import seq_tools.plot4seq as p
/Users/alexsha/miniconda3/envs/seq_tools/lib/python3.6/site-packages/Bio/SearchIO/__init__.py:211: BiopythonExperimentalWarning: Bio.SearchIO is an experimental submodule which may undergo significant changes prior to its future official release. BiopythonExperimentalWarning)
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
import seq_tools.hist_ss as st
import numpy as np
#import get_hist_ss_in_aln_for_shade
human_h2a_z_core=Seq('SRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLI-KATIAGGGVIPHIHKSLIG')
xenopus_h2a_core=Seq('TRSSRAGLQFPVGRVHRLLRKGNYAE-RVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLP')
msa=MultipleSeqAlignment([SeqRecord(xenopus_h2a_core,id='H2A',name='H2A'),SeqRecord(human_h2a_z_core,id='H2Ah',name='H2Ah')])
from importlib import reload
reload(st)
<module 'seq_tools.hist_ss' from '/Users/alexsha/work_HD/seq_tools/seq_tools/hist_ss.py'>
reload(st)
features=st.get_hist_ss_in_aln_for_shade(msa,below=True)
SingleLetterAlphabet() alignment with 2 rows and 129 columns SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHR-LLRKGNYAERV...KSK H2A ---------------XRSXRAGLQFPVGRXHRXLXXXXXXXXRV...--- Query Type detected= H2A
reload(p)
p.plot_prof4seq('default',list(map(np.abs,map(np.sin,range(len(msa[0]))))),msa,features,axis='conservation')
Chosen splitting parameters 2 20 Launcning Latex: pdflatex --file-line-error --synctex=1 -output-directory=/tmp --save-size=10000 /tmp/align.tex > /dev/null mv /tmp/align.pdf /tmp/tempshade.pdf Converting PDF to PNG convert -density 150 /tmp/tempshade.pdf -trim -bordercolor White -border 0.000%x0% /tmp/tempprofseq.png
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<img src="default.png" alt="Plot" >