$res holds a string of the predicted sites in tabular format.
$data_ref is a reference to an array of hashes. Each element in the array represents a predicted phosphorylation site. The hash keys are the names of the data fields,i.e.,
which returns an array of Bio::SeqFeatureI compliant objects with primary tag value Site and tag names of motif, score, sequence, zscore as above.
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Please direct usage questions or support issues to the mailing list:
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.
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:
Richard Adams, Richard.Adams@ed.ac.uk,
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Name : result Usage : $job->result (...) Returns : a result created by running an analysis Args : none (but an implementation may choose to add arguments for instructions how to process the raw result)
The method returns a scalar representing a result of an executed job. If the job was terminated by an error, the result may contain an error message instead of the real data.
This implementation returns differently processed data depending on argument:
undef Returns the raw ASCII data stream but without HTML tags Bio::SeqFeatureI The argument string defined the type of bioperl objects returned in an array. The objects are Bio::SeqFeature::Generic. parsed Returns a reference to an array of hashes containing the data of one phosphorylation site prediction. Key values are:
motif, percentile, position, protein, score, site, zscore, sequence.
Usage : $job->stringency(...) Returns : The significance stringency of a prediction Args : None (retrieves value) or High, Medium or Low. Purpose : Get/setter of the stringency to be sumitted for analysis.
Usage : $job->protein_id(...) Returns : The sequence id of the protein or unnamed if not set. Args : None Purpose : Getter of the seq_id. Returns the display_id of the sequence object.
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