diff --git a/gtf_processing/pre_bedtools.py b/gtf_processing/pre_bedtools.py
index 20889478f604b5e409b2220c494a7e57176cb8de..cc69d5b3fae683a6b61ccf5e2ed21aef48c5b11d 100644
--- a/gtf_processing/pre_bedtools.py
+++ b/gtf_processing/pre_bedtools.py
@@ -12,22 +12,36 @@ import pandas as pd
from gtfparse import read_gtf
parser = argparse.ArgumentParser(
- prog = 'pre_bedtools',
- description = 'extracts ordered information from gtf file and for transcripts in the negative strand, flips the order in which exons are ordered.')
-parser.add_argument('--input_gtf_file',
- help='ordered and processed gtf file')
-parser.add_argument('--output_bed_file',
- help='bed file with only exons with strandedness taken into account')
+ prog="pre_bedtools",
+ description="extracts ordered information from gtf file and for transcripts in the negative strand, flips the order in which exons are ordered.",
+)
+parser.add_argument("--input_gtf_file", help="ordered and processed gtf file")
+parser.add_argument(
+ "--output_bed_file",
+ help="bed file with only exons with strandedness taken into account",
+)
args = parser.parse_args()
gtf = read_gtf(args.input_gtf_file)
gtf_exons = gtf[gtf["feature"] == "exon"]
-gtf_exons = gtf_exons[["seqname", "start", "end", "transcript_id", "score", "strand", "gene_id"]]
+gtf_exons = gtf_exons[
+ ["seqname", "start", "end", "transcript_id", "score", "strand", "gene_id"]
+]
gtf_df_neg = gtf_exons[gtf_exons["strand"] == "-"]
-gtf_df_neg = gtf_df_neg.sort_values(['transcript_id','start'],ascending=False).groupby('transcript_id').head(len(gtf_df_neg. transcript_id))
+gtf_df_neg = (
+ gtf_df_neg.sort_values(["transcript_id", "start"], ascending=False)
+ .groupby("transcript_id")
+ .head(len(gtf_df_neg.transcript_id))
+)
gtf_df_pos = gtf_exons[gtf_exons["strand"] == "+"]
-gtf_df_pos = gtf_df_pos.sort_values(['transcript_id','start'],ascending=True).groupby('transcript_id').head(len(gtf_df_pos. transcript_id))
-
-pd.concat([gtf_df_pos, gtf_df_neg]).to_csv(args.output_bed_file,sep="\t",index=False) #gtf_df_pos and gtf_df_neg must be dataframes
+gtf_df_pos = (
+ gtf_df_pos.sort_values(["transcript_id", "start"], ascending=True)
+ .groupby("transcript_id")
+ .head(len(gtf_df_pos.transcript_id))
+)
+
+pd.concat([gtf_df_pos, gtf_df_neg]).to_csv(
+ args.output_bed_file, sep="\t", index=False
+) # gtf_df_pos and gtf_df_neg must be dataframes
diff --git a/sequence_extractor/cli.py b/sequence_extractor/cli.py
index 73062da3fb84f18f67391f490203612d65c4f0e2..b3bfeab5176ae3fd05fae2475b28e2f72488e5a8 100644
--- a/sequence_extractor/cli.py
+++ b/sequence_extractor/cli.py
@@ -5,15 +5,15 @@ from exon_concatenation import exon_concatenation
from poly_a import poly_a_addition_to_fasta_list
parser = argparse.ArgumentParser(
- prog = 'transcript_sequence_extractor',
- description = 'extracts transcript sequences from genome sequence and ouputs transcripts with PolyA tail added to them')
-parser.add_argument('--input_fasta_file',
- help='fasta file obtained from bedtools')
-parser.add_argument('--output_file_name',
- help='Name of the output fasta file')
+ prog="transcript_sequence_extractor",
+ description="extracts transcript sequences from genome sequence and ouputs transcripts with PolyA tail added to them",
+)
+parser.add_argument("--input_fasta_file", help="fasta file obtained from bedtools")
+parser.add_argument("--output_file_name", help="Name of the output fasta file")
args = parser.parse_args()
+
def main():
"""Runs on the output from bedtools and concatenates the exons together and adds a polyA tail and outputs a fasta file.
@@ -26,11 +26,12 @@ def main():
LOG.info("sequence_extractor begins")
fasta_list = exon_concatenation(args.input_fasta_file)
final_list = poly_a_addition_to_fasta_list(fasta_list)
- with open(args.output_file_name, 'w', encoding="utf-8") as fasta_out:
- fasta_out.write('\n'.join('%s\n%s' % x for x in final_list))
+ with open(args.output_file_name, "w", encoding="utf-8") as fasta_out:
+ fasta_out.write("\n".join("%s\n%s" % x for x in final_list))
LOG.info("sequence_extractor ends")
-if ___name__ == 'main':
+
+if ___name__ == "main":
logging.basicConfig(
format='[%(asctime)s: %(levelname)s] %(message)s (module "%(module)s")',
level=logging.INFO,
diff --git a/sequence_extractor/exon_concatenation.py b/sequence_extractor/exon_concatenation.py
index d9f3266e90d058c0698c029aec2cf5811fceca2a..88377f27ee5ee0a01c63a503596b854066123ea2 100644
--- a/sequence_extractor/exon_concatenation.py
+++ b/sequence_extractor/exon_concatenation.py
@@ -1,4 +1,6 @@
"""Script containing the function to concatenate exons and output the results in a list of tuples"""
+
+
def exon_concatenation(
post_bedtools_fasta: str,
) -> list:
@@ -10,10 +12,10 @@ def exon_concatenation(
Returns:
A list containing transcript ID and concatenated exons in tuples.
"""
- with open(post_bedtools_fasta,'r', encoding="utf-8") as fasta:
+ with open(post_bedtools_fasta, "r", encoding="utf-8") as fasta:
annotation = []
fasta_format_list = []
- for line1,line2 in zip(fasta,fasta):
+ for line1, line2 in zip(fasta, fasta):
if len(annotation) == 0:
annotation.append(line1[0:16])
read = line2[:-1]
@@ -21,8 +23,8 @@ def exon_concatenation(
if annotation[-1] == line1[0:16]:
read += line2[:-1]
elif annotation[-1] != line1[0:16]:
- fasta_format_list.append((annotation[-1],read))
+ fasta_format_list.append((annotation[-1], read))
annotation.append(line1[0:16])
read = line2[:-1]
- fasta_format_list.append((annotation[-1],read))
+ fasta_format_list.append((annotation[-1], read))
return fasta_format_list
diff --git a/sequence_extractor/poly_a.py b/sequence_extractor/poly_a.py
index 60b299788743a192f984a2d580ac139a42c35a7b..d1975628337d4b0e5bb6f5c90f55c6981ca34dde 100644
--- a/sequence_extractor/poly_a.py
+++ b/sequence_extractor/poly_a.py
@@ -1,31 +1,35 @@
""" This script contains two functions and the first function is called by the second function and used to add poly A tail to the concatenated exon"""
import numpy as np
+
# To do: Taking probabilities of nucleotides from user and raising error if sum != 1
def poly_a_generator(
- exon: str,
+ exon: str,
) -> str:
"""Adds a PolyA tail to an exon sequence input into the function.
- Args:
- exon: RNA sequence, obtained from concatenation of exons, that needs polyA to be added to its 3' end.
+ Args:
+ exon: RNA sequence, obtained from concatenation of exons, that needs polyA to be added to its 3' end.
+
+ Returns:
+ RNA with polyA tail added to its 3' end.
+ """
+ list_of_nucleotides = ["A", "T", "G", "C"]
+ poly_a_string = "".join(
+ np.random.choice(list_of_nucleotides, 250, p=[0.914, 0.028, 0.025, 0.033])
+ )
+ return exon + poly_a_string
- Returns:
- RNA with polyA tail added to its 3' end.
- """
- list_of_nucleotides = ['A','T','G','C']
- poly_a_string = ''.join(np.random.choice(list_of_nucleotides,250,p=[0.914,0.028,0.025,0.033]))
- return exon+poly_a_string
def poly_a_addition_to_fasta_list(
- fasta_list: list,
+ fasta_list: list,
) -> list:
"""Takes in a list of tuples with annotations and exons and outputs a list where polyA tail has been added to all the exon 3' ends.
- Args:
- fasta_list: List contaning tuples of annotations and exons
+ Args:
+ fasta_list: List contaning tuples of annotations and exons
- Returns:
- A list like the initial list, this time with polyA tail added onto it.
- """
- mature_rna_list = [(i[0],poly_a_generator(i[1])) for i in fasta_list]
+ Returns:
+ A list like the initial list, this time with polyA tail added onto it.
+ """
+ mature_rna_list = [(i[0], poly_a_generator(i[1])) for i in fasta_list]
return mature_rna_list