From 26ee85bf2651b157e1779a71c7920d298628dfe7 Mon Sep 17 00:00:00 2001
From: gayaldassanayake <g.c.dassanayake@gmail.com>
Date: Tue, 16 Nov 2021 22:16:25 +0530
Subject: [PATCH] Move preprocess logic to a sub dir

---
 pipeline.py                               | 4 ++--
 preprocess/__init__.py                    | 0
 fragment.py => preprocess/fragment.py     | 0
 kmer.py => preprocess/kmer.py             | 0
 preprocess.py => preprocess/preprocess.py | 4 ++--
 progress_bar.py                           | 1 -
 6 files changed, 4 insertions(+), 5 deletions(-)
 create mode 100644 preprocess/__init__.py
 rename fragment.py => preprocess/fragment.py (100%)
 rename kmer.py => preprocess/kmer.py (100%)
 rename preprocess.py => preprocess/preprocess.py (91%)

diff --git a/pipeline.py b/pipeline.py
index 3728a1a..8876809 100644
--- a/pipeline.py
+++ b/pipeline.py
@@ -2,7 +2,7 @@
 import argparse
 
 from constants import *
-from preprocess import preprocess
+from preprocess.preprocess import preprocess
 
 def parse_user_arguements():
     parser = argparse.ArgumentParser(
@@ -42,4 +42,4 @@ def main(args):
 
 if __name__ == "__main__":
     args = parse_user_arguements()
-    main(args)
\ No newline at end of file
+    main(args)
diff --git a/preprocess/__init__.py b/preprocess/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/fragment.py b/preprocess/fragment.py
similarity index 100%
rename from fragment.py
rename to preprocess/fragment.py
diff --git a/kmer.py b/preprocess/kmer.py
similarity index 100%
rename from kmer.py
rename to preprocess/kmer.py
diff --git a/preprocess.py b/preprocess/preprocess.py
similarity index 91%
rename from preprocess.py
rename to preprocess/preprocess.py
index be3c6dc..2358a46 100644
--- a/preprocess.py
+++ b/preprocess/preprocess.py
@@ -1,7 +1,7 @@
 import os
 
-from fragment import fragment
-from kmer import count_kmers
+from preprocess.fragment import fragment
+from preprocess.kmer import count_kmers
 from constants import *
 from helpers import print_error
 
diff --git a/progress_bar.py b/progress_bar.py
index 14dfcae..16065f1 100644
--- a/progress_bar.py
+++ b/progress_bar.py
@@ -15,4 +15,3 @@ def update_progress_bar(pbar,i):
 
 def close_progress_bar(pbar):
     pbar.close()
- 
\ No newline at end of file