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Add a metadata parameter to Alignment datatypes which stores chromosome information found in the alignment for each species.

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GMAJ tool no longer needs to have the chromosome specified for annotations.
This commit is contained in:
Daniel Blankenberg
2008-08-28 15:12:53 -04:00
parent e8ae9e040a
commit 5073bfb57a
4 changed files with 62 additions and 28 deletions
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lib/galaxy/datatypes/metadata.py
+21
View File
@@ -66,6 +66,7 @@ class MetadataParameter( object ):
value = str( value )
self.value = value
self.context = context
self.display = True
def __str__(self):
if self.value is None:
@@ -264,4 +265,24 @@ class ColumnTypesParameter( MetadataParameter ):
def __str__(self):
return ",".join( map( str, self.value ) )
class PythonObjectParameter( MetadataParameter ):
def __init__( self, spec, value, context ):
MetadataParameter.__init__( self, spec, value, context )
self.value = value
self.display = False
def __str__(self):
if not self.value:
return self.spec.to_string( self.spec.no_value )
return self.spec.to_string( self.value )
def get_html_field( self, value=None, other_values={} ):
return form_builder.TextField( self.spec.name, value=str( self ) )
def get_html( self ):
return str( self )
@classmethod
def marshal( cls, value ):
return value
lib/galaxy/datatypes/sequence.py
+9 -2
View File
@@ -24,6 +24,7 @@ class Alignment( Sequence ):
"""Add metadata elements"""
MetadataElement( name="species", desc="Species", default=[], param=metadata.SelectParameter, multiple=True, readonly=True, no_value=None )
MetadataElement( name="species_chromosomes", desc="Species Chromosomes", value={}, param=metadata.PythonObjectParameter, readonly=True, no_value={}, to_string=str )
class Fasta( Sequence ):
"""Class representing a FASTA sequence"""
@@ -165,9 +166,10 @@ class Maf( Alignment ):
def set_meta( self, dataset, first_line_is_header=False, **kwd ):
"""
Parses and returns species from MAF files.
Parses and sets species and chromosomes from MAF files.
"""
species = []
species_chromosomes = {}
try:
for i, m in enumerate( bx.align.maf.Reader( open(dataset.file_name) ) ):
for c in m.components:
@@ -176,15 +178,20 @@ class Maf( Alignment ):
# "src_split" finds the rightmost dot, which is probably
# wrong in general, and certainly here.
spec = c.src
chrom = None
if "." in spec:
spec = spec.split( "." )[0]
spec, chrom = spec.split( ".", 1 )
if spec not in species:
species.append(spec)
species_chromosomes[spec] = []
if chrom and chrom not in species_chromosomes[spec]:
species_chromosomes[spec].append( chrom )
# only check first 100,000 blocks for species
if i > 100000: break
except:
pass
dataset.metadata.species = species
dataset.metadata.species_chromosomes = species_chromosomes
def missing_meta( self, dataset ):
"""Checks to see if species is set"""
templates/dataset/edit_attributes.mako
+10 -8
View File
@@ -39,15 +39,17 @@
<div style="clear: both"></div>
</div>
%for element in metadata:
<div class="form-row">
<label>
${element.spec.desc}:
</label>
<div style="float: left; width: 250px; margin-right: 10px;">
${element.get_html()}
%if element.display:
<div class="form-row">
<label>
${element.spec.desc}:
</label>
<div style="float: left; width: 250px; margin-right: 10px;">
${element.get_html()}
</div>
<div style="clear: both"></div>
</div>
<div style="clear: both"></div>
</div>
%endif
%endfor
<div class="form-row">
<input type="submit" name="save" value="Save">
tools/visualization/GMAJ.xml
+22 -18
View File
@@ -10,7 +10,6 @@
<filter type="data_meta" ref="maf_input" key="species" />
</options>
</param>
<param name="chromosome" label="Chromosome" value="" type="text"/>
<param name="exons_file" type="data" format="bed,gff" label="Exons File" optional="True"/>
<param name="highlights_file" type="data" format="bed,gff" label="Highlights File" optional="True"/>
<param name="underlays_file" type="data" format="bed,gff" label="Underlays File" optional="True"/>
@@ -81,48 +80,53 @@ tabext = .bed .gff .gtf
nowarn = $nowarn
#end if
#for $seq_count, $annotation in $enumerate( $annotations ):
seq ${seq_count}:
#if $annotation['chromosome'].value:
seqname = $annotation['species'].$annotation['chromosome']
#else:
seqname = $annotation['species']
#set $seq_count = 0
#for $spec_count, $annotation in $enumerate( $annotations ):
#if $annotation['species'].value in $maf_input.metadata.species_chromosomes and $maf_input.metadata.species_chromosomes[$annotation['species'].value]:
#set $seq_names = [ "%s.%s" % ( $annotation['species'].value, $chrom ) for $chrom in $maf_input.metadata.species_chromosomes[$annotation['species'].value]]
#else
#set $seq_names = [$annotation['species'].value]
#end if
#for $seq_name in $seq_names:
seq ${seq_count}:
seqname = $seq_name
#if $annotation['exons_file'].dataset:
exons = ${seq_count}.exons.${annotation['exons_file'].extension}
exons = ${spec_count}.exons.${annotation['exons_file'].extension}
#end if
#if $annotation['repeats_file'].dataset:
repeats = ${seq_count}.repeats.${annotation['repeats_file'].extension}
repeats = ${spec_count}.repeats.${annotation['repeats_file'].extension}
#end if
#if $annotation['links_file'].dataset:
links = ${seq_count}.links.${annotation['links_file'].extension}
links = ${spec_count}.links.${annotation['links_file'].extension}
#end if
#if $annotation['underlays_file'].dataset:
underlays = ${seq_count}.underlays.${annotation['underlays_file'].extension}
underlays = ${spec_count}.underlays.${annotation['underlays_file'].extension}
#end if
#if $annotation['highlights_file'].dataset:
highlights = ${seq_count}.highlights.${annotation['highlights_file'].extension}
highlights = ${spec_count}.highlights.${annotation['highlights_file'].extension}
#end if
offset = $annotation['offset']
#set $seq_count = $seq_count + 1
#end for
#end for
</configfile>
<configfile name="filenames_file">
#for $seq_count, $annotation in $enumerate( $annotations ):
#for $spec_count, $annotation in $enumerate( $annotations ):
#if $annotation['exons_file'].dataset:
$annotation['exons_file'] = ${seq_count}.exons.${annotation['exons_file'].extension}
$annotation['exons_file'] = ${spec_count}.exons.${annotation['exons_file'].extension}
#end if
#if $annotation['repeats_file'].dataset:
$annotation['repeats_file'] = ${seq_count}.repeats.${annotation['repeats_file'].extension}
$annotation['repeats_file'] = ${spec_count}.repeats.${annotation['repeats_file'].extension}
#end if
#if $annotation['links_file'].dataset:
$annotation['links_file'] = ${seq_count}.links.${annotation['links_file'].extension}
$annotation['links_file'] = ${spec_count}.links.${annotation['links_file'].extension}
#end if
#if $annotation['underlays_file'].dataset:
$annotation['underlays_file'] = ${seq_count}.underlays.${annotation['underlays_file'].extension}
$annotation['underlays_file'] = ${spec_count}.underlays.${annotation['underlays_file'].extension}
#end if
#if $annotation['highlights_file'].dataset:
$annotation['highlights_file'] = ${seq_count}.highlights.${annotation['highlights_file'].extension}
$annotation['highlights_file'] = ${spec_count}.highlights.${annotation['highlights_file'].extension}
#end if
#end for
</configfile>