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update
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@ziadbkh
ziadbkh committed May 13, 2024
1 parent 2d349a9 commit 7a183c8
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Showing 2 changed files with 93 additions and 13 deletions.
14 changes: 7 additions & 7 deletions assets/alphafold_template.html
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Original file line number Diff line number Diff line change
Expand Up @@ -412,13 +412,13 @@ <h3> Download </h3>
</div>
</div>
</div>
<table width="100%">
<tr>
<td width="33%" style="align-content: center;"><img width="400px" id="seq_cov_img" src="seq_coverage.png"></img></td>
<td width="33%" style="align-content: center;"><img id="lddt_img" width="400px" src="coverage_LDDT_0.png"></img></td>
<!--<td width="33%" style="align-content: center;"><img id="pae_img" width="400px" src=""></img></td>-->
</tr>
</table>
<div class="row">
<div class="flex">
<div class="col" style="padding: 20px;"><img width="400px" id="seq_cov_img" src="seq_coverage.png"></img></div>
<div class="col" style="padding: 20px;"><img id="lddt_img" width="400px" src="coverage_LDDT_0.png"></img></div>
<!--<div class="col" style="padding: 20px;"><img id="pae_img" width="400px" src=""></img></div>-->
</div>
</div>
</div>
</body>

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92 changes: 86 additions & 6 deletions assets/generat_plots_2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,10 @@
import argparse
from collections import OrderedDict
import base64
import os
from collections import OrderedDict
import plotly.graph_objects as go
from plotly.subplots import make_subplots

def generate_output_images(msa_path, plddt_paths, name, out_dir):
msa = []
Expand Down Expand Up @@ -102,6 +106,71 @@ def generate_output_images(msa_path, plddt_paths, name, out_dir):
##################################################################


def generate_plots(msa_path, plddt_paths, name, out_dir):
msa = []
with open(msa_path, 'r') as in_file:
for line in in_file:
msa.append([int(x) for x in line.strip().split()])

seqid = []
for sequence in msa:
matches = [1.0 if first == other else 0.0 for first, other in zip(msa[0], sequence)]
seqid.append(sum(matches) / len(matches))

seqid_sort = sorted(range(len(seqid)), key=seqid.__getitem__)

non_gaps = []
for sequence in msa:
non_gaps.append([float(num != 21) if num != 21 else float('nan') for num in sequence])

sorted_non_gaps = [non_gaps[i] for i in seqid_sort]
final = []
for sorted_seq, identity in zip(sorted_non_gaps, [seqid[i] for i in seqid_sort]):
final.append([value * identity if not isinstance(value, str) else value for value in sorted_seq])

# Plotting Sequence Coverage using Plotly
fig = go.Figure()
fig.add_trace(go.Heatmap(
z=final,
colorscale="Rainbow",
zmin=0,
zmax=1,
))
fig.update_layout(
title="Sequence coverage",
xaxis_title="Positions",
yaxis_title="Sequences"
)
# Save as interactive HTML instead of an image
fig.savefig(f"{out_dir}/{name+('_' if name else '')}seq_coverage.png")
"""
#fig.to_html(full_html=False).write_html(f"{out_dir}/{name+('_' if name else '')}seq_coverage.html")
with open (f"{out_dir}/{name+('_' if name else '')}seq_coverage.html", "w") as out_plt:
out_plt.write(fig.to_html(full_html=False))
"""
# Plotting Predicted LDDT per position using Plotly
plddt_per_model = OrderedDict()
plddt_paths.sort()
for plddt_path in plddt_paths:
with open(plddt_path, 'r') as in_file:
plddt_per_model[os.path.basename(plddt_path)[:-4]] = [float(x) for x in in_file.read().strip().split()]

i = 0
for model_name, value_plddt in plddt_per_model.items():
fig = go.Figure()
fig.add_trace(go.Scatter(
x=list(range(len(value_plddt))),
y=value_plddt,
mode='lines',
name=model_name
))
fig.update_layout(title="Predicted LDDT per Position")
fig.savefig(f"{out_dir}/{name+('_' if name else '')}coverage_LDDT_{i}.png")
"""
with open (f"{out_dir}/{name+('_' if name else '')}coverage_LDDT_{i}.html", "w") as out_plt:
out_plt.write(fig.to_html(full_html=False).replace("\"", "\\\""))
"""
i += 1

print("Starting..")
parser = argparse.ArgumentParser()
Expand All @@ -118,6 +187,8 @@ def generate_output_images(msa_path, plddt_paths, name, out_dir):

generate_output_images(args.msa, args.plddt, args.name, args.output_dir)

#generate_plots(args.msa, args.plddt, args.name, args.output_dir)

print("generating html report...")
structures = args.pdb
structures.sort()
Expand All @@ -130,14 +201,23 @@ def generate_output_images(msa_path, plddt_paths, name, out_dir):
alphfold_template = alphfold_template.replace(f"*_data_ranked_{i}.pdb*", open(structure, "r").read().replace("\n", "\\n"))
i += 1

with open(f"{args.output_dir}/{args.name + ('_' if args.name else '')}seq_coverage.png", "rb") as in_file:
alphfold_template = alphfold_template.replace(f"seq_coverage.png", f"data:image/png;base64,{base64.b64encode(in_file.read()).decode('utf-8')}")

for i in range(0, 5):
with open(f"{args.output_dir}/{args.name + ('_' if args.name else '')}coverage_LDDT_{i}.png", "rb") as in_file:
alphfold_template = alphfold_template.replace(f"coverage_LDDT_{i}.png", f"data:image/png;base64,{base64.b64encode(in_file.read()).decode('utf-8')}")
if True:
with open(f"{args.output_dir}/{args.name + ('_' if args.name else '')}seq_coverage.png", "rb") as in_file:
alphfold_template = alphfold_template.replace(f"seq_coverage.png", f"data:image/png;base64,{base64.b64encode(in_file.read()).decode('utf-8')}")

for i in range(0, 5):
with open(f"{args.output_dir}/{args.name + ('_' if args.name else '')}coverage_LDDT_{i}.png", "rb") as in_file:
alphfold_template = alphfold_template.replace(f"coverage_LDDT_{i}.png", f"data:image/png;base64,{base64.b64encode(in_file.read()).decode('utf-8')}")


"""
with open(f"{args.output_dir}/{args.name + ('_' if args.name else '')}seq_coverage.html", "r") as in_file:
alphfold_template = alphfold_template.replace(f"seq_coverage.png", f"{in_file.read()}")
for i in range(0, 5):
with open(f"{args.output_dir}/{args.name + ('_' if args.name else '')}coverage_LDDT_{i}.html", "r") as in_file:
alphfold_template = alphfold_template.replace(f"coverage_LDDT_{i}.png", f"{in_file.read()}")
"""
with open(f"{args.output_dir}/{args.name}_alphafold.html", "w") as out_file:
out_file.write(alphfold_template)

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