colorMSAwithSSE

Generate an image from a multiple sequence alignment (MSA) colored by the secondary structures elements (SSE)

Usage

Please note that you need a strict match between the sequences in the fasta file AND your structrure files. It will not work if there is a mismatch.

You will need a fasta where the header countain the PDB filename
And all the structures used

formats

For now only those file extension and associated formats are supported:

.fa -> fasta
.faa -> fasta
.fasta -> fasta
.clw -> clustal
.aln -> clustal
.clustal -> clustal
.phy -> phylip
.phylip -> phylip

Coloring

You can change the color of the Gaps, Coil, ɑ-helix and β-sheet with the argument -c.
Use the HEX code or the matplotlib color name here (https://matplotlib.org/stable/gallery/color/named_colors.html).
The color order should follow this : GAP, COIL, HELICES, BSHEET.
Example: -c "white, bisque, red, yellow"

Font

You can change the font style with the parameter -fs. It can be with Serif (serif) or sans-serif (sans)

Example

You can run an example within the test folder.

python ../colorMSAwithSSE/colorMSAwithSSE.py -f SH2.fasta -s structures/ -o SH2.png -w 60 -c 'white, bisque, red, yellow' -a 0.6 -ft sans

Output example

help

usage: python colorMSAwithSSE.py -f file.fasta -t structuresfolder -o alignment.png

This program is made to generate a picture (SVG/PNG/PDF) of a multiple
sequence alignement with secondary structure element coloration

optional arguments:
  -h, --help            show this help message and exit
  -f FILE, --file FILE  alignment file (FASTA only for now)
  -s STRUCTURES, --structures STRUCTURES
                        structures FOLDER
  -w LINEWIDTH, --linewidth LINEWIDTH
                        line width. Default = 50, choose 0 if you want the
                        picture one 1 line
  -i INTERSPACE, --interspace INTERSPACE
                        interspace between two lines
  -fs FONTSTYLE, --fontstyle FONTSTYLE
                        fontstyle (serif/sans). Default: serif.
  -o OUTPUT, --output OUTPUT
                        output file
  -sort SORT, --sort SORT
                        Sort indexes (Y/N) (A->Z)
  -r RANGE, --range RANGE
                        output range of the alignment. Example '30:70'.
                        default='all'

  -p TICKPOSITION, --tickPosition TICKPOSITION
                        Put the position in the alignment every {tickPosition}
  -c COLOR, --color COLOR
                        Color for the secondary structure in this order
                        'GAP,COIL,HELICES,BSHEET'. default is 'white, bisque,
                        red, yellow'. You can use color name (See https://matp
                        lotlib.org/stable/gallery/color/named_colors.html) or
                        HEX code
  -a ALPHA, --alpha ALPHA
                        Transparency of the color background

Dependancies:

Biopython
matplotlib
DSSP
argparse

You can the dependancies with conda install -c conda-forge -c salilab dssp biopython matplotlib

Support

Please ask your question/feedback through Github :-)

tubiana / colormsawithsse Goto Github PK