From 04be1470a934176dc097e5443af5462058850d8d Mon Sep 17 00:00:00 2001
From: Dan Fornika <dfornika@gmail.com>
Date: Tue, 2 Jul 2024 19:12:52 -0700
Subject: [PATCH] Handle case where segment is missing while plotting scaffold
 (#33)

* Handle case where segment is missing while plotting scaffold

* fill in docstring for make_plots

* Update usage in README
---
 README.md             |  6 ++++--
 fluviewer/__init__.py |  2 +-
 fluviewer/plots.py    | 17 +++++++++++++++++
 3 files changed, 22 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 4d82d17..432dcc0 100644
--- a/README.md
+++ b/README.md
@@ -106,8 +106,8 @@ pip3 install git+https://github.com/BCCDC-PHL/FluViewer.git
 ## Usage
 
 ```
-usage: fluviewer [-h] -f FORWARD_READS -r REVERSE_READS -d DATABASE [-o OUTDIR] -n OUTPUT_NAME [-i [0-100]] [-l [32-]] [-D [1-]] [-q [0-]] [-v [0-1]] [-V [0-1]] [-N [1-]] [-L [1-]]
-                 [-t [1-]] [-M [1-]] [-g] [--log-level {info,debug}]
+usage: fluviewer [-h] -f FORWARD_READS -r REVERSE_READS -d DB [-o OUTDIR] -n OUTPUT_NAME [-i [0-100]] [-l [32-]] [-D [1-]] [-q [0-]] [-v [0-1]] [-V [0-1]] [-N [1-]] [-L [1-]] [-t [1-]] [-M [1-]] [-g] [--force]
+                 [--log-level {info,debug}] [--version]
 
 BCCDC-PHL/FluViewer: Influenza A virus consensus sequence generation and variant calling
 
@@ -145,8 +145,10 @@ optional arguments:
                         Gigabytes of memory allocated for normalizing reads (default=max)
   -g, --disable-garbage-collection
                         Disable garbage collection and retain intermediate analysis files
+  --force               Allow overwrite of existing files and directories.
   --log-level {info,debug}
                         Log level (default=info)
+  --version             show program's version number and exit
 ```
 
 
diff --git a/fluviewer/__init__.py b/fluviewer/__init__.py
index 71998e8..cfe0fe0 100644
--- a/fluviewer/__init__.py
+++ b/fluviewer/__init__.py
@@ -1 +1 @@
-__version__ = '0.1.11-2'
+__version__ = '0.1.11-3'
diff --git a/fluviewer/plots.py b/fluviewer/plots.py
index c721218..9669a9a 100644
--- a/fluviewer/plots.py
+++ b/fluviewer/plots.py
@@ -185,6 +185,18 @@ def make_scaffolding_plots(alignment: list[dict], scaffold: dict, output: Path)
 def make_plots(inputs, outdir, out_name):
     """
     Generate plots for the analysis.
+
+    :param inputs: The inputs dictionary. Expected keys are:
+                   ['depth_of_cov_freebayes', 'alignment', 'depth_of_cov_freebayes',
+                    'low_coverage_positions', 'ambiguous_positions', 'variant_positions',
+                    'segment_contigs_alignments', 'scaffolds']
+    :type inputs: dict
+    :param outdir: The output directory.
+    :type outdir: str
+    :param out_name: The output name.
+    :type out_name: str
+    :return: The analysis summary. Keys are ['timestamp_analysis_start', 'inputs', 'outputs', 'timestamp_analysis_complete']
+    :rtype: dict
     """
     timestamp_analysis_start = datetime.datetime.now().isoformat()
     analysis_summary = {
@@ -222,6 +234,11 @@ def make_plots(inputs, outdir, out_name):
     ]
     outputs['scaffold_alignment_plots'] = {}
     for segment in segments:
+
+        if segment not in inputs['segment_contigs_alignments']:
+            log.warning(f'No contig alignment file found for segment {segment}. Skipping...')
+            continue
+
         contig_alignment_path  = inputs['segment_contigs_alignments'][segment]
         if not os.path.exists(contig_alignment_path):
             log.warning(f'Contig alignment file {contig_alignment_path} does not exist. Skipping...')