Add clade selection into the workflow

chrishah · Jan 20, 2023 · 592e2ea · 592e2ea
1 parent fafcca0
commit 592e2ea
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diff --git a/.gitignore b/.gitignore
@@ -1,2 +1,3 @@
 orthodb
 .snakemake
+clades
diff --git a/Snakefile b/Snakefile
@@ -4,6 +4,67 @@ orthoDBlinks = [
     ("level2species.tab", "https://data.orthodb.org/download/odb11v0_level2species.tab.gz"),
     ("levels.tab", "https://data.orthodb.org/download/odb11v0_levels.tab.gz")]
 
+
+rule selectViridiplantae:
+    input:
+        "clades/Eukaryota.fa",
+        "orthodb/levels.tab",
+        "orthodb/level2species.tab"
+    output:
+        "clades/Viridiplantae.fa"
+    shell:
+        "./selectClade.py {input} Viridiplantae > {output}"
+
+rule selectFungi:
+    input:
+        "clades/Eukaryota.fa",
+        "orthodb/levels.tab",
+        "orthodb/level2species.tab"
+    output:
+        "clades/Fungi.fa"
+    shell:
+        "./selectClade.py {input} Fungi > {output}"
+
+rule selectVertebrata:
+    input:
+        "clades/Eukaryota.fa",
+        "orthodb/levels.tab",
+        "orthodb/level2species.tab"
+    output:
+        "clades/Vertebrata.fa"
+    shell:
+        "./selectClade.py {input} Vertebrata > {output}"
+
+rule selectMetazoa:
+    input:
+        "clades/Eukaryota.fa",
+        "orthodb/levels.tab",
+        "orthodb/level2species.tab"
+    output:
+        "clades/Metazoa.fa"
+    shell:
+        "./selectClade.py {input} Metazoa > {output}"
+
+rule selectArthropoda:
+    input:
+        "clades/Eukaryota.fa",
+        "orthodb/levels.tab",
+        "orthodb/level2species.tab"
+    output:
+        "clades/Arthropoda.fa"
+    shell:
+        "./selectClade.py {input} Arthropoda > {output}"
+
+rule selectEukaryota:
+    input:
+        "orthodb/raw.fasta",
+        "orthodb/levels.tab",
+        "orthodb/level2species.tab"
+    output:
+        "clades/Eukaryota.fa"
+    shell:
+        "./selectClade.py {input} Eukaryota > {output}"
+
 rule unzip:
     input:
         ["orthodb/{f}.gz".format(f=filename) for (filename, _) in orthoDBlinks]