Mercurial > repos > jay > pdaug_tsvtofasta

annotate PDAUG_Peptide_Length_Distribution/PDAUG_Peptide_Length_Distribution.py @ 11:7e6c49b99153 draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit d396d7ff89705cc0dd626ed32c45a9f4029b1b05"
author jay
date Mon, 10 Jan 2022 04:15:37 +0000
parents c3f0b3a6339e
children
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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)