Mercurial > repos > jay > pdaug_ml_models

annotate PDAUG_Peptide_Length_Distribution/PDAUG_Peptide_Length_Distribution.py @ 0:0973f093d98f draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author jay
date Wed, 28 Oct 2020 02:31:40 +0000
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1 import matplotlib.pyplot as plt
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2 import Bio
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3 from Bio import SeqIO
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4 import os
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7 def LegnthDestribution(InFile, OutFile):
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10 sizes = [len(rec.seq) for rec in SeqIO.parse(InFile, "fasta")]
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12 plt.hist(sizes, bins=20)
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13 plt.title("%i Negative bacteriocin sequences\nLengths %i to %i" \
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14 % (len(sizes),min(sizes),max(sizes)))
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15 plt.xlabel("Sequence length (bp)")
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16 plt.ylabel("Count")
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18 plt.savefig(OutFile)
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22 if __name__=="__main__":
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24 import argparse
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26 parser = argparse.ArgumentParser()
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28 parser.add_argument("-I", "--InFile", required=True, default=None, help="Input file name")
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29 parser.add_argument("-O", "--OutFile", required=False, default="Out.png", help="Input file name")
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30 args = parser.parse_args()
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31 LegnthDestribution(args.InFile, args.OutFile)