From b2f1355c457f6b83090c2bb0ab5fb6b081a3c136 Mon Sep 17 00:00:00 2001
From: "U-STI\\morika" <morika@TPH-L17108.sti.local>
Date: Mon, 29 Nov 2021 22:37:18 +0100
Subject: [PATCH] fixed ranges to correct # of reads
---
src/read_sequencing.py | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/src/read_sequencing.py b/src/read_sequencing.py
index aaec0e9..f970db3 100644
--- a/src/read_sequencing.py
+++ b/src/read_sequencing.py
@@ -40,7 +40,10 @@ def read_sequencing(frag_file_name, output_file_name, num_reads, read_len, num_s
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 = ""
else:
@@ -60,7 +63,7 @@ def read_sequencing(frag_file_name, output_file_name, num_reads, read_len, num_s
sum_frags = sum(map(len, frag_list))
# Repeat the read process for given number of cycles
- for j in range(1, num_seq_cyc):
+ for j in range(0, num_seq_cyc):
# Loop through fasta fragments that start with 5'
for frag in frag_list:
@@ -70,7 +73,7 @@ def read_sequencing(frag_file_name, output_file_name, num_reads, read_len, num_s
# TODO resolve this issue
num_frag_reads = round((len(frag)/sum_frags) * num_reads)
- for i in range(1, num_frag_reads):
+ for i in range(0, num_frag_reads):
# Obtain random first position for the read on the fragment
rand_start = randrange(0, len(frag))
--
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