Mercurial > repos > jay > pdaug_sequence_similarity_network
comparison PDAUG_Peptide_Length_Distribution/PDAUG_Peptide_Length_Distribution.py @ 0:e650de82bcc7 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author | jay |
---|---|
date | Wed, 28 Oct 2020 01:50:00 +0000 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:e650de82bcc7 |
---|---|
1 import matplotlib.pyplot as plt | |
2 import Bio | |
3 from Bio import SeqIO | |
4 import os | |
5 | |
6 | |
7 def LegnthDestribution(InFile, OutFile): | |
8 | |
9 | |
10 sizes = [len(rec.seq) for rec in SeqIO.parse(InFile, "fasta")] | |
11 | |
12 plt.hist(sizes, bins=20) | |
13 plt.title("%i Negative bacteriocin sequences\nLengths %i to %i" \ | |
14 % (len(sizes),min(sizes),max(sizes))) | |
15 plt.xlabel("Sequence length (bp)") | |
16 plt.ylabel("Count") | |
17 | |
18 plt.savefig(OutFile) | |
19 | |
20 | |
21 | |
22 if __name__=="__main__": | |
23 | |
24 import argparse | |
25 | |
26 parser = argparse.ArgumentParser() | |
27 | |
28 parser.add_argument("-I", "--InFile", required=True, default=None, help="Input file name") | |
29 parser.add_argument("-O", "--OutFile", required=False, default="Out.png", help="Input file name") | |
30 args = parser.parse_args() | |
31 LegnthDestribution(args.InFile, args.OutFile) |