From 5cb10fef3d17315281460c7131cc7fb7338ba5e3 Mon Sep 17 00:00:00 2001
From: VinzentRisch <risch.vinzent@gmail.com>
Date: Wed, 24 Jul 2024 15:00:34 +0200
Subject: [PATCH] fix annotationformat twice bug

---
 q2_amr/amrfinderplus/feature_data.py | 14 +++++++-------
 q2_amr/amrfinderplus/utils.py        |  2 --
 q2_amr/plugin_setup.py               |  2 +-
 3 files changed, 8 insertions(+), 10 deletions(-)

diff --git a/q2_amr/amrfinderplus/feature_data.py b/q2_amr/amrfinderplus/feature_data.py
index 9d6f712..2ba921e 100644
--- a/q2_amr/amrfinderplus/feature_data.py
+++ b/q2_amr/amrfinderplus/feature_data.py
@@ -59,14 +59,14 @@ def _get_file_paths(file, mags, proteins, loci):
 
 
 def _move_or_create_files(src_dir: str, mag_id: str, file_operations: dict):
-    for file_name, condition, target_dir in file_operations:
-        if condition:
+    for file_name, target_dir in file_operations:
+        if os.path.exists(os.path.join(src_dir, file_name)):
             shutil.move(
                 os.path.join(src_dir, file_name),
                 os.path.join(str(target_dir), f"{mag_id}_{file_name}"),
             )
         else:
-            with open(os.path.join(str(target_dir), file_name), "w"):
+            with open(os.path.join(str(target_dir), f"{mag_id}_{file_name}"), "w"):
                 pass
 
 
@@ -134,10 +134,10 @@ def annotate_feature_data_amrfinderplus(
             # directory format, if organism, dna_sequence and proteins parameters
             # are specified. Else create empty placeholder files.
             file_operations = [
-                ("amr_annotations.tsv", True, amr_annotations),
-                ("amr_all_mutations.tsv", organism, amr_all_mutations),
-                ("amr_genes.fasta", mags, amr_genes),
-                ("amr_proteins.fasta", proteins, amr_proteins),
+                ("amr_annotations.tsv", amr_annotations),
+                ("amr_all_mutations.tsv", amr_all_mutations),
+                ("amr_genes.fasta", amr_genes),
+                ("amr_proteins.fasta", amr_proteins),
             ]
 
             # Loop through each file operation
diff --git a/q2_amr/amrfinderplus/utils.py b/q2_amr/amrfinderplus/utils.py
index 10c6f03..51dfcb3 100644
--- a/q2_amr/amrfinderplus/utils.py
+++ b/q2_amr/amrfinderplus/utils.py
@@ -34,8 +34,6 @@ def run_amrfinderplus_n(
         "-o",
         f"{working_dir}/amr_annotations.tsv",
         "--print_node",
-        "--annotation_format",
-        "prodigal",
     ]
     # Creates nucleotide fasta output if DNA sequences are given as input
     if dna_sequences:
diff --git a/q2_amr/plugin_setup.py b/q2_amr/plugin_setup.py
index c40fa44..35deeae 100644
--- a/q2_amr/plugin_setup.py
+++ b/q2_amr/plugin_setup.py
@@ -34,8 +34,8 @@
 
 from q2_amr import __version__
 from q2_amr.amrfinderplus.database import fetch_amrfinderplus_db
+from q2_amr.amrfinderplus.feature_data import annotate_feature_data_amrfinderplus
 from q2_amr.amrfinderplus.sample_data import annotate_sample_data_amrfinderplus
-from q2_amr.amrfinderplus.sequences import annotate_feature_data_amrfinderplus
 from q2_amr.amrfinderplus.types._format import (
     AMRFinderPlusAnnotationFormat,
     AMRFinderPlusAnnotationsDirFmt,