Mercurial > repos > drosofff > msp_fasta_tabular_converter

annotate fasta_tabular_converter.py @ 0:951cb6b3979b draft

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author drosofff
date Sun, 21 Jun 2015 14:28:49 -0400
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children 2f7278120be9
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0
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1 #!/usr/bin/python
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2 #
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3 import sys
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4 from collections import defaultdict
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5
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6 def readfasta_writetabular(fasta, tabular):
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7 F = open(fasta, "r")
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8 for line in F:
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9 if line[0] == ">": continue
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10 else:
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11 seqdic[line[:-1]] += 1
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12 F.close()
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13 F = open(tabular, "w")
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14 for seq in sorted(seqdic, key=seqdic.get, reverse=True):
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15 print >> F, "%s\t%s" % (seq, seqdic[seq])
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16 F.close()
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17
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18
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19 def readtabular_writefasta(tabular, fasta):
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20 F = open(tabular, "r")
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21 Fw = open(fasta, "w")
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22 counter = 0
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23 for line in F:
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24 fields = line.split()
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25 for i in range(int(fields[1])):
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26 counter += 1
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27 print >> Fw, ">%s\n%s" % (counter, fields[0])
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28 F.close()
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29 Fw.close()
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30
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31 def readtabular_writefastaweighted (tabular, fasta):
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32 F = open(tabular, "r")
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33 Fw = open(fasta, "w")
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34 counter = 0
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35 for line in F:
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36 counter += 1
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37 fields = line[:-1].split()
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38 print >> Fw, ">%s_%s\n%s" % (counter, fields[1], fields[0])
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39 F.close()
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40 Fw.close()
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41
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42 def readfastaeighted_writefastaweighted(fastaweigthed_input, fastaweigthed_reparsed):
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43 F = open(fastaweigthed_input, "r")
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44 number_reads = 0
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45 for line in F:
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46 if line[0] == ">":
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47 weigth = int(line[1:-1].split("_")[-1])
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48 number_reads += weigth
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49 else:
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50 seqdic[line[:-1]] += weigth
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51 F.close()
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52 F = open(fastaweigthed_reparsed, "w")
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53 n=0
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54 for seq in sorted(seqdic, key=seqdic.get, reverse=True):
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55 n += 1
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56 print >> F, ">%s_%s\n%s" % (n, seqdic[seq], seq)
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57 F.close()
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58 print "%s reads collapsed" % number_reads
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59
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60 def readfastaeighted_writefasta(fastaweigthed, fasta):
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61 F = open(fastaweigthed, "r")
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62 Fw = open(fasta, "w")
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63 counter = 0
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64 for line in F:
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65 if line[0] == ">":
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66 weigth = int(line[1:-1].split("_")[-1])
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67 else:
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68 seq = line[:-1]
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69 for i in range (weigth):
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70 counter += 1
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71 print >> Fw, ">%s\n%s" % (counter, seq)
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72 F.close()
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73 Fw.close()
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74
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75
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76 seqdic = defaultdict(int)
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77 option = sys.argv[3]
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78
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79 if option == "fasta2tabular":
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80 readfasta_writetabular(sys.argv[1], sys.argv[2])
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81 elif option == "tabular2fasta":
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82 readtabular_writefasta(sys.argv[1], sys.argv[2])
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83 elif option == "tabular2fastaweight":
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84 readtabular_writefastaweighted (sys.argv[1], sys.argv[2])
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85 elif option == "fastaweight2fastaweight":
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86 readfastaeighted_writefastaweighted(sys.argv[1], sys.argv[2])
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87 elif option == "fastaweight2fasta":
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88 readfastaeighted_writefasta(sys.argv[1], sys.argv[2])