[Biopython] meddling with GeneDiagram
A M Torres, Hugo
mnemonico at posthocergopropterhoc.net
Wed Mar 7 16:18:37 UTC 2012
Fellow biopythoneers,
I've been playing around with GenomeDiagram trying to draw a gene's
features. My impressions are this is a very nifty tool indeed.
However I see a problem in the way I would can draw a gene though it might
be just my inexperience with as a user: The sigil don't
automatically distinguish between a FeatureLocation with fuzzy
position(i.e. BeforePosition(0)) and a feature with an exact position (i.e.
ExactPosition(6475)).
As example suppose I would like to draw the genes from a SeqRecord object
built from the TP53 genbank file:
def
draw_gene(seqrec):
diagram = GenomeDiagram.Diagram(seqrec.id)
gene_track = diagram.new_track(1, name='Genes:
')
gene_set =
gene_track.new_set()
····
genes = ( i for i in seqrec.features if i.type ==
'gene')
color =
colors.green
for gene in
genes:
if gene.strand ==
1:
angle = 0
#
else:
angle =
180
gene_set.add_feature(gene,·
sigil='ARROW',·
color=color,·
arrowshaft_height=1,
arrowhead_length=0.2,
label=True,
label_size=14,·
label_angle=angle,
)
diagram.draw(format='linear',·
pagesize='A4',·
fragments=1,·
start=0,·
end=len(seqrec)
)
diagram.write('gene_diagram.svg', 'SVG')
The resulting image looks like gene_diagram.svg. There seems to be a WRAP53
gene on the minus strand and the sigil represents it as awhole gene. but
its only a portion of it. Maybe we could represent its just a piece by
drawing the arrowhead pointing inwards instead of outwards as in
gene_arrow.png.
Is that possible to implement?
--
.''`. Hugo A. M. Torres
: :' :
`. `' “Talk is cheap,
`- show me the code. ” -- L. Torvalds.
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