Make src/poly_a.py runnable, added fasta processing. Initial transcript generation workflow.

src/generate_transcripts.nf

+#!/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}
+    """
+}

src/poly_a.py

 """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()