diff fasta2fastq.py @ 0:8ab09593f2eb draft default tip

planemo upload commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fasta2fastq.py	Wed Oct 07 18:48:40 2020 +0000
@@ -0,0 +1,57 @@
+#!/usr/bin/env python
+
+"""fasta2fastq.py
+
+Author -- Monika Heinzl
+Contact -- [e-mail]
+
+Takes a fasta file and converts it to fastq file with a fake quality score.
+
+=======  ==========  =================  ================================
+Version  Date        Author             Description
+1.0.0    2020-10-07  Monika Heinzl    
+=======  ==========  =================  ================================
+
+USAGE: python fasta2fastq.py -i in.fasta -o out.fastq -s 40
+"""
+
+import argparse
+import sys, os
+from Bio import SeqIO
+
+
+def make_argparser():
+    parser = argparse.ArgumentParser(description='Takes a fasta file and converts it to fastq file with a fake quality score.')
+    parser.add_argument('-i', '--infile', required = True,
+                        help='Input FASTA file.')
+    parser.add_argument('-o', '--outfile', required = True,
+                        help='Output FASTQ file.')
+    parser.add_argument('-s', '--score', type=int, default=40,
+                        help='Quality score added to each base in the read. Default 40.')
+    return parser
+
+def fasta2fastq(argv):
+    parser = make_argparser()
+    args = parser.parse_args(argv[1:])
+
+    infasta = args.infile
+    outfastq = args.outfile
+    score = args.score
+
+    if os.path.isfile(infasta) is False:
+        sys.exit("Error: Could not find '{}'".format(infasta))
+    if os.path.isfile(outfastq) is False:
+        sys.exit("Error: Could not find '{}'".format(outfastq))
+    if score < 0:
+        sys.exit("Error: score is '{}', but only non-negative integers allowed".format(score))
+
+	# make fastq
+    with open(infasta, "r") as fasta, open(outfastq, "w") as fastq:
+        for record in SeqIO.parse(fasta, "fasta"):
+            record.letter_annotations["phred_quality"] = [score] * len(record)
+            SeqIO.write(record, fastq, "fastq")
+
+
+if __name__ == '__main__':
+    sys.exit(fasta2fastq(sys.argv))
+