"""
Created on 16 Nov 2018
@author: jmht
"""
from mrparse.mr_topcons import TM
from mrparse.mr_deepcoil import CC
from mrparse.mr_jpred import HELIX, SHEET
from mrparse.mr_annotation import get_annotation_chunks
from builtins import range
import colorsys
[docs]def get_N_HexCol(N=5):
HSV_tuples = [(x * 1.0 / N, 0.5, 0.5) for x in range(N)]
hex_out = []
for rgb in HSV_tuples:
rgb = map(lambda x: int(x * 255), colorsys.hsv_to_rgb(*rgb))
hex_out.append("".join(map(lambda x: chr(x).encode('hex'), rgb)))
return ['#' + h for h in hex_out]
[docs]def add_pfam_dict_to_homologs(homologs, sequence_length):
# Need a better way of getting the number of regions
nregions = len(set([h.region_id for h in homologs.values()]))
region_colors = get_N_HexCol(nregions)
for h in homologs.values():
start = h.query_start
stop = h.query_stop
name = h.name
region_id = h.region_id
search_engine = h.hit.search_engine
d = {'startStyle': "curved",
'endStyle': "curved",
'start': start,
'end': stop,
'aliStart': start,
'aliEnd': stop,
'colour': region_colors[h.region_index],
'text': name,
'metadata': {"description": "Homolog {} from region #{}".format(name, region_id),
"database": "{} search".format(search_engine.upper()),
"start": start,
"end": stop}
}
jdict = {'length': sequence_length,
'regions': [d]}
h._pfam_json = jdict
[docs]def add_pfam_dict_to_models(models, sequence_length):
# Need a better way of getting the number of regions
for m in models.values():
start = m.query_start
stop = m.query_stop + 1
name = m.name
region_id = m.region_id
plddt_regions = m.plddt_regions
# 'colour': '#193f90'
d = {'startStyle': "curved",
'endStyle': "curved",
'start': start,
'end': stop,
'aliStart': start,
'aliEnd': stop,
'colour': '#d3d3d3',
'text': "",
'metadata': {"description": "Model {} from region #{}".format(name, region_id),
"database": "EBI AlphaFold database",
"start": start,
"end": stop}
}
motifs = []
colors = {'v_low': "ff7d45",
"low": "ffdb13",
"confident": "65cbf3",
"v_high": "0053d6"}
for quality in plddt_regions.keys():
for plddt_region in plddt_regions[quality]:
plddt_region_start, plddt_region_end = plddt_region
md = {'colour': colors[quality],
'metadata': {"description": quality,
"database": "EBI AlphaFold database",
"type": "Quality",
"end": plddt_region_end,
"start": plddt_region_start},
"type": "pLDDT",
"display": "true",
"end": plddt_region_end,
"start": plddt_region_start
}
motifs.append(md)
jdict = {'length': sequence_length,
'regions': [d],
'motifs': motifs
}
m._pfam_json = jdict
[docs]def pfam_dict_from_annotation(annotation):
annotation_chunks = get_annotation_chunks(annotation)
return pfam_dict_from_chunks(annotation_chunks, len(annotation))
[docs]def pfam_dict_from_chunks(chunk_data, seqlen):
if not chunk_data:
return None
regions = []
for i, chunk in enumerate(chunk_data):
idx = i + 1
if chunk.annotation == CC:
colour = "#00ff00"
text = CC.name
meta_desc = "Coiled-coil region #%d" % idx
elif chunk.annotation == TM:
colour = "#aaaaaa"
text = TM.name
meta_desc = "Transmembrane region #%d" % idx
elif chunk.annotation == HELIX:
colour = "#ff0000"
text = HELIX.name
meta_desc = "Helix region #%d" % idx
elif chunk.annotation == SHEET:
colour = "#0000ff"
text = SHEET.name
meta_desc = "Beta strand region #%d" % idx
d = {'startStyle': "straight",
'endStyle': "straight",
'start': chunk.start,
'end': chunk.end,
'aliStart': chunk.start,
'aliEnd': chunk.end,
'colour': colour,
'text': text,
'metadata': {"description": meta_desc,
"database": chunk.annotation.source,
"start": chunk.start,
"end": chunk.end,
}
}
regions.append(d)
vis_data = {'length': seqlen,
'regions': regions}
return vis_data
