Bio::Prospect::Thread - Representation of a Prospect thread.
$Id: Thread.pm,v 1.28 2003/11/18 19:45:45 rkh Exp $
my $in = new IO::File $ARGV[0] or die( "can't open $ARGV[0] for reading" ); my $out = new IO::File ">$ARGV[1]" or die( "can't open $ARGV[1] for writing" ); my $xml = ''; while(<$in>) { $xml .= $_; } close($in); my $t = new Bio::Prospect::Thread( $xml ); print "tseq: " . $t->tseq() . "\n"; print "qseq: " . $t->qseq() . "\n"; print "raw: " . $t->raw_score() . "\n"; print "svm: " . $t->svm_score() . "\n"; print "align: " . $t->alignment() . "\n"; $t->write_xml( $out ); exit(0);
Bio::Prospect::Thread -- Representation of a full Prospect thread this is really just a set of methods associated with the hash structure returned by XML::Simple.
Name: new() Purpose: return Thread object Arguments: Prospect XML string Returns: Bio::Prospect::Thread
Name: qname() Purpose: return the name of the query sequence Arguments: none Returns: string
Name: qseq() Purpose: return the query sequence Arguments: none Returns: string
Name: qseq_align() Purpose: return the aligned query sequence Arguments: none Returns: string
Name: qss() Purpose: return the secondary structure of the aligned query sequence Arguments: none Returns: string
Name: qlen() Purpose: return the length of the query sequence Arguments: none Returns: integer
Name: qstart() Purpose: return the start of the alignment on the query sequence Arguments: none Returns: integer
Name: qend() Purpose: return the end of the alignment on the query sequence Arguments: none Returns: integer
Name: target_start() Purpose: return the start position of the query sequence Arguments: none Returns: integer
Name: target_end() Purpose: return the end position of the query sequence Arguments: none Returns: integer
Name: tname() Purpose: return the name of the template sequence Arguments: none Returns: string
Name: pdbcode() Purpose: return the PDB id Arguments: none Returns: string
Name: tseq() Purpose: return the template sequence Arguments: none Returns: string
Name: tseq_align() Purpose: return the aligned template sequence Arguments: none Returns: string
Name: tss() Purpose: return the secondary structure of the aligned template sequence Arguments: none Returns: string
Name: tlen() Purpose: return the length of the template sequence Arguments: none Returns: integer
Name: tstart() Purpose: return the start of the alignment on the template sequence. CURRENTLY, tstart and template_start are the same. Because the template residue numbering is not necessarily sequential (due to missing residues in the structure), I would need to parse the template xml files to correctly handle the tstart value. Arguments: none Returns: integer
Name: tend() Purpose: return the end of the alignment on the template sequence. CURRENTLY, tend and template_start are the same. Because the template residue numbering is not necessarily sequential (due to missing residues in the structure), I would need to parse the template xml files to correctly handle the tend value. Arguments: none Returns: integer
Name: template_start() Purpose: return the start position of the template sequence Arguments: none Returns: integer
Name: target_end() Purpose: return the end position of the template sequence Arguments: none Returns: integer
Name: isGlobal() Purpose: return whether the alignment is global (1) or local (0) Arguments: none Returns: integer
Name: align() Purpose: return the raw alignment from the prospect output Arguments: none Returns: string
Name: align_len() Purpose: return the alignment length Arguments: none Returns: float
Name: identities() Purpose: return the number of identities Arguments: none Returns: float
Name: svm_score() Purpose: get/set the svm score Arguments: none Returns: float
Name: raw_score() Purpose: return the raw score Arguments: none Returns: float
Name: gap_score() Purpose: return the gap score Arguments: none Returns: float
Name: mutation_score() Purpose: return the mutation score Arguments: none Returns: float
Name: ssfit_score() Purpose: return the ssfit score Arguments: none Returns: float
Name: pair_score() Purpose: return the pairwise score Arguments: none Returns: float
Name: singleton_score() Purpose: return the singletonwise score Arguments: none Returns: float
Name: rgyr() Purpose: return the radius of gyration Arguments: none Returns: float
Name: alignment() Purpose: return the threading alignment as a set of line-wrapped rows. Arguments: query tag (optional), template tag (optional), width (optional) Returns: string
Name: write_xml() Purpose: output the xml to a file Arguments: IO::File object Returns: none
Name: output_rasmol_script Purpose: return a rasmol script for displaying a threaded structure Arguments: Bio::Structure::IO::Entry object Returns: rasmol script
Name: thread_structure Purpose: modify a Bio::Structure::IO::Entry object to reflect a prospect threading alignment Arguments: Bio::Prospect::Thread object, Bio::Structure::IO::Entry object Returns: nada
Name: get_mismatches Purpose: return array of mismatches Argument: nada Returns: array of residue ids
Name: get_similarities Purpose: return array of similarities Argument: nada Returns: array of residue ids
Name: get_deletions Purpose: return array of deletions Argument: nada Returns: array of residue ids
Name: get_inserts Purpose: return array of inserts Argument: nada Returns: array of residue ids
Name: get_inserted_residues Purpose: return identities of inserted residues Argument: position of insert Returns: array of residue ids
Name: get_identities Purpose: return array of identities Argument: nada Returns: array of residue ids
Name: pdb_model() Purpose: return a rudimentary 3D backbone model in PDB format Arguments: none Returns: text
Name: _add_similarity Purpose: add residue id to list of similarities Arguments: residue id Returns: nada
Name: _add_mismatch Purpose: add residue id to list of mismatches Arguments: residue id Returns: nada
Name: _add_deletion Purpose: add residue id to list of deletions Arguments: residue id Returns: nada
Name: _add_insert Purpose: add residue id to list of inserts Arguments: template residue id at which insert occurs optional: inserted query residues Returns: nada
Name: _add_identity Purpose: add residue id to list of identities Arguments: residue id Returns: nada
Name: _a_to_aaa_code Purpose: convert a single amino acid code (e.g. W) to its three letter amino acid code (e.g. TRP) Arguments: single amino acid code Returns: triple amino acid code
Name: _format_select Purpose: handle the rasmol buffer limit Arguments: array of ids to select Returns: rasmol select statement
Name: _parse_xml_file() Purpose: parse the input XML file. Arguments: [self] Returns: self
Name: _parse_structure Purpose: parse the pdb model and determine identities, similarities, deletions Arguments: scalar containing coordinates in pdb format Returns: nada
To install Bio::Prospect::File, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Prospect::File
CPAN shell
perl -MCPAN -e shell install Bio::Prospect::File
For more information on module installation, please visit the detailed CPAN module installation guide.