diff trycycler.py @ 0:85658cabbbed draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trycycler.py	Thu Feb 11 19:25:20 2021 +0000
@@ -0,0 +1,40 @@
+#!/usr/bin/env python3
+
+from os import path, walk
+from sys import argv
+
+
+def cluster(output_folder):
+    counter = 1
+    for root, dir, files in walk(output_folder):
+        if root.endswith('1_contigs'):
+            output_path = path.join(output_folder, f"cluster_0{counter}.fasta")
+            with open(output_path, "a") as out_cluster:
+                for fasta in files:
+                    fasta_path = path.join(root, fasta)
+                    fasta = open(fasta_path).read()
+                    out_cluster.write(fasta)
+            counter += 1
+
+
+def reconcile(input_file):
+    number_cluster = [x for x in input_file[-1:0:-1] if x.isdigit()][0]
+    full_path = f"selected_cluster/cluster_0{number_cluster}/1_contigs/"
+    with open(input_file) as tmp:
+        for line in tmp:
+            if ">" in line:
+                filename = line[1:].strip()
+                output_fasta = f"{full_path}{filename}.fasta"
+            with open(output_fasta, "a") as handle:
+                handle.write(line)
+
+
+def main():
+    if argv[1] == "cluster":
+        cluster(argv[2])
+    if argv[1] == "reconcile":
+        reconcile(argv[2])
+
+
+if __name__ == "__main__":
+    main()