def __init__(self, all_transcripts, region, options):
# call superclass constructor
super(GenesTrack, self).__init__(region, options)
self.transcripts = all_transcripts
self.n_fwd_rows = None
self.n_rev_rows = None
self.row_assignment = None
self.color = options['color']
self.utr_color = options['utr_color']
# get all transcripts that overlap region
self.overlap_trs = coord.get_coord_overlaps(self.region,
self.transcripts,
use_strand=False)
# assign rows to the transcripts
padding = region.length() * 0.2
self.assign_feature_rows(self.overlap_trs, padding=padding)
if self.height <= 0.0:
# assign height based on how many rows of transcripts
# there are
self.height = float(self.n_row) * 0.5
def __init__(self, all_transcripts, region, options):
# call superclass constructor
super(GenesTrack, self).__init__(region, options)
self.transcripts = all_transcripts
self.n_fwd_rows = None
self.n_rev_rows = None
self.row_assignment = None
self.color = options['color']
self.utr_color = options['utr_color']
if 'draw_label' in options:
self.draw_label = self.parse_bool_str(options['draw_label'])
else:
self.draw_label = True
# get all transcripts that overlap region
self.overlap_trs = coord.get_coord_overlaps(self.region,
self.transcripts,
use_strand=False)
if 'longest_isoform_only' in options:
longest_only = self.parse_bool_str(options['longest_isoform_only'])
else:
longest_only = False
if longest_only:
sys.stderr.write(" only drawing longest isoform of each gene\n")
gene_groups = genome.gene.group_transcripts(self.overlap_trs)
sys.stderr.write(" grouped %d transcripts into %d genes\n" % (len(self.overlap_trs), len(gene_groups)))
longest_trs = []
for gene in gene_groups:
longest_trs.append(gene.get_longest_transcript())
self.overlap_trs = longest_trs
# assign rows to the transcripts
if self.draw_label:
padding = region.length() * 0.2
else:
padding = region.length() * 0.01
self.assign_feature_rows(self.overlap_trs, padding=padding)
if self.height <= 0.0:
# assign height based on how many rows of transcripts
# there are
self.height = float(self.n_row) * 0.5
def __init__(self, all_genes, region, options):
# call superclass constructor
super(GenesTrack, self).__init__(region, options)
self.genes = all_genes
self.n_fwd_rows = None
self.n_rev_rows = None
self.row_assignment = None
self.color = options['color']
self.utr_color = options['utr_color']
self.longest_isoform_only = self.parse_bool_str(
options['longest_isoform_only'])
if 'draw_label' in options:
self.draw_label = self.parse_bool_str(options['draw_label'])
else:
self.draw_label = True
sys.stderr.write("%d genes total\n" % len(all_genes))
# get all genes that overlap region
self.overlap_genes = coord.get_coord_overlaps(self.region,
self.genes,
use_strand=False)
sys.stderr.write("%d genes overlap region\n" % len(self.overlap_genes))
self.overlap_trs = []
for g in self.overlap_genes:
if self.longest_isoform_only:
# only longest transcript for each gene
self.overlap_trs.append(g.get_longest_transcript())
else:
# use all transcripts
self.overlap_trs.extend(gene.transcripts)
sys.stderr.write("%d transcripts overlap region" %
len(self.overlap_trs))
# assign rows to the transcripts
if self.draw_label:
padding = region.length() * 0.2
else:
padding = region.length() * 0.01
self.assign_feature_rows(self.overlap_trs, padding=padding)
if self.height <= 0.0:
# assign height based on how many rows of transcripts
# there are
self.height = float(self.n_row) * 0.5
def __init__(self, all_genes, region, options):
# call superclass constructor
super(GenesTrack, self).__init__(region, options)
self.genes = all_genes
self.n_fwd_rows = None
self.n_rev_rows = None
self.row_assignment = None
self.color = options['color']
self.utr_color = options['utr_color']
self.longest_isoform_only = self.parse_bool_str(options['longest_isoform_only'])
if 'draw_label' in options:
self.draw_label = self.parse_bool_str(options['draw_label'])
else:
self.draw_label = True
sys.stderr.write("%d genes total\n" % len(all_genes))
# get all genes that overlap region
self.overlap_genes = coord.get_coord_overlaps(self.region,
self.genes,
use_strand=False)
sys.stderr.write("%d genes overlap region\n" % len(self.overlap_genes))
self.overlap_trs = []
for g in self.overlap_genes:
if self.longest_isoform_only:
# only longest transcript for each gene
self.overlap_trs.append(g.get_longest_transcript())
else:
# use all transcripts
self.overlap_trs.extend(gene.transcripts)
sys.stderr.write("%d transcripts overlap region" % len(self.overlap_trs))
# assign rows to the transcripts
if self.draw_label:
padding = region.length() * 0.2
else:
padding = region.length() * 0.01
self.assign_feature_rows(self.overlap_trs, padding=padding)
if self.height <= 0.0:
# assign height based on how many rows of transcripts
# there are
self.height = float(self.n_row) * 0.5