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1 #! /bin/python
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2
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3
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4 import sys
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5 from os.path import basename
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6
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7 fasta = sys.argv[1]
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8 linesize = int(sys.argv[2])
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9
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10 if len(sys.argv[1:])>=3:
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11 outfastaname = sys.argv[3]
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12 else:
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13 outfastaname = "adjusted_%d_%s" % (linesize,basename(fasta))
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14
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15
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16 if len(sys.argv[1:])>=4:
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17 outplotname = sys.argv[4]
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18 else:
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19 outplotname = "%s_nt_counts.pdf" % (basename(fasta))
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20
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21
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22 #fasta = "/Users/boris/Desktop/mouse/mouse_reference_mtDNA.fasta"
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23 #linesize = 200
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24
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25 fastaheader = ">noname"
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26 fastaseq = ""
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27
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28 with open(fasta) as fa:
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29 for line in fa:
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30 if line.strip().startswith(">"):
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31 fastaheader = line.strip()
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32 else:
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33 fastaseq+= line.strip()
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34
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35
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36 #outfastaname = "adjusted_%d_%s" % (linesize,basename(fasta))
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37 outfile = open(outfastaname,"w+")
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38
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39 outfile.write(fastaheader+"\n")
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40 for i in range(0,len(fastaseq),linesize):
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41 outfile.write(fastaseq[i:i+linesize]+'\n')
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42 outfile.close()
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43
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44 ############################################################################
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45 import matplotlib.pyplot as plt
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46 import numpy as np
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47
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48 bases=['A','C','G','T','N']
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49 counts = np.array([fastaseq.upper().count(nt) for nt in bases])
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50
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51 index = np.array(range(len(counts)))
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52 bar_width = 0.7
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53 plt.bar(index,counts,bar_width,color=['red','green','orange','blue','grey'])
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54
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55 plt.axis([-1,5,0,max(counts)+1000])
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56 plt.xlabel('Nucleotide')
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57 plt.ylabel('Count')
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58 plt.title('Fasta nucleotide content')
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59 plt.xticks(index+bar_width/2, bases)
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60
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61 plt.savefig(outplotname,format="pdf")
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62
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