PAZAR

Update of /cvsroot/pazar/XML
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv16767

Added Files:
	example_xmlparser.pl 
Removed Files:
	pazarxmlparser.pl 
Log Message:
renaming an earlier xml parser file to avoid confusion

--- pazarxmlparser.pl DELETED ---

--- NEW FILE: example_xmlparser.pl ---
#!/usr/bin/perl -w

use strict;

use XML::Parser;
use XML::SimpleObject;

#This file parses files that comply with the pazar DTD
#All it needs is code to insert the attribute data

my $file = 'pazarexample.xml';

my $parser = XML::Parser->new(ErrorContext => 2, Style => "Tree");
my $xso = XML::SimpleObject->new( $parser->parsefile($file) );


sub handle_params
{
    my $parent = new XML::SimpleObject;
    $parent = shift;    
    my @params = $parent->children('parameter');

    #param attributes: tag, value
    foreach my $param (@params)
    {
	#do something
    }
}


sub handle_transcript
{
    my $transcript = shift;
    handle_params($transcript);

    #attributes:db_subset,db_name
    my $transcript_dbsource = $transcript->child('db_source');
    handle_params($transcript_dbsource);

    #attributes: class,edit_date,family,pazar_id
    my $transcript_tf = $transcript->child('tf');
    if($transcript_tf)
    {
	handle_params($transcript_tf);
    }
}


sub handle_coordinate
{
    my $coord = shift;
    # do coordinate stuff

    handle_params($coord);
    my $coord_location = $coord->child('location');
    handle_params($coord_location);
    my $coord_location_dbsource = $coord_location->child('db_source');
    if($coord_location_dbsource)
    {
	handle_params($coord_location_dbsource);
    }
}

sub handle_regseq
{
    my $regseq = shift;
    handle_params($regseq);
    my $regseq_coord = $regseq->child('coordinate');
    handle_coordinate($regseq_coord);


    # do mutation set stuff
    my @regseq_mutation_sets = $regseq->children('mutation_set');
    if(@regseq_mutation_sets)
    {
	foreach my $mutation_set (@regseq_mutation_sets)
	{
	    handle_params($mutation_set);
	    my $mutation_set_coord = $mutation_set->child('coordinate');
	    handle_coordinate($mutation_set_coord);
	    
	    my $mutation_set_method = $mutation_set->child('method');
	    handle_params($mutation_set_method);
	    
	    my $mutation_set_ref = $mutation_set->child('ref');
	    if($mutation_set_ref)
	    {
		handle_params($mutation_set_ref);
	    }

	    #handle mutations
	    my @mutation_set_mutations = $mutation_set->children('mutation');
	    foreach my $mutation_set_mutation (@mutation_set_mutations)
	    {
		handle_params($mutation_set_mutation);
	    }
	    
	}
    }

    #do construct stuff
    my @regseq_constructs = $regseq->children('construct');
    foreach my $regseq_construct (@regseq_constructs)
    {
	handle_params($regseq_construct);
    }
}


sub handle_gene_source
{
    my $gene_source = shift;
    #   print $gene_source->attribute('description');

    handle_params($gene_source);
    #attributes:db_name,db_subset
    my $gene_source_db_source = $gene_source->child('db_source');
    handle_params($gene_source_db_source);

    #attributes:predominant_start,fuzzy_start,fuzzy_end,pazar_id
    my @gene_source_tsrs = $gene_source->children('TSR');
    if(@gene_source_tsrs)
    {
	foreach my $gene_source_tsr (@gene_source_tsrs)
	{
	    handle_params($gene_source_tsr);
	    my $gene_source_tsr_transcript = $gene_source_tsr->child('transcript');
	    if($gene_source_tsr_transcript)
	    {
		handle_transcript($gene_source_tsr_transcript);
	    }
    
	    #attributes:TFBS_name,quality,pazar_id,sequence
	    my @gene_source_tsr_regseqs = $gene_source_tsr->children('reg_seq');
	    
	    if(@gene_source_tsr_regseqs)
	    {
		foreach my $gene_source_tsr_regseq (@gene_source_tsr_regseqs)
		{
		    handle_regseq($gene_source_tsr_regseq);
		}
	    }
	}
    }

    #attributes:edit_date,pazar_id
    my @gene_source_transcripts = $gene_source->children('transcript');
    
    
    foreach my $gene_source_transcript (@gene_source_transcripts)
    {
	handle_transcript($gene_source_transcript);
    } 

}

#########################handle project section######################

#attributes:edit_date,project_name,pazar_id,status
my $project = $xso->child('pazar')->child('project');
#print $project->attribute('edit_date');

#user details
#attributes: affiliation,first_name,last_name,pazar_id,username
my $user = $project->child('user');
#print $user->attribute('affiliation');


#########################handle data######################
my $data = $xso->child('pazar')->child('data');

if($data)
{

#matrixes
#matrix attributes: pazar_id,name,db_accn,vectorA,vectorC,vectorG,vectorT,description
    my @matrixes = $data->children('matrix');
    #In my experience XML::SimpleObject returns with this example empty string 
    #as a first array element, which breaks XML::Parser
    if ((@matrixes)&&($matrixes[0] ne '')) 
    {
	foreach my $matrix (@matrixes)
	{
	    handle_params($matrix);
	    my $matrix_dbsource = $matrix->child('db_source');
	    handle_params($matrix_dbsource);
	    
	    my $matrix_info = $matrix->child('matrix_info');
	    handle_params($matrix_info);
	    
	    #handle regseqs
	    my @matrix_reg_seqs = $matrix->children('reg_seq');
	    if(@matrix_reg_seqs)
	    {
		foreach my $matrix_reg_seq (@matrix_reg_seqs)
		{
		    handle_reg_seq($matrix_reg_seq);
		}
	    }
	}
    }


    #homologs
    my @homologs = $data->children('homolog');
    if((@homologs)&&($homologs[0] ne '')) 
    {
	foreach my $homolog (@homologs)
	{
	    handle_params($homolog);
	    
	    my $homolog_dbsource = $homolog->child('db_source');
	    handle_params($homolog_dbsource);
	    
	    my @homolog_gene_sources = $homolog->children('gene_source');
	    foreach my $homolog_gene_source (@homolog_gene_sources)
	    {
		handle_gene_source($homolog_gene_source);
	    }
	    
	    my @homolog_conserved_els = $homolog->children('conserved_el');
	    if(@homolog_conserved_els)
	    {
		foreach my $homolog_conserved_el (@homolog_conserved_els)
		{
		    handle_params($homolog_conserved_el);
		}
	    }
	}
    }

    #gene sources
    my @gene_sources = $data->children('gene_source');

    #attributes
    #pazar_id, db_accn, description
    if((@gene_sources)&&($gene_sources[0] ne '')) 
    {
	foreach my $gene_source (@gene_sources) 
	{
	    handle_gene_source($gene_source);
	} #for each gene source

    }


    #attributes: dataset_name
    my @datasets = $data->children('dataset');
    if((@datasets)&&($datasets[0] ne '')) 
    {
	foreach my $dataset (@datasets)
	{
	    handle_params($dataset);
	    my @dataset_regseqs = $dataset->children('reg_seq');
	    foreach my $dataset_regseq (@dataset_regseqs)
	    {
		handle_regseq($dataset_regseq);
	    }
	}	
    }


    #sample attributes: pazar_id, sample_type
    my @samples = $data->children('sample');
    if((@samples)&&($samples[0] ne '')) 
    {
	foreach my $sample (@samples)
	{
	    handle_params($sample);
	    
	    my $cell = $sample->child('cell');
	    handle_params($cell);
	    #do something with cell attributes

	    my $time = $sample->child('time');
	    handle_params($time);
	    #do something with time attributes
	}
    }

    #funct_tf attributes: pazar_id, tf_ids, funct_TF_name, modifications
    my @funct_tfs = $data->children('funct_tf');
    if((@funct_tfs)&&($funct_tfs[0] ne '')) 
    {
	foreach my $funct_tf (@funct_tfs)
	{
	    handle_params($funct_tf);
	    my $funct_tf_ref = $funct_tf->child('ref');
	    if($funct_tf_ref)
	    {
		handle_params($funct_tf_ref);	    
	    }
	}
    }


    #attributes: pazar_id, construct_name, description, sequence
    my @constructs = $data->children('construct');
    if((@constructs)&&($constructs[0] ne '')) 
    {
	foreach my $construct (@constructs)
	{
	    handle_params($construct);
	}
    }

    #attributes: pazar_id, cond_type, molecule, description, concentration
    my @conditions = $data->children('condition');
    if((@conditions)&&($conditions[0] ne '')) 
    {
	foreach my $condition (@conditions)
	{
	    handle_params($condition);
	}
    }

    #attributes: scale,comments,quantitative,qualitative,pazar_id
    my @expressions = $data->children('expression');
    if((@expressions)&&($expressions[0] ne '')) 
    {
	foreach my $expression (@expressions)
	{
	    handle_params($expression);
	}
    }
    

    #attributes:scale,comments,quantitative,qualitative,pazar_id
    my @interactions = $data->children('interaction');
    if((@interactions)&&($expressions[0] ne '')) 
    {
	foreach my $interaction (@interactions)
	{
	    handle_params($interaction);
	}
    }

    #attributes: type_evid,status_evid
    my @evidences = $data->children('evidence');
    if((@evidences)&&($evidences[0] ne '')) 
    {
	foreach my $evidence (@evidences)
	{
	    handle_params($evidence);
	}
    }


    #attributes: description,method
    my @methods = $data->children('method');
    if((@methods)&&($methods[0] ne '')) 
    {
	foreach my $method (@methods)
	{
	    handle_params($method);
	}
    }

    #attributes: pmid
    my @refs = $data->children('ref');
    if((@refs)&&($refs[0] ne '')) 
    {
	foreach my $ref (@refs)
	{
	    handle_params($ref);
	}      
    }


    #attributes: pazar_id,name,tissue_ontology,description,species,status
    my @cells = $data->children('cell');
    if((@cells)&&($cells[0] ne '')) 
    {
	foreach my $cell (@cells)
	{
	    handle_params($cell);
	}       
    }

    #attributes: pazar_id,name,description,scale
    my @times = $data->children('time');
    if((@times)&&($times[0] ne '')) 
    {
	foreach my $time (@times)
	{
	    handle_params($time);
	}
    }
}# if data


#########################handle analysis######################
my @analyses = $xso->child('pazar')->children('analysis');

if((@analyses)&&($analyses[0] ne '')) 
{
    #analysis attributes: name,comments
    foreach my $analysis (@analyses)
    {

	#attributes: type_evid,status_evid
	my $evidence = $analysis->child('evidence');
	handle_params($evidence);

	#attributes: description,method
	my $method = $analysis->child('method');
	handle_params($method);

	#attributes: pmid
	my $ref = $analysis->child('ref');
	if($ref)
	{
	    handle_params($ref);
	}


	#attributes: pazar_id,name,tissue_ontology,description,species,status
	my $cell = $analysis->child('cell');
	if($cell)
	{
	    handle_params($cell);
	}
	
	#attributes: pazar_id,name,description,scale
	my $time = $analysis->child('time');
	if($time)
	{
	    handle_params($time);
	}

	#handle multiple input_outputs

	my @input_outputs = $analysis->children('input_output');
	#attributes: edit_date
	foreach my $input_output (@input_outputs)
	{
	    #attributes: inputs
	    my @inputs = $input_output->children('input');
	    foreach my $input (@inputs)
	    {
		#do something
	    }
	    #attributes: outputs
	    my @outputs = $input_output->children('output');
	    foreach my $output (@outputs)
	    {
		#do something
	    }
	}
    }
}

2005	Jan	Feb	Mar	Apr	May	Jun	Jul	Aug	Sep	Oct	Nov (42)	Dec (93)
2006	Jan (74)	Feb (149)	Mar (202)	Apr (94)	May (113)	Jun (88)	Jul	Aug (13)	Sep (25)	Oct (44)	Nov (25)	Dec (12)
2007	Jan (8)	Feb (13)	Mar (6)	Apr (13)	May (35)	Jun (74)	Jul (61)	Aug (47)	Sep (17)	Oct (3)	Nov (1)	Dec
2008	Jan (3)	Feb (12)	Mar (12)	Apr	May (7)	Jun (27)	Jul (13)	Aug (24)	Sep (3)	Oct (17)	Nov (2)	Dec (2)
2009	Jan (3)	Feb (3)	Mar (4)	Apr	May (33)	Jun (18)	Jul (20)	Aug (23)	Sep	Oct (4)	Nov (15)	Dec
2010	Jan (2)	Feb	Mar	Apr (4)	May	Jun	Jul	Aug (5)	Sep (5)	Oct (2)	Nov (1)	Dec (17)
2011	Jan (4)	Feb	Mar	Apr (1)	May (3)	Jun	Jul (6)	Aug (1)	Sep (13)	Oct (6)	Nov (7)	Dec
2012	Jan (46)	Feb (1)	Mar	Apr (1)	May (1)	Jun	Jul (11)	Aug	Sep	Oct (25)	Nov	Dec (9)
2013	Jan	Feb	Mar	Apr	May	Jun (4)	Jul	Aug	Sep	Oct	Nov	Dec
2015	Jan	Feb	Mar	Apr	May	Jun	Jul	Aug (1)	Sep	Oct	Nov	Dec

S	M	T	W	T	F	S
		1	2	3	4 (2)	5
6	7 (3)	8	9 (2)	10 (4)	11 (4)	12
13	14	15	16	17 (1)	18 (1)	19
20	21 (1)	22 (1)	23 (2)	24	25 (7)	26
27	28 (7)	29	30	31

Thanks for helping keep SourceForge clean.

PAZAR

Brought to you by: elodiepc, j_lim, jaysnoddy, kirovs

pazar-guts — internal development communication list