From 061f425fd02125e479399dd7878e428bf0ec509a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Boris=20Juri=C4=8D?= <499542@mail.muni.cz>
Date: Fri, 1 Apr 2022 11:56:30 +0000
Subject: [PATCH] Make src/poly_a.py runnable, added fasta processing. Initial
transcript generation workflow.
---
src/generate_transcripts.nf | 51 +++++++++++++++++++++++++++++++++++++
src/poly_a.py | 26 +++++++++++++++++++
2 files changed, 77 insertions(+)
create mode 100644 src/generate_transcripts.nf
diff --git a/src/generate_transcripts.nf b/src/generate_transcripts.nf
new file mode 100644
index 0000000..36b1f67
--- /dev/null
+++ b/src/generate_transcripts.nf
@@ -0,0 +1,51 @@
+#!/usr/bin/env nextflow
+
+params.fasta = "/inputs/ref_genome.fa"
+params.gtf = "/inputs/ref_annotation.gtf"
+params.outdir = "/tests"
+params.tail_length = "100"
+params.weights = "1.0 0.0 0.0 0.0"
+
+project_dir = projectDir
+
+process getTranscriptGTF {
+
+ input:
+ path gtf from params.gtf
+
+ output:
+ file "transcripts.gtf" into transcripts_gtf
+
+ """
+ awk '\$3 == "transcript"' ${gtf} > transcripts.gtf
+ """
+}
+
+process getTranscripts {
+
+ input:
+ path fasta from params.fasta
+ file gtf from transcripts_gtf
+
+ output:
+ file "transcripts.fa" into transcripts_fa
+
+ """
+ bedtools getfasta -fi ${fasta} -bed ${gtf} -fo transcripts.fa
+ """
+}
+
+process addPolyA {
+publishDir params.outdir, mode: 'copy', pattern: 'transcripts_with_polyA.fa'
+
+ input:
+ file transcripts from transcripts_fa
+
+ output:
+ file "transcripts_with_polyA.fa" into transcripts_polyA
+
+ script:
+ """
+ python3 $project_dir/poly_a.py -i ${transcripts} -o transcripts_with_polyA.fa --length ${params.tail_length} --weights ${params.weights}
+ """
+}
diff --git a/src/poly_a.py b/src/poly_a.py
index 2c3ee30..72dacb1 100644
--- a/src/poly_a.py
+++ b/src/poly_a.py
@@ -1,7 +1,11 @@
"""Generate a poly(A) tail."""
+from Bio import SeqIO
+from Bio.SeqRecord import SeqRecord
+from Bio.Seq import Seq
from random import choices
from typing import (List, Tuple)
+import argparse
def generate_poly_a(
@@ -65,3 +69,25 @@ def generate_poly_a(
norm_weights: List[float] = [freq/s for freq in weights]
tail_bases: List[str] = choices(bases, weights=norm_weights, k=length)
return "".join(tail_bases)
+
+def main():
+ parser = argparse.ArgumentParser(description='Process some integers.')
+ parser.add_argument('-i', '--input', required=True,
+ help='Fasta file to add tails to')
+ parser.add_argument('-o', '--output', default="out.fa",
+ help='Name of the output Fasta file (default = out.fa)')
+ parser.add_argument('--length', default=100, type=int,
+ help='Length of the desired tail (max value = 200)')
+ parser.add_argument('--weights', default=(0.914, 0.028, 0.025, 0.033), type=float, nargs='+',
+ help="Tuple of relative A, C, G and U frequencies in the tail")
+ args = parser.parse_args()
+
+ new_records = []
+ for fasta in SeqIO.parse(open(args.input),'fasta'):
+ new_seq = fasta.seq + Seq(generate_poly_a(args.length, args.weights))
+ new_records.append(SeqRecord(new_seq, id=fasta.id, description=fasta.description))
+ print(new_records[0].seq)
+ SeqIO.write(new_records, args.output, "fasta")
+
+if __name__ == '__main__':
+ main()
--
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