzabo::Create::ColumnDefinition" object which holds this column's type information. set_definition ("Alzabo::Create::ColumnDefinition" object) Sets the "Alzabo::Create::ColumnDefinition" object which holds this column's type information. former_name If the column's name has been changed since the last time the schema was instantiated, this method returns the column's previous name. comment Returns the comment associated with the column object, if any. set_comment ($comment) Set the comment for the column object. perl v5.8.8 2007-12-23 Alzabo::Create::Column(3pm)
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