seequence

Display/explore (bio)sequences with Bokeh

Example:

from seequence.view import *
from seequence.color import *

sequence_nt = 'GCTAGTGGTGCTAGCCCCGCGAAATTAATACGACTCACTATAGGGTCTAGAAATAATTTTGTTTAACTTTAAGAAGGAGATATACATATGCAAAGCCCAGCACCTGCCGCAGCGCCTGCCCCTGCGGCACGTTCCATCGCAGCTACGCCTCCTAAACTGATCGTGGCAATTAGCGTGGACCAGTTTAGTGCAGACTTGTTCTCGGAGTATCGTCAATATTACACCGGAGGTTTAAAGCGTCTTACATCCGAAGGAGCTGTGTTCCCACGTGGTTATCAGAGTCATGCGGCAACAGAAACGTGTCCTGGTCACTCAACGATCCTGACAGGATCACGTCCGTCACGTACGGGTATTATCGCTAATAACTGGTTCGACTTGGACGCAAAGCGTGAGGATAAAAATCTGTACTGTGCTGAGGATGAATCCCAACCCGGTAGTTCGTCTGACAAGTACGAAGCTTCGCCACTGCACTTAAAGGTACCCACCCTGGGGGGACGCATGAAAGCCGCCAATCCTGCGACTCGTGTCGTCTCTGTTGCCGGCAAGGATCGCGCGGCCATTATGATGGGTGGCGCCACAGCGGATCAGGTCTGGTGGTTAGGGGGGCCTCAGGGGTATGTTTCGTATAAGGGTGTAGCGCCAACTCCCCTTGTAACACAGGTCAATCAGGCCTTTGCACAGCGCTTAGCTCAGCCGAACCCGGGATTTGAGTTGCCTGCTCAGTGCGTCAGCAAGGACTTTCCTGTTCAAGCGGGAAATCGCACAGTGGGTACCGGCCGCTTCGCCCGTGATGCTGGTGACTACAAAGGTTTTCGCATTTCCCCGGAGCAGGATGCTATGACGCTTGCATTCGCTGCCGCGGCCATTGAAAATATGCAATTAGGGAAGCAGGCCCAGACCGATATTATTAGCATTGGACTGAGCGCTACGGATTACGTGGGACACACCTTCGGCACGGAGGGTACGGAGAGTTGCATCCAAGTGGATCGTTTAGACACGGAGCTTGGTGCATTCTTTGATAAACTGGATAAGGATGGGATTGACTACGTAGTAGTGCTGACTGCAGATCATGGAGGACACGATCTGCCCGAACGTCATCGTATGAATGCCATGCCGATGGAACAGCGCGTAGACATGGCCCTGACACCTAAAGCTCTGAATGCTACCATCGCTGAGAAAGCTGGCCTTCCGGGCAAAAAGGTTATTTGGTCAGATGGACCTTCTGGCGATATTTACTATGATAAGGGCCTTACAGCCGCTCAACGTGCCCGTGTTGAAACCGAGGCGTTAAAATACTTGCGCGCGCATCCCCAAGTACAGACTGTATTCACTAAGGCGGAAATCGCGGCTACCCCTTCTCCGTCGGGACCACCTGAGAGCTGGAGTTTGATCCAGGAAGCTCGCGCGTCATTTTACCCGTCGCGCTCCGGGGACCTGTTACTTTTATTGAAACCTCGTGTGATGAGCATTCCTGAGCAAGCAGTCATGGGCTCGGTTGCAACCCATGGATCTCCATGGGATACGGATCGCCGTGTGCCTATCCTGTTTTGGCGCAAAGGTATGCAGCATTTCGAACAACCCTTAGGAGTAGAGACTGTTGATATTTTGCCCTCCTTGGCTGCACTTATTAAGCTTCCTGTTCCTAAGGATCAGATCGACGGCCGCTGTCTGGACTTGGTCGCCGGCAAGGATGATTCCTGTGCTGGACAGGGAGGAGGGTCTGGGGGAGGAGGCAGTGGCATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACC'
mutreg_aa = 'QSPAPAAAPAPAARSIAATPPKLIVAISVDQFSADLFSEYRQYYTGGLKRLTSEGAVFPRGYQSHAATETCPGHSTILTGSRPSRTGIIANNWFDLDAKREDKNLYCAEDESQPGSSSDKYEASPLHLKVPTLGGRMKAANPATRVVSVAGKDRAAIMMGGATADQVWWLGGPQGYVSYKGVAPTPLVTQVNQAFAQRLAQPNPGFELPAQCVSKDFPVQAGNRTVGTGRFARDAGDYKGFRISPEQDAMTLAFAAAAIENMQLGKQAQTDIISIGLSATDYVGHTFGTEGTESCIQVDRLDTELGAFFDKLDKDGIDYVVVLTADHGGHDLPERHRMNAMPMEQRVDMALTPKALNATIAEKAGLPGKKVIWSDGPSGDIYYDKGLTAAQRARVETEALKYLRAHPQVQTVFTKAEIAATPSPSGPPESWSLIQEARASFYPSRSGDLLLLLKPRVMSIPEQAVMGSVATHGSPWDTDRRVPILFWRKGMQHFEQPLGVETVDILPSLAALIKLPVPKDQIDGRCLDLVAGKDDSCAGQ'

f_ls = []
f_ls.append(view_seq(seq = sequence_nt,
                     layer = 'seq_nt',
                     start = -90))
f_ls.append(view_seq(seq = mutreg_aa,
                     layer = 'mutreg_aa',
                     start = 0,
                     scale = 3,
                     xr = f_ls[0].x_range))
f_ls = list(reversed(f_ls))
gp = gridplot(f_ls, ncols=1,
              toolbar_location='left', toolbar_options={'logo':None})
show(gp)

Features:

• visualization:
  • align to x-axis with start, scale
  • hover text with indices
  • character -> color mappings (default dicts in color.py)
  • zoom-sensitive character visibility
• interactivity:
  • x-zoom: scroll
  • x-pan: click + drag
  • reset: double click

Install:
pip install git+https://github.com/FordyceLab/seequence.git

to edit locally:
pip install -e git+https://github.com/FordyceLab/seequence.git#egg=seequence