Mercurial > repos > cpt > cpt_gbk_adjacent

annotate adjacent_features.py @ 1:e29c36ee61e0 draft

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:42:35 +0000
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1 #!/usr/bin/env python
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2 from Bio import SeqIO
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3 from Bio.Seq import Seq
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4 from Bio.Data import CodonTable
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5 from Bio.SeqRecord import SeqRecord
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6 from Bio.SeqFeature import SeqFeature, FeatureLocation
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7 from Bio.Alphabet import generic_dna, generic_protein
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8 import argparse
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9 import logging
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10
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11 logging.basicConfig(level=logging.INFO)
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12 log = logging.getLogger()
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13
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14
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15 def extract_features(
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16 genbankFiles=None,
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17 fastaFiles=None,
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18 upOut=None,
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19 downOut=None,
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20 genesOnly=False,
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21 cdsOnly=True,
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22 forceSeqID=False,
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23 forward=1,
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24 behind=1,
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25 outProt=True,
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26 tTable=11,
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27 fTable=11,
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28 ):
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29
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30 genList = []
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31 fastaList = []
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32
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33 for fileX in genbankFiles:
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34 opener = SeqIO.parse(fileX, "genbank")
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35 for (
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36 openRec
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37 ) in (
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38 opener
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39 ): # To turn the generator into objects (or else we end up with a list of generators)
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40 genList.append(openRec)
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41
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42 for fileX in fastaFiles:
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43 opener = SeqIO.parse(fileX, "fasta")
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44 for openRec in opener: # Technically flattens multifastas too
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45 fastaList.append(openRec)
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46
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47 for seqMatch in fastaList:
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48 longOut = seqMatch.description
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49 protID = seqMatch.id
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50 if fTable != 0:
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51 fSeq = seqMatch.seq.translate(table=fTable, cds=False)
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52 else:
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53 fSeq = seqMatch.seq
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54
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55 for gbk in genList:
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56 sourceOut = gbk.id
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57 num = -1
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58 for feat in gbk.features:
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59 num += 1
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60
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61 if (genesOnly and feat.type != "gene") or (
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62 cdsOnly and feat.type != "CDS"
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63 ):
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64 continue
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65
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66 if "codon_start" in feat.qualifiers:
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67 offset = 1 - int(feat.qualifiers["codon_start"][0])
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68 else:
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69 offset = 0
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70
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71 temp = gbk.seq[feat.location.start : feat.location.end]
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72 if feat.location.strand == -1:
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73 temp = gbk.seq[feat.location.start : feat.location.end - offset]
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74 temp = temp.reverse_complement()
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75 else:
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76 temp = gbk.seq[feat.location.start + offset : feat.location.end]
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77
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78 if tTable != 0:
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79 try:
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80 gSeq = temp.translate(table=tTable, cds=True)
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81 except CodonTable.TranslationError as cte:
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82 # log.info("Translation issue at %s", cte)
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83 gSeq = temp.translate(table=tTable, cds=False)
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84 else:
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85 gSeq = temp
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86
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87 if not ("protein_id" in feat.qualifiers):
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88 feat.qualifiers["protein_id"] = [
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89 "++++++++"
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90 ] # Junk value for genesOnly flag
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91
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92 if (gSeq == fSeq) and (
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93 protID == feat.qualifiers["protein_id"][0] or forceSeqID == False
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94 ):
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95 goBack = num - 1
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96 goAhead = num + 1
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97 numBack = behind
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98 numAhead = forward
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99 backList = []
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100 aheadList = []
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101
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102 while numBack != 0 and goBack >= 0:
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103 if (genesOnly and gbk.features[goBack].type != "gene") or (
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104 cdsOnly and gbk.features[goBack].type != "CDS"
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105 ):
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106 goBack -= 1
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107 continue
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108 backList.append(gbk.features[goBack])
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109 numBack -= 1
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110 goBack -= 1
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111
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112 while numAhead != 0 and goAhead < len(gbk.features):
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113 if (genesOnly and gbk.features[goAhead].type != "gene") or (
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114 cdsOnly and gbk.features[goAhead].type != "CDS"
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115 ):
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116 goAhead += 1
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117 continue
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118 aheadList.append(gbk.features[goAhead])
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119 numAhead -= 1
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120 goAhead += 1
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121
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diff changeset
122 backList.reverse()
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
123 if feat.location.strand == -1:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
124 tmpList = aheadList
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
125 aheadList = backList
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
126 backList = tmpList
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
127
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
128 for item in backList:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
129 addition = ""
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
130 header = ""
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
131 if "product" in item.qualifiers:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
132 addition = " -" + str(item.qualifiers["product"][0]) + "-"
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
133 if "protein_id" in item.qualifiers:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
134 header = (
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
135 ">"
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
136 + (item.qualifiers["protein_id"][0])
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
137 + addition
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
138 + " (5' of "
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
139 + longOut
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
140 + " found within "
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
141 + sourceOut
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
142 + ")\n"
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
143 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
144 else:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
145 header = (
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
146 ">"
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
147 + (item.qualifiers["locus_tag"][0])
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
148 + addition
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
149 + " (5' of "
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
150 + longOut
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
151 + " found within "
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
152 + sourceOut
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
153 + ")\n"
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
154 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
155 if outProt == True:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
156 if "translation" in item.qualifiers:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
157 upOut.write(header)
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
158 upOut.write(
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
159 str(item.qualifiers["translation"][0]) + "\n\n"
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
160 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
161 else:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
162 modS = 0
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
163 modE = 0
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
164 if "codon_start" in item.qualifiers:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
165 if item.location.strand > 0:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
166 modS = (
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
167 int(item.qualifiers["codon_start"][0]) - 1
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
168 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
169 else:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
170 modE = (
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
171 int(item.qualifiers["codon_start"][0]) - 1
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
172 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
173
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
174 seqHold = gbk.seq[
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
175 item.location.start
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
176 + modS : item.location.end
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
177 - modE
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
178 ]
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
179 if item.location.strand == -1:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
180 seqHold = seqHold.reverse_complement()
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
181 if cdsOnly:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
182 try:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
183 finalSeq = ""
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
184 if tTable != 0:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
185 finalSeq = (
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
186 str(
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
187 seqHold.translate(
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
188 table=tTable, cds=True
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
189 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
190 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
191 + "\n\n"
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
192 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
193 else:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
194 finalSeq = str(seqHold) + "\n\n"
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
195 # upOut.write(header)
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
196 # upOut.write(finalSeq)
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
197 except Exception as bdct:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
198 log.warn(
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
199 "ERROR %s %s",
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
200 item.qualifiers["locus_tag"][0],
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
201 bdct,
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
202 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
203 finalSeq = ""
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
204 if tTable != 0:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
205 finalSeq = (
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
206 str(
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
207 seqHold.translate(
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
208 table=tTable, cds=False
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
209 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
210 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
211 + "\n\n"
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
212 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
213 else:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
214 finalSeq = str(seqHold) + "\n\n"
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
215 header = (
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
216 ">"
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
217 + (item.qualifiers["locus_tag"][0])
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
218 + addition
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
219 + " [INCOMPLETE] (5' of "
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
220 + longOut
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
221 + " found within "
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
222 + sourceOut
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
223 + ")\n"
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
224 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
225 upOut.write(header)
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
226 upOut.write(finalSeq)
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
227 else:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
228
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
229 if tTable != 0:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
230 upOut.write(header)
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
231 upOut.write(
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
232 str(
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
233 seqHold.translate(
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
234 table=tTable, cds=False
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
235 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
236 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
237 + "\n\n"
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
238 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
239 else:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
240 upOut.write(header)
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
241 upOut.write(str(seqHold) + "\n\n")
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
242 else:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
243 upOut.write(header)
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
244 upOut.write(
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
245 str(gbk.seq[item.location.start : item.location.end])
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
246 + "\n\n"
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
247 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
248
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
249 for item in aheadList:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
250 addition = ""
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
251 header = ""
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
252 if "product" in item.qualifiers:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
253 addition = " -" + str(item.qualifiers["product"][0]) + "-"
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
254 if "protein_id" in item.qualifiers:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
255 header = (
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
256 ">"
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
257 + (item.qualifiers["protein_id"][0])
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
258 + addition
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
259 + " (3' of "
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
260 + longOut
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
261 + " found within "
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
262 + sourceOut
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
263 + ")\n"
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
264 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
265 else:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
266 header = (
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
267 ">"
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
268 + (item.qualifiers["locus_tag"][0])
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
269 + addition
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
270 + " (3' of "
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
271 + longOut
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
272 + " found within "
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
273 + sourceOut
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
274 + ")\n"
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
275 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
276 if outProt == True:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
277 if "translation" in item.qualifiers:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
278 downOut.write(header)
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
279 downOut.write(
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
280 str(item.qualifiers["translation"][0]) + "\n\n"
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
281 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
282 else:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
283 modS = 0
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
284 modE = 0
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
285 if "codon_start" in item.qualifiers:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
286 if item.location.strand > 0:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
287 modS = (
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
288 int(item.qualifiers["codon_start"][0]) - 1
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
289 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
290 else:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
291 modE = (
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
292 int(item.qualifiers["codon_start"][0]) - 1
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
293 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
294
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
295 seqHold = gbk.seq[
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
296 item.location.start
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
297 + modS : item.location.end
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
298 - modE
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
299 ]
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
300 if item.location.strand == -1:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
301 seqHold = seqHold.reverse_complement()
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
302 if cdsOnly:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
303 try:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
304 finalSeq = ""
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
305 if tTable != 0:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
306 finalSeq = (
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
307 str(
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
308 seqHold.translate(
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
309 table=tTable, cds=True
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
310 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
311 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
312 + "\n\n"
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
313 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
314 else:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
315 finalSeq = str(seqHold) + "\n\n"
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
316 # downOut.write(header)
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
317 # downOut.write(finalSeq)
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
318 except Exception as bdct:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
319 log.warn(
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
320 "ERROR %s %s",
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
321 item.qualifiers["locus_tag"][0],
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
322 bdct,
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
323 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
324 finalSeq = ""
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
325 if tTable != 0:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
326 finalSeq = (
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
327 str(
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
328 seqHold.translate(
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
329 table=tTable, cds=False
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
330 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
331 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
332 + "\n\n"
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
333 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
334 else:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
335 finalSeq = str(seqHold) + "\n\n"
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
336 header = (
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
337 ">"
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
338 + (item.qualifiers["locus_tag"][0])
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
339 + addition
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
340 + " [INCOMPLETE] (3' of "
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
341 + longOut
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
342 + " found within "
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
343 + sourceOut
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
344 + ")\n"
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
345 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
346 downOut.write(header)
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
347 downOut.write(finalSeq)
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
348 else:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
349
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
350 if tTable != 0:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
351 downOut.write(header)
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
352 downOut.write(
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
353 str(
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
354 seqHold.translate(
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
355 table=tTable, cds=False
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
356 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
357 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
358 + "\n\n"
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
359 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
360 else:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
361 downOut.write(header)
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
362 downOut.write(str(seqHold) + "\n\n")
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
363 else:
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
364 downOut.write(header)
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
365 downOut.write(
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
366 str(gbk.seq[item.location.start : item.location.end])
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
367 + "\n\n"
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
368 )
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
369 # print(longOut)
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
370
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
371 return
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
372
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
373
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
374 if __name__ == "__main__":
e29c36ee61e0 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
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375 parser = argparse.ArgumentParser(
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376 description="Export a subset of features from a Genbank file", epilog=""
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377 )
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378 parser.add_argument(
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379 "-genbankFiles", nargs="+", type=argparse.FileType("r"), help="Genbank file"
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380 )
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381 parser.add_argument(
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382 "-fastaFiles",
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383 nargs="+",
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384 type=argparse.FileType("r"),
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385 help="Fasta file to match against",
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386 )
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387 parser.add_argument(
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388 "-tTable",
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389 type=int,
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390 default=11,
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391 help="Translation table to use",
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392 choices=range(0, 23),
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393 )
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394 parser.add_argument(
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395 "-fTable",
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396 type=int,
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397 default=11,
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398 help="Translation table to use",
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399 choices=range(0, 23),
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400 )
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401 parser.add_argument(
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402 "-upOut",
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403 type=argparse.FileType("w"),
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404 help="Upstream Fasta output",
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405 default="test-data/upOut.fa",
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406 )
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407 parser.add_argument(
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408 "-downOut",
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409 type=argparse.FileType("w"),
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410 help="Downstream Fasta output",
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411 default="test-data/downOut.fa",
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412 )
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413 parser.add_argument(
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414 "--genesOnly",
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415 action="store_true",
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416 help="Search and return only Gene type features",
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417 )
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418 parser.add_argument(
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419 "--cdsOnly",
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420 action="store_true",
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421 help="Search and return only CDS type features",
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422 )
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423 parser.add_argument(
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424 "--forceSeqID",
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425 action="store_true",
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426 help="Search and return only CDS type features",
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427 )
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428 parser.add_argument(
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429 "--outProt", action="store_true", help="Output the translated sequence"
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430 )
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431 parser.add_argument(
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432 "--forward",
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433 type=int,
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434 default=1,
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435 help="Number of features upstream from the hit to return",
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436 )
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437 parser.add_argument(
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438 "--behind",
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439 type=int,
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440 default=1,
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441 help="Number of features downstream from the hit to return",
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442 )
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443 args = parser.parse_args()
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444 extract_features(**vars(args))