From 68ee6cff322925fa15af5bcba2f1d352e1bd7f1c Mon Sep 17 00:00:00 2001
From: Sage Wright <sage.wright@theiagen.com>
Date: Wed, 7 Aug 2024 19:11:56 +0000
Subject: [PATCH] prevent flu-specific items from being dropped from non-flu
 tables

---
 Dockerfile          | 2 +-
 README.md           | 6 +++---
 mercury/Table.py    | 5 +++--
 mercury/__init__.py | 2 +-
 4 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index a7e03bd..37c618d 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-ARG MERCURY_VER="1.0.6"
+ARG MERCURY_VER="1.0.7"
 
 FROM google/cloud-sdk:480.0.0-slim
 
diff --git a/README.md b/README.md
index 19473c6..ead2a2e 100644
--- a/README.md
+++ b/README.md
@@ -27,16 +27,16 @@ Default databases by organism:
 We highly recommend using the following Docker image to run Mercury:
 
 ```bash
-docker pull us-docker.pkg.dev/general-theiagen/theiagen/mercury:1.0.6
+docker pull us-docker.pkg.dev/general-theiagen/theiagen/mercury:1.0.7
 ```
 
 The entrypoint for this Docker image is the Mercury help message. To run this container interactively, use the following command:
 
 ```bash
-docker run -it --entrypoint=/bin/bash us-docker.pkg.dev/general-theiagen/theiagen/mercury:1.0.6
+docker run -it --entrypoint=/bin/bash us-docker.pkg.dev/general-theiagen/theiagen/mercury:1.0.7
 # Once inside the container interactively, you can run the tbp-parser tool
 python3 /mercury/mercury/mercury.py -v
-# v1.0.6
+# v1.0.7
 ```
 
 ### Locally with Python
diff --git a/mercury/Table.py b/mercury/Table.py
index 489ece4..6661bb4 100644
--- a/mercury/Table.py
+++ b/mercury/Table.py
@@ -200,8 +200,9 @@ def make_biosample_csv(self):
       # strip off "Type_" from beginning of Type, e.g. "Type_A" -> "A"
       self.logger.debug("DEBUG:User did not supply isolate or strain metadata columns, creating isolate column for Flu samples now...")
       biosample_metadata["isolate"] = (biosample_metadata["abricate_flu_type"].str.replace("Type_","") + "/" + biosample_metadata["state"] + "/" + biosample_metadata["sample_name"] + "/" + biosample_metadata["year"] + " (" + biosample_metadata["abricate_flu_subtype"] + ")")
-    # Remove 4 extra columns from the output table prior to creating TSV file (these are simply used to create the isolate column)
-    biosample_metadata.drop(["abricate_flu_type", "abricate_flu_subtype", "year", "state"], axis=1, inplace=True)
+      
+      # Remove 4 extra columns from the output table prior to creating TSV file (these are simply used to create the isolate column)
+      biosample_metadata.drop(["abricate_flu_type", "abricate_flu_subtype", "year", "state"], axis=1, inplace=True)
 
     biosample_metadata.to_csv(self.output_prefix + "_biosample_metadata.tsv", sep='\t', index=False)
     self.logger.debug("TABLE:BioSample metadata file created")
diff --git a/mercury/__init__.py b/mercury/__init__.py
index 2e1805c..bef6d07 100644
--- a/mercury/__init__.py
+++ b/mercury/__init__.py
@@ -1 +1 @@
-__VERSION__ = "v1.0.6"
\ No newline at end of file
+__VERSION__ = "v1.0.7"
\ No newline at end of file