changeset 1:60e768cf5101 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fasta_to_fastq.py	Tue Jul 23 14:28:53 2024 +0000
@@ -0,0 +1,53 @@
+#!/usr/bin/python
+#-*- coding: utf-8 -*-
+
+"""
+
+Scripts ayant pour rôle l'extraction de tous les noms de segment contenus dans un fichier genbank.
+Réalisé par Pierrick Lucas.
+Usage : python fastq_to_fastq.py -i sequences.fasta -s 40 -o output_file.fastq
+
+"""
+
+# Import
+import argparse
+import sys
+import os
+from Bio import SeqIO
+
+##### MAIN
+def __main__():
+  # Options :
+  parser = argparse.ArgumentParser(description="""Takes a fasta file and converts it to fastq file with a fake quality score.""",
+                                   epilog="""This script need few options, use -h to see it.""")
+  parser.add_argument("-i", "--infile", dest="infile", help="Input fasta file.")
+  parser.add_argument("-s", "--score", type=int, default=40, dest="score", help="Quality score you wanted for each base in all reads. (default: 40)")
+  parser.add_argument("-o", "--outfile", dest="outfile", help="Output file in fastq format.")
+
+  if len(sys.argv) == 1 or len(sys.argv) < 5 or len(sys.argv) > 7:
+    parser.print_help()
+    sys.exit(1)
+
+  # Get options :
+  options = parser.parse_args()
+  infile = options.infile
+  score = options.score
+  outfile = options.outfile
+
+  outputfile = open(outfile,"w")
+
+  # Check score
+  if score < 0:
+    sys.exit("Error: only positive integers for the score".format(score))
+
+  # Create fastq output file
+  with open(infile, "r") as inf:
+    for record in SeqIO.parse(inf, "fasta"):
+      record.letter_annotations["phred_quality"] = [score] * len(record)
+      SeqIO.write(record, outputfile, "fastq")
+
+  # Close output file
+  outputfile.close()
+
+#### MAIN END
+if __name__ == "__main__": __main__()