diff PDAUG_Peptide_Length_Distribution/PDAUG_Peptide_Length_Distribution.py @ 0:7557b48b2872 draft

"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PDAUG_Peptide_Length_Distribution/PDAUG_Peptide_Length_Distribution.py	Wed Oct 28 02:10:12 2020 +0000
@@ -0,0 +1,31 @@
+import matplotlib.pyplot as plt
+import Bio
+from Bio import SeqIO
+import os
+
+
+def LegnthDestribution(InFile, OutFile):
+
+
+    sizes = [len(rec.seq) for rec in SeqIO.parse(InFile, "fasta")]
+
+    plt.hist(sizes, bins=20)
+    plt.title("%i Negative bacteriocin sequences\nLengths %i to %i" \
+                % (len(sizes),min(sizes),max(sizes)))
+    plt.xlabel("Sequence length (bp)")
+    plt.ylabel("Count")
+
+    plt.savefig(OutFile)
+
+
+
+if __name__=="__main__":
+
+    import argparse
+    
+    parser = argparse.ArgumentParser()
+    
+    parser.add_argument("-I", "--InFile", required=True, default=None, help="Input file name")
+    parser.add_argument("-O", "--OutFile", required=False, default="Out.png", help="Input file name")
+    args = parser.parse_args()
+    LegnthDestribution(args.InFile, args.OutFile)