BioGraPy - Biological Graphical Library in Python

Quick examples

Simple test

>>> from biograpy import Panel, tracks, features
>>> panel=Panel(fig_width=1000,fig_dpi=100)#initialize a drawer
>>> test_track = tracks.BaseTrack(name = 'test') 

Create 5 graphicfeatures

>>> feat1=features.Simple(name='feat1',start=100,end=756,fc='r',aplha=0.5,height=1)
>>> feat2=features.Simple(name='feat2',start=300,end=1056,fc='pink',aplha=0.5,height=1)
>>> feat3=features.Simple(name='feat3',start=600,end=1356,fc='y',aplha=0.5,height=1)
>>> feat4=features.Simple(name='feat4',start=800,end=1356,fc='g',aplha=0.5,height=1)
>>> feat5=features.Simple(name='feat5',start= 1357,end=1806,fc='b',aplha=0.5,height=1)

Add the features to the track::

>>> test_track.append(feat1)
>>> test_track.append(feat2)
>>> test_track.append(feat3)
>>> test_track.append(feat4)
>>> test_track.append(feat5)

Add the track to the panel::

>>> panel.add_track(test_track)

Save the drawn image in PDF format::

>>> panel.save('test.pdf')

or in short, using default styles, and saving as PNG::

>>> from biograpy import Panel, tracks, features
>>> panel=Panel(fig_width=1000)#initialize a drawer
>>> test_track = tracks.BaseTrack(features.Simple(name='feat1',start=100,end=756,),
        features.Simple(name='feat2',start=300,end=1056,),
        features.Simple(name='feat3',start=600,end=1356,),
        features.Simple(name='feat4',start=800,end=1356,),
        features.Simple(name='feat5',start= 1357,end=1806,),
        name = 'test')
>>> panel.add_track(test_track)
>>> panel.save('test.png')

draw a SeqRecord

>>> from biograpy.seqrecord import SeqRecordDrawer
>>> from Bio import SeqIO
>>> seqrec = SeqIO.read(open('biograpy/tests/test_uniprot.xml'),'uniprot-xml')
>>> grseqrec = SeqRecordDrawer(seqrec)
>>> grseqrec.save('biograpy/tests/test_uniprot.svg')