<reponame>StephenRogers1/cogent3
"""
Draw sequence logos
===================

Sequence logo's display sequence information. They're extensively applied to transcription factor binding site (TFBS) display. They can also be applied to sequence alignments more generally.
"""
#%%
# Drawing logo for a TFBS
# #######################
# 
# We use the TFBS for the TAT box binding protein.

from cogent3 import load_aligned_seqs
from cogent3.parse import jaspar


_, pwm = jaspar.read("../../data/tbp.jaspar")
freqarr = pwm.to_freq_array()
freqarr[:5]  # illustrating the contents of the MotifFreqsArray


# %%
logo = freqarr.logo()
logo.show(height=250, width=500)

#%%
# Drawing a sequence logo from a multiple sequence alignment
# ##########################################################
# 
# This can be done for an entire alignment, but bear in mind it can take some time to render. Note that we include gap characters in the display.


aln = load_aligned_seqs("../../data/brca1-bats.fasta", moltype="dna")
l = aln[:311].seqlogo(height=300, width=500, wrap=60, vspace=0.05)
l.show()

#%%
# Sequence logo of protein alignment
# ##################################
# 
# No difference here except it uses the built-in colour scheme from the protein `MolType`.

aa = aln.get_translation(incomplete_ok=True)[:120]
logo = aa.seqlogo(width=500, height=300, wrap=50, vspace=0.1)
logo.show()

"""
Draw sequence logos
===================

Sequence logo's display sequence information. They're extensively applied to transcription factor binding site (TFBS) display. They can also be applied to sequence alignments more generally.
"""
#%%
# Drawing logo for a TFBS
# #######################
# 
# We use the TFBS for the TAT box binding protein.

from cogent3 import load_aligned_seqs
from cogent3.parse import jaspar


_, pwm = jaspar.read("../../data/tbp.jaspar")
freqarr = pwm.to_freq_array()
freqarr[:5]  # illustrating the contents of the MotifFreqsArray


# %%
logo = freqarr.logo()
logo.show(height=250, width=500)

#%%
# Drawing a sequence logo from a multiple sequence alignment
# ##########################################################
# 
# This can be done for an entire alignment, but bear in mind it can take some time to render. Note that we include gap characters in the display.


aln = load_aligned_seqs("../../data/brca1-bats.fasta", moltype="dna")
l = aln[:311].seqlogo(height=300, width=500, wrap=60, vspace=0.05)
l.show()

#%%
# Sequence logo of protein alignment
# ##################################
# 
# No difference here except it uses the built-in colour scheme from the protein `MolType`.

aa = aln.get_translation(incomplete_ok=True)[:120]
logo = aa.seqlogo(width=500, height=300, wrap=50, vspace=0.1)
logo.show()
Draw sequence logos ===================  Sequence logo's display sequence information. They're extensively applied to transcription factor binding site (TFBS) display. They can also be applied to sequence alignments more generally. #%% # Drawing logo for a TFBS # ####################### # # We use the TFBS for the TAT box binding protein. # illustrating the contents of the MotifFreqsArray # %% #%% # Drawing a sequence logo from a multiple sequence alignment # ########################################################## # # This can be done for an entire alignment, but bear in mind it can take some time to render. Note that we include gap characters in the display. #%% # Sequence logo of protein alignment # ################################## # # No difference here except it uses the built-in colour scheme from the protein `MolType`.