From 2c8cbd0dbf8600ae4b0ddbc793c83588c6459a59 Mon Sep 17 00:00:00 2001
From: "hugo.madgeleon" <hugo.madgeleon@stud.unibas.ch>
Date: Sun, 13 Nov 2022 11:14:54 +0100
Subject: [PATCH] Clean package imports
---
frag_package/fragmentation.py | 3 +-
frag_package/fragmentation_2.py | 57 ++++++++++++++++++++++++++++++++-
2 files changed, 57 insertions(+), 3 deletions(-)
diff --git a/frag_package/fragmentation.py b/frag_package/fragmentation.py
index 6ea8cdf..7dba609 100644
--- a/frag_package/fragmentation.py
+++ b/frag_package/fragmentation.py
@@ -1,6 +1,5 @@
-import pandas as pd
import random
-import numpy as np
+
dna_seq = {
"ATAACATGTGGATGGCCAGTGGTCGGTTGTTACACGCCTACCGCGATGCTGAATGACCCGGACTAGAGTGGCGAAATTTATGGCGTGTGACCCGTTATGC": 100,
diff --git a/frag_package/fragmentation_2.py b/frag_package/fragmentation_2.py
index 4a20a85..69329ef 100644
--- a/frag_package/fragmentation_2.py
+++ b/frag_package/fragmentation_2.py
@@ -1 +1,56 @@
-import pandas as pd
import random
import numpy as np
import re
dna_seq = {
"ATAACATGTGGATGGCCAGTGGTCGGTTGTTACACGCCTACCGCGATGCTGAATGACCCGGACTAGAGTGGCGAAATTTATGGCGTGTGACCCGTTATGC": 100,
"TCCATTTCGGTCAGTGGGTCATTGCTAGTAGTCGATTGCATTGCCATTCTCCGAGTGATTTAGCGTGACAGCCGCAGGGAACCCATAAAATGCAATCGTA": 100
}
nucs = ['A','T','G','C']
mononuc_freqs = [0.22, 0.25, 0.23, 0.30]
# A_dinuc_freqs = {'AA':0.27,'AT':0.25, 'AG':0.22, 'AC':0.26}
# T_dinuc_freqs = {'TA':0.27, 'TT':0.24, 'TG':0.24, 'TC':0.25}
# C_dinuc_freqs = {'CA':0.23, 'CT':0.21, 'CG':0.35, 'CC':0.21}
# G_dinuc_freqs = {'GA':0.25, 'GT':0.25, 'GG':0.23, 'GC':0.27}
mean_length = 12
std = 1
term_frags = []
for seq, counts in dna_seq.items():
for _ in range(counts):
n_cuts = int(len(seq)/mean_length)
# non-random DNA fragmentation implementation based on https://www.nature.com/articles/srep04532#Sec1
# assume fragmentation by sonication for NGS workflow
cuts = []
cut_nucs = np.random.choice(nucs, n_cuts, p=mononuc_freqs)
for nuc in cut_nucs:
nuc_pos = [x.start() for x in re.finditer(nuc, seq)]
pos = np.random.choice(nuc_pos)
while pos in cuts:
pos = np.random.choice(nuc_pos)
cuts.append(pos)
cuts.sort()
cuts.insert(0,0)
term_frag = ""
for i, val in enumerate(cuts):
if i == len(cuts)-1:
fragment = seq[val+1:cuts[-1]]
else:
fragment = seq[val:cuts[i+1]]
if mean_length-std <= len(fragment) <= mean_length+std:
term_frag = fragment
if term_frag == "":
continue
else:
term_frags.append(term_frag)
with open('terminal_frags.txt', 'w') as f:
for line in term_frags:
f.write(line)
f.write('\n')
\ No newline at end of file
+import re
+
+import numpy as np
+
+dna_seq = {
+ "ATAACATGTGGATGGCCAGTGGTCGGTTGTTACACGCCTACCGCGATGCTGAATGACCCGGACTAGAGTGGCGAAATTTATGGCGTGTGACCCGTTATGC": 100,
+ "TCCATTTCGGTCAGTGGGTCATTGCTAGTAGTCGATTGCATTGCCATTCTCCGAGTGATTTAGCGTGACAGCCGCAGGGAACCCATAAAATGCAATCGTA": 100
+}
+nucs = ['A','T','G','C']
+mononuc_freqs = [0.22, 0.25, 0.23, 0.30]
+
+# A_dinuc_freqs = {'AA':0.27,'AT':0.25, 'AG':0.22, 'AC':0.26}
+# T_dinuc_freqs = {'TA':0.27, 'TT':0.24, 'TG':0.24, 'TC':0.25}
+# C_dinuc_freqs = {'CA':0.23, 'CT':0.21, 'CG':0.35, 'CC':0.21}
+# G_dinuc_freqs = {'GA':0.25, 'GT':0.25, 'GG':0.23, 'GC':0.27}
+
+mean_length = 12
+std = 1
+
+term_frags = []
+for seq, counts in dna_seq.items():
+ for _ in range(counts):
+ n_cuts = int(len(seq)/mean_length)
+
+ # non-random DNA fragmentation implementation based on https://www.nature.com/articles/srep04532#Sec1
+ # assume fragmentation by sonication for NGS workflow
+ cuts = []
+ cut_nucs = np.random.choice(nucs, n_cuts, p=mononuc_freqs)
+ for nuc in cut_nucs:
+ nuc_pos = [x.start() for x in re.finditer(nuc, seq)]
+ pos = np.random.choice(nuc_pos)
+ while pos in cuts:
+ pos = np.random.choice(nuc_pos)
+ cuts.append(pos)
+
+ cuts.sort()
+ cuts.insert(0,0)
+ term_frag = ""
+ for i, val in enumerate(cuts):
+ if i == len(cuts)-1:
+ fragment = seq[val+1:cuts[-1]]
+ else:
+ fragment = seq[val:cuts[i+1]]
+ if mean_length-std <= len(fragment) <= mean_length+std:
+ term_frag = fragment
+ if term_frag == "":
+ continue
+ else:
+ term_frags.append(term_frag)
+
+with open('terminal_frags.txt', 'w') as f:
+ for line in term_frags:
+ f.write(line)
+ f.write('\n')
+
+
--
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