From aba597a11e236768df580efd0b0c6b2c67d6beb7 Mon Sep 17 00:00:00 2001
From: Eric Boittier <ericdavid.boittier@unibas.ch>
Date: Wed, 23 Nov 2022 11:11:45 +0100
Subject: [PATCH] reformatted with black
---
cdna/cdna.py | 50 ++++++++++++++++++++++----------------------------
1 file changed, 22 insertions(+), 28 deletions(-)
diff --git a/cdna/cdna.py b/cdna/cdna.py
index 97208d1..c4b1ae3 100644
--- a/cdna/cdna.py
+++ b/cdna/cdna.py
@@ -1,20 +1,18 @@
import sys
+
def translate(res):
- translate_dict = {"A": "T", "U": "A", "G": "C", "C":"G"}
+ translate_dict = {"A": "T", "U": "A", "G": "C", "C": "G"}
if res not in translate_dict.keys():
print("cDNA residue not A,T,U or G ")
sys.exit(1)
return translate_dict[res]
+
class cDNA_Gen:
- def __init__(self,
- fasta,
- gtf,
- cpn,
- output_fasta = "cDNA.fasta",
- output_csv = "cDNA.csv"
- ):
+ def __init__(
+ self, fasta, gtf, cpn, output_fasta="cDNA.fasta", output_csv="cDNA.csv"
+ ):
# inputs
self.fasta = fasta
self.gtf = gtf
@@ -26,27 +24,25 @@ class cDNA_Gen:
self.fasta_seq = ""
self.fasta_id = ""
self.copy_numbers = {}
-
+
self.run()
-
+
def run(self):
self.read_fasta()
self.read_gtf()
-
+
def order_priming_sites(self):
pass
-
+
def generate_cdna(self):
pass
-
-
+
def read_fasta(self):
fasta = open(self.fasta).readlines()
self.fasta_id = fasta[0]
print(fasta[0])
self.fasta_seq = "".join([_.rstrip() for _ in fasta[1:]])
-
-
+
def read_gtf(self):
with open(self.gtf) as gtf_file:
gtf_lines = gtf_file.readlines()
@@ -58,7 +54,7 @@ class cDNA_Gen:
def write_fasta(self):
pass
-
+
def read_copy_numbers(self):
with open(self.cpn) as cpn_file:
cpn_lines = cpn_file.readlines()
@@ -69,11 +65,10 @@ class cDNA_Gen:
gene_id = csv[1]
count = csv[2]
self.copy_numbers[gene_id] = count
-
-
+
def return_output(self):
return self.output_fasta, self.output_csv
-
+
class GTF_entry:
def __init__(self, string):
@@ -82,19 +77,18 @@ class GTF_entry:
self.id = self.values[0]
self.start = int(self.values[3])
self.end = int(self.values[4])
- self.score = float(0.5) #self.values[5]
+ self.score = float(0.5) # self.values[5]
self.sequence = "no sequence set"
self.length = self.end - self.start
-
+
def __repr__(self):
return self.sequence[:10] + "..." + f" len={self.length} score={self.score}"
-
+
def set_sequence(self, full_sequence):
- self.sequence = full_sequence[self.start:self.end]
-
-
+ self.sequence = full_sequence[self.start : self.end]
+
+
if __name__ == "__main__":
import argparse
+
pass
-
-
--
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