pytexshade

A python wrapper for TexShade sequence alignment shader

Installation via conda

conda install -c intbio -c conda-forge -c bioconda pytexshade

Usage

In Jupyter

For Jupyter use see example.ipynb - THIS IS RECOMMENDED

Stand alone

from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Align import MultipleSeqAlignment

from pytexshade.shade import shade_aln2png

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='H2AZ',name='H2AZ')])

features=[{'style':'fill:$\\uparrow$','sel':[5,10],'text':'test'}]
shade_aln2png(msa,filename='shaded.png',shading_modes=['charge_functional'], legend=False,features=features,title='',logo=False,hideseqs=False,splitN=20,setends=[],ruler=False,show_seq_names=False,show_seq_length=False)
    

Result is

Main function is

shade_aln2png(msa,filename='default',shading_modes=['similar'],features=[],title='',legend=True, logo=False,hideseqs=False,splitN=20,setends=[],ruler=False,show_seq_names=True,show_seq_length=True,funcgroups=None,rotate=False,threshold=[80,50],resperline=0,margins=None, density=150)

It will convert MultipleSequenceAlignment to a shaded image.

• shading_modes: similar, ... see write_texshade code
• features - a list of dictionaries: {'style':'shaderegion','shadeblock','frameblock','helix','loop','-->','---','<--',',-,' - all texshade features types of features

• frameblock + shaderegion + shadeblock 'position':'top','bottom','ttop','bbottom', etc. if no - automatic 'seqref':number of sequence for selection - default consensus 'sel':[begin,end] - region selection, this is in 0 based numbering (as in msa - we override here the TexShade 1-based numbering) 'text':'text' 'color':'Red' this is for frame block 'thickness':1.5 -1.5pt also for frameblock 'rescol':'Black' this is for \shaderegion{ seqref }{ selection }{ res.col. }{ shad.col. } 'shadcol':'Green' - the same funcgroup example fg="\funcgroup{xxx}{CT}{White}{Green}{upper}{up} \funcgroup{xxx}{GA}{White}{Blue}{upper}{up}" }

Debuging and common problems

• In case of problems use the degub=True option. This will copy all the intermediate files in the debug folder, you can adjust and modify it.
• If you see an error TeX capacity exceeded, sorry [main memory size=5000000] decrease slitN parameter. Or try to tweak your Latex compiler.

Alternative installation notes

TeX distro for Mac http://www.tug.org/mactex/morepackages.html and then add TeXShade via

sudo tlmgr update --self
sudo tlmgr install texshade

• ImageMagic has to be installed - the convert command at least should be available systemwide. The Ghostscript should be installed - the gs command at least should be available systemwide.

Via brew:

brew install im
brew install gs

For developers

• Testing can be done as

git clone https://github.com/intbio/pytexshade.git
docker run   --workdir "/wd" -v "$PWD/pytexshade:/wd" intbio/pytexshade_test pytest

See test_results folder for results.