From 2d349a925d67d2218db0c473b796d78d212d333b Mon Sep 17 00:00:00 2001
From: ziadbkh <ziadbkh@gmail.com>
Date: Sun, 12 May 2024 21:21:58 +1000
Subject: [PATCH] add figs to report

---
 assets/alphafold_template.html | 16 ++++++++--------
 assets/generat_plots_2.py      | 11 +++++++++++
 tower.yml                      |  2 --
 3 files changed, 19 insertions(+), 10 deletions(-)

diff --git a/assets/alphafold_template.html b/assets/alphafold_template.html
index 32be8829..8477b6f5 100755
--- a/assets/alphafold_template.html
+++ b/assets/alphafold_template.html
@@ -414,9 +414,9 @@ <h3> Download </h3>
       </div>
       <table width="100%">
         <tr>
-          <td width="33%" style="align-content: center;"><img  width="400px" id="seq_cov_img" src="*sample_name_here*_seq_coverage.png"></img></td>
-          <td width="33%" style="align-content: center;"><img id="lddt_img"  width="400px" src="*sample_name_here*_coverage_LDDT_0.png"></img></td>
-          <td width="33%" style="align-content: center;"><img id="pae_img"  width="400px" src="*model_pae*"></img></td>
+          <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>
@@ -475,11 +475,11 @@ <h3> Download </h3>
     ] 
 
     const LDDT_IMGS = [
-      "*sample_name_here*_coverage_LDDT_0.png",
-      "*sample_name_here*_coverage_LDDT_1.png",
-      "*sample_name_here*_coverage_LDDT_2.png",
-      "*sample_name_here*_coverage_LDDT_3.png",
-      "*sample_name_here*_coverage_LDDT_4.png"
+      "coverage_LDDT_0.png",
+      "coverage_LDDT_1.png",
+      "coverage_LDDT_2.png",
+      "coverage_LDDT_3.png",
+      "coverage_LDDT_4.png"
     ]
 
     const REPRESENTATIONS = [
diff --git a/assets/generat_plots_2.py b/assets/generat_plots_2.py
index c0948dd6..3b2ac1d8 100644
--- a/assets/generat_plots_2.py
+++ b/assets/generat_plots_2.py
@@ -4,6 +4,7 @@
 from matplotlib import pyplot as plt
 import argparse
 from collections import OrderedDict
+import base64
 
 def generate_output_images(msa_path, plddt_paths, name, out_dir):
     msa = []
@@ -123,10 +124,20 @@ def generate_output_images(msa_path, plddt_paths, name, out_dir):
 
 alphfold_template = open(args.html_template, "r").read()
 alphfold_template = alphfold_template.replace(f"*sample_name_here*", args.name)
+
 i = 0
 for structure in structures:
     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')}")
+        
+
+
 with open(f"{args.output_dir}/{args.name}_alphafold.html", "w") as out_file:
     out_file.write(alphfold_template)
diff --git a/tower.yml b/tower.yml
index 16a92fd3..c0b95ad4 100755
--- a/tower.yml
+++ b/tower.yml
@@ -5,5 +5,3 @@ reports:
     display: "Auto-created samplesheet with collated metadata and FASTQ paths"
   "*_alphafold.html":
     display: "Predected structures"
-  "*.png":
-    display: "Plots"
\ No newline at end of file