Mercurial > repos > matthias > longorf

annotate getLongestORF.py @ 0:e09750baa9ac draft default tip

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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/ commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
author matthias
date Wed, 20 Jun 2018 10:55:21 -0400
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e09750baa9ac planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/ commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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1 #!/usr/bin/env python
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3 """
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4 usage: getLongestORF.py input output.fas output.tab
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7 input.fas: a amino acid fasta file of all open reading frames (ORF) listed by transcript (output of GalaxyTool "getorf")
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8 output.fas: fasta file with all longest ORFs per transcript
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9 output.tab: table with information about seqID, start, end, length, orientation, longest for all ORFs
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11 example:
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13 >253936-254394(+)_1 [28 - 63]
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14 LTNYCQMVHNIL
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15 >253936-254394(+)_2 [18 - 77]
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16 HKLIDKLLPNGAQYFVKSTQ
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17 >253936-254394(+)_3 [32 - 148]
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18 QTTAKWCTIFCKKYPVAPFHTMYLNYAVTWHHRSLLVAV
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19 >253936-254394(+)_4 [117 - 152]
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20 LGIIVPSLLLCN
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21 >248351-252461(+)_1 [14 - 85]
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22 VLARKYPRCLSPSKKSPCQLRQRS
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23 >248351-252461(+)_2 [21 - 161]
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24 PGNTHDASAHRKSLRVNSDKEVKCLFTKNAASEHPDHKRRRVSEHVP
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25 >248351-252461(+)_3 [89 - 202]
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26 VPLHQECCIGAPRPQTTACVRACAMTNTPRSSMTSKTG
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27 >248351-252461(+)_4 [206 - 259]
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28 SRTTSGRQSVLSEKLWRR
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29 >248351-252461(+)_5 [263 - 313]
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30 CLSPLWVPCCSRHSCHG
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31 """
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33 import sys,re
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35 def findlongestOrf(transcriptDict,old_seqID):
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36 #write for previous seqID
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37 prevTranscript = transcriptDict[old_seqID]
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38 i_max = 0
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39 #find longest orf in transcript
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40 for i in range(0,len(prevTranscript)):
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41 if(prevTranscript[i][2] >= prevTranscript[i_max][2]):
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42 i_max = i
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43 for i in range(0,len(prevTranscript)):
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44 prevStart = prevTranscript[i][0]
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45 prevEnd = prevTranscript[i][1]
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46 prevLength = prevTranscript[i][2]
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47 output = str(old_seqID) + "\t" + str(prevStart) + "\t" + str(prevEnd) + "\t" + str(prevLength)
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48 if (end - start > 0):
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49 output+="\tForward"
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50 else:
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51 output+="\tReverse"
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52 if(i == i_max):
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53 output += "\ty\n"
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54 else:
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55 output += "\tn\n"
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56 OUTPUT_ORF_SUMMARY.write(output)
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57 transcriptDict.pop(old_seqID, None)
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58 return None
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59
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60 INPUT = open(sys.argv[1],"r")
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61 OUTPUT_FASTA = open(sys.argv[2],"w")
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62 OUTPUT_ORF_SUMMARY = open(sys.argv[3],"w")
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63
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64 seqID = ""
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65 old_seqID = ""
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66 lengthDict = {}
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67 seqDict = {}
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68 headerDict = {}
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69 transcriptDict = {}
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70 skip = False
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71
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72 OUTPUT_ORF_SUMMARY.write("seqID\tstart\tend\tlength\torientation\tlongest\n")
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73
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74 for line in INPUT:
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75 line = line.strip()
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76 # print line
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77 if(re.match(">",line)): #header
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78 seqID = "_".join(line.split(">")[1].split("_")[:-1])
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79 #seqID = line.split(">")[1].split("_")[0]
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80 start = int (re.search('\ \[(\d+)\ -', line).group(1))
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81 end = int (re.search('-\ (\d+)\]',line).group(1))
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82 length = abs(end - start)
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83 if(seqID not in transcriptDict and old_seqID != ""): #new transcript
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84 findlongestOrf(transcriptDict,old_seqID)
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85 if seqID not in transcriptDict:
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86 transcriptDict[seqID] = []
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87 transcriptDict[seqID].append([start,end,length])
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88 if(seqID not in lengthDict and old_seqID != ""): #new transcript
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89 #write FASTA
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90 OUTPUT_FASTA.write(headerDict[old_seqID]+"\n"+seqDict[old_seqID]+"\n")
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91 #delete old dict entry
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92 headerDict.pop(old_seqID, None)
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93 seqDict.pop(old_seqID, None)
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94 lengthDict.pop(old_seqID, None)
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95 #if several longest sequences exist with the same length, the dictionary saves the last occuring.
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96 if(seqID not in lengthDict or length >= lengthDict[seqID]):
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97 headerDict[seqID] = line
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98 lengthDict[seqID] = length
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99 seqDict[seqID] = ""
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100 skip = False
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101 else:
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102 skip = True
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103 next
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104 old_seqID = seqID
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105 elif(skip):
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106 next
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107 else:
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108 seqDict[seqID] += line
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109
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110 OUTPUT_FASTA.write(headerDict[old_seqID]+"\n"+seqDict[old_seqID])
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111 findlongestOrf(transcriptDict,old_seqID)
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112 INPUT.close()
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113 OUTPUT_FASTA.close()
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114 OUTPUT_ORF_SUMMARY.close()