added vsearch path

iobis · Nov 6, 2024 · 9a440a7 · 9a440a7
1 parent 3d3f8f0
commit 9a440a7
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Showing 2 changed files with 5 additions and 3 deletions.
diff --git a/README.md b/README.md
@@ -68,7 +68,7 @@ Build the fasta file, occurrence sqlite database, and bowtie2 database:
 ### Upload data
 
 ```sh
-rsync -r data ***@***:/data/sequence-search/data
+rsync -r data [email protected]:/data/sequence-search
 ```
 
 ### Run the API

diff --git a/api/search.py b/api/search.py
@@ -12,6 +12,10 @@
 logging.basicConfig(level=logging.INFO)
 
 
+os.environ["PATH"] += os.pathsep + "/Users/pieter/IPOfI Dropbox/Pieter Provoost/werk/projects/OBIS pipeline/sequence-search/vsearch-2.29.1-macos-aarch64/bin"
+os.environ["PATH"] += os.pathsep + "/data/vsearch-2.29.1/bin"
+
+
 def search_sequences(seq, strategy="vsearch"):
 
     with tempfile.TemporaryDirectory() as tmpdir:
@@ -65,8 +69,6 @@ def search_sequences(seq, strategy="vsearch"):
 
             blast_file_path = os.path.join(tmpdir, "output.blast")
 
-            vsearch_path = "/Users/pieter/IPOfI Dropbox/Pieter Provoost/werk/projects/OBIS pipeline/sequence-search/vsearch-2.29.1-macos-aarch64/bin"
-            os.environ["PATH"] += os.pathsep + vsearch_path
             os.system(f"vsearch --usearch_global {input_file_path} --db ../data/sequences.udb --id 0.9 --query_cov 0.9 --maxaccepts 100 --maxrejects 100 --maxhits 100 --blast6out {blast_file_path}")
 
             con = sqlite3.connect(sqlite_file_path)