From 958f7e41e1c6f87e67d7836ec8025d07bda819c2 Mon Sep 17 00:00:00 2001
From: "kathleen.moriarty" <kathleen.moriarty@unibas.ch>
Date: Mon, 3 Jan 2022 12:20:19 +0100
Subject: [PATCH] replace readline() to use file handle as iterator
---
src/read_sequencing.py | 42 +++++++++++++++++++++---------------------
1 file changed, 21 insertions(+), 21 deletions(-)
diff --git a/src/read_sequencing.py b/src/read_sequencing.py
index d6dfc47..a008f19 100644
--- a/src/read_sequencing.py
+++ b/src/read_sequencing.py
@@ -37,27 +37,27 @@ def read_sequencing(
frag_desc = [] # type: List[str]
with open(frag_file_name, 'r') as f:
- frag_line = f.readline()
- # Store all fragments as a list to parse later
- frag_list = [] # type: List[str]
- # Store combined fragment lines
- frag_str = ""
- while frag_line != "":
- # To stop when the end of file is reached
- if frag_line.startswith('>'):
- # Determine if this is the first fragment in the file
- # Ignore the description line (starting with >) of the first fragment
- if not (len(frag_list) == 0 and frag_str == ""):
- # Not the first fragment. Append to list.
- frag_list.append(frag_str)
- frag_str = ""
- # Store description line for output file
- frag_desc.append(frag_line)
- else:
- frag_str = frag_str + frag_line.rstrip("\n")
- # Read next line
- frag_line = f.readline()
- frag_list.append(frag_str)
+ for frag_line in f:
+ # Store all fragments as a list to parse later
+ frag_list = [] # type: List[str]
+ # Store combined fragment lines
+ frag_str = ""
+ while frag_line != "":
+ # To stop when the end of file is reached
+ if frag_line.startswith('>'):
+ # Determine if this is the first fragment in the file
+ # Ignore the description line (starting with >) of the first fragment
+ if not (len(frag_list) == 0 and frag_str == ""):
+ # Not the first fragment. Append to list.
+ frag_list.append(frag_str)
+ frag_str = ""
+ # Store description line for output file
+ frag_desc.append(frag_line)
+ else:
+ frag_str = frag_str + frag_line.rstrip("\n")
+ # Read next line
+ frag_line = f.readline()
+ frag_list.append(frag_str)
# Store list of random nucleotides from which to sample when read length is too short
nucleotides = ['A', 'C', 'G', 'T']
--
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