Bio::Tools::Primer3 - Create input for and work with the output from the program primer3
Chad will put synopses here by the end of the second week of october, 2002.
Bio::Tools::Primer3 creates the input files needed to design primers using primer3 and provides mechanisms to access data in the primer3 output files.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new() Usage : Function: Returns : Args : Notes :
Title : Usage : Function: Returns : Args : Notes :
Title : next_primer() Usage : $primer3 = $stream->next_primer() Function: returns the next primer in the stream Returns : Bio::Seq::PrimedSeq containing: - 2 Bio::SeqFeature::Primer representing the primers - 1 Bio::Seq representing the target sequence - 1 Bio::Seq representing the amplified region Args : NONE Notes :
Title : _create_primer_features() Usage : &_create_primer_features() Function: This is an internal method used by next_seq() to create the Bio::SeqFeature::Primer objects necessary to represent the primers themselves. Returns : An array of 2 Bio::SeqFeature::Primer objects. Args : None. Notes : This is an internal method. Do not call this method.
Title : get_amplified_region() Usage : $primer->get_amplified_region() Function: Returns a Bio::Seq object representing the sequence amplified Returns : (I think) A Bio::Seq object Args : None. Notes : This is not implemented at this time. Note to chad: implement this simple getter. Developer notes: There obviously isn't a way for a single primer to know about its amplified region unless it is paired with another primer. At this time these object will generally be created with another so I will put in this method. If there is no sequence null is returned. THIS DOES NOT BELONG HERE. Put this into something else.
Title : get_amplification_error() Usage : Function: Returns : Args : Notes : Developer Notes: THIS DOES NOT BELONG HERE. Put this into something else.
Title : _set_target() Usage : &_set_target($self); Function: Returns : Args : Notes : Developer Notes: Really I have no idea why I put this in here. It can is referenced by new_deprecated and by run_primer3
Title : _read_file($self,$filename) Usage : Function: Returns : A scalar containing the contents of $filename Args : $self and the name of a file to parse. Notes : Developer notes: Honestly, I have no idea what this is for.
Title : _parse_report() Usage : &_parse_report($self,$filename); Function: Parse a primer3 outfile and place everything into an object under {primers} with PRIMER_SEQUENCE_ID being the name of the keys for the {primers} hash. Returns : Nothing. Args : $self and the name of a file to parse. Notes :
Title : _construct_empty() Usage : &_construct_empty($self); Function: Construct an empty object that will be used to construct a primer3 input "file" so that it can be run. Returns : Args : Notes :
Title : add_target(%stuff) Usage : $o_primer->add_target(%stuff); Function: Add an target to the infile constructor. Returns : Args : A hash. Looks something like this: $o_primer2->add_target( -PRIMER_SEQUENCE_ID => "sN11902", -PRIMER_COMMENT => "3831", -SEQUENCE => "some_sequence", -TARGET => "513,26", -PRIMER_PRODUCT_SIZE_RANGE => "100-500", -PRIMER_FILE_FLAG => "0", -PRIMER_LIBERAL_BASE => "1", -PRIMER_NUM_RETURN => "1", -PRIMER_FIRST_BASE_INDEX => "1", -PRIMER_EXPLAIN_FLAG => "1"); The add_target() method does not validate the things you put into this parameter hash. Read the docs for Primer3 to see which fields do what and how they should be used. Notes : To design primers, first create a new CSM::Primer3 object with the -construct_infile parameter. Then, add targets using this method (add_target()) with the target hash as above in the Args: section. Be careful. No validation will be done here. All of those parameters will be fed straight into primer3. Once you are done adding targets, invoke the function run_primer3(). Then retrieve the results using something like a loop around the array from get_primer_sequence_IDs();
Title : get_primer_sequence_IDs() Usage : $o_phred->get_primer_sequence_IDs(); Function: Return the primer sequence ID's. These normally correspond to the name of a sequence in a database but can be whatever was used when the primer3 infile was constructed. Returns : An array containing the names of the primer sequence ID's Args : None. Notes : This would be used as the basis for an iterator to loop around each primer that was designed.
Title : dump_hash() Usage : $o_primer->dump_hash(); Function: Dump out the CSM::Primer3 object. Returns : Nothing. Args : None. Notes : Used extensively in debugging.
Title : dump_infile_hash() Usage : $o_primer->dump_infile_hash(); Function: Dump out the contents of the infile hash. Returns : Nothing. Args : None. Notes : Used for debugging the construction of the infile.
Title : This is a place holder so chad can cut and paste Usage : Function: Returns : Args : Notes :
perl(1).
To install LocalConfig, copy and paste the appropriate command in to your terminal.
cpanm
cpanm LocalConfig
CPAN shell
perl -MCPAN -e shell install LocalConfig
For more information on module installation, please visit the detailed CPAN module installation guide.