[2] | 1 | #!/usr/bin/env python
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| 2 | #Dan Blankenberg
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| 3 |
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| 4 | import sys
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| 5 |
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| 6 | assert sys.version_info[:2] >= ( 2, 4 )
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| 7 |
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| 8 | #genbank_to_bed
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| 9 | class Region:
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| 10 | def __init__( self ):
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| 11 | self.qualifiers = {}
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| 12 | self.start = None
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| 13 | self.end = None
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| 14 | self.strand = '+'
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| 15 | def set_coordinates_by_location( self, location ):
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| 16 | location = location.strip().lower().replace( '..', ',' )
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| 17 | if "complement(" in location: #if part of the sequence is on the negative strand, it all is?
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| 18 | self.strand = '-' #default of + strand
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| 19 | for remove_text in ["join(", "order(", "complement(", ")"]:
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| 20 | location = location.replace( remove_text, "" )
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| 21 | for number in location.split( ',' ):
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| 22 | number = number.strip('\n\r\t <>,()')
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| 23 | if number:
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| 24 | if "^" in number:
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| 25 | #a single point
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| 26 | #check that this is correct for points, ie: 413/NC_005027.gbk: misc_feature 6636286^6636287 ===> 6636285,6636286
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| 27 | end = int( number.split( '^' )[0] )
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| 28 | start = end - 1
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| 29 | else:
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| 30 | end = int( number )
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| 31 | start = end - 1 #match BED coordinates
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| 32 | if self.start is None or start < self.start:
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| 33 | self.start = start
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| 34 | if self.end is None or end > self.end:
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| 35 | self.end = end
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| 36 |
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| 37 | class GenBankFeatureParser:
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| 38 | """Parses Features from Single Locus GenBank file"""
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| 39 | def __init__( self, fh, features_list = [] ):
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| 40 | self.fh = fh
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| 41 | self.features = {}
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| 42 | fh.seek(0)
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| 43 | in_features = False
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| 44 | last_feature_name = None
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| 45 | base_indent = 0
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| 46 | last_indent = 0
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| 47 | last_attr_name = None
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| 48 | for line in fh:
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| 49 | if not in_features and line.startswith('FEATURES'):
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| 50 | in_features = True
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| 51 | continue
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| 52 | if in_features:
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| 53 | lstrip = line.lstrip()
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| 54 | if line and lstrip == line:
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| 55 | break #end of feature block
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| 56 | cur_indent = len( line ) - len( lstrip )
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| 57 | if last_feature_name is None:
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| 58 | base_indent = cur_indent
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| 59 | if cur_indent == base_indent:
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| 60 | #a new feature
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| 61 | last_attr_name = None
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| 62 | fields = lstrip.split( None, 1 )
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| 63 | last_feature_name = fields[0].strip()
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| 64 | if not features_list or ( features_list and last_feature_name in features_list ):
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| 65 | if last_feature_name not in self.features:
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| 66 | self.features[last_feature_name] = []
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| 67 | region = Region()
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| 68 | region.set_coordinates_by_location( fields[1] )
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| 69 | self.features[last_feature_name].append( region )
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| 70 | else:
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| 71 | #add info to last known feature
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| 72 | line = line.strip()
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| 73 | if line.startswith( '/' ):
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| 74 | fields = line[1:].split( '=', 1 )
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| 75 | if len( fields ) == 2:
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| 76 | last_attr_name, content = fields
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| 77 | else:
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| 78 | #No data
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| 79 | last_attr_name = line[1:]
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| 80 | content = ""
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| 81 | content = content.strip( '"' )
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| 82 | if last_attr_name not in self.features[last_feature_name][-1].qualifiers:
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| 83 | self.features[last_feature_name][-1].qualifiers[last_attr_name] = []
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| 84 | self.features[last_feature_name][-1].qualifiers[last_attr_name].append( content )
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| 85 | elif last_attr_name is None and last_feature_name:
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| 86 | # must still be working on location
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| 87 | self.features[last_feature_name][-1].set_coordinates_by_location( line )
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| 88 | else:
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| 89 | #continuation of multi-line qualifier content
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| 90 | if last_feature_name.lower() in ['translation']:
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| 91 | self.features[last_feature_name][-1].qualifiers[last_attr_name][-1] = "%s%s" % ( self.features[last_feature_name][-1].qualifiers[last_attr_name][-1], line.rstrip( '"' ) )
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| 92 | else:
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| 93 | self.features[last_feature_name][-1].qualifiers[last_attr_name][-1] = "%s %s" % ( self.features[last_feature_name][-1].qualifiers[last_attr_name][-1], line.rstrip( '"' ) )
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| 94 |
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| 95 |
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| 96 | def get_features_by_type( self, feature_type ):
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| 97 | if feature_type not in self.features:
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| 98 | return []
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| 99 | else:
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| 100 | return self.features[feature_type]
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| 101 |
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| 102 | # Parse A GenBank file and return arrays of BED regions for the corresponding features
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| 103 | def get_bed_from_genbank(gb_file, chrom, feature_list):
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| 104 | genbank_parser = GenBankFeatureParser( open( gb_file ) )
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| 105 | features = {}
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| 106 | for feature_type in feature_list:
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| 107 | features[feature_type]=[]
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| 108 | for feature in genbank_parser.get_features_by_type( feature_type ):
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| 109 | name = ""
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| 110 | for name_tag in ['gene', 'locus_tag', 'db_xref']:
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| 111 | if name_tag in feature.qualifiers:
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| 112 | if name: name = name + ";"
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| 113 | name = name + feature.qualifiers[name_tag][0].replace(" ","_")
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| 114 | if not name:
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| 115 | name = "unknown"
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| 116 |
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| 117 | features[feature_type].append( "%s\t%s\t%s\t%s\t%s\t%s" % ( chrom, feature.start, feature.end, name, 0, feature.strand ) )#append new bed field here
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| 118 | return features
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| 119 |
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| 120 | #geneMark to bed
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| 121 | import sys
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| 122 |
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| 123 | #converts GeneMarkHMM to bed
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| 124 | #returns an array of bed regions
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| 125 | def get_bed_from_GeneMark(geneMark_filename, chr):
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| 126 | orfs = open(geneMark_filename).readlines()
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| 127 | while True:
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| 128 | line = orfs.pop(0).strip()
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| 129 | if line.startswith("--------"):
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| 130 | orfs.pop(0)
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| 131 | break
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| 132 | orfs = "".join(orfs)
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| 133 | ctr = 0
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| 134 | regions = []
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| 135 | for block in orfs.split("\n\n"):
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| 136 | if block.startswith("List of Regions of interest"): break
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| 137 | best_block = {'start':0,'end':0,'strand':'+','avg_prob':-sys.maxint,'start_prob':-sys.maxint,'name':'DNE'}
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| 138 | ctr+=1
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| 139 | ctr2=0
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| 140 | for line in block.split("\n"):
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| 141 | ctr2+=1
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| 142 | fields = line.split()
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| 143 | start = int(fields.pop(0))-1
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| 144 | end = int(fields.pop(0))
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| 145 | strand = fields.pop(0)
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| 146 | if strand == 'complement':
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| 147 | strand = "-"
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| 148 | else:
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| 149 | strand = "+"
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| 150 | frame = fields.pop(0)
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| 151 | frame = frame + " " + fields.pop(0)
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| 152 | avg_prob = float(fields.pop(0))
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| 153 | try:
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| 154 | start_prob = float(fields.pop(0))
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| 155 | except:
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| 156 | start_prob = 0
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| 157 | name = "orf_"+str(ctr)+"_"+str(ctr2)
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| 158 | if avg_prob >= best_block['avg_prob']:
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| 159 | if start_prob > best_block['start_prob']:
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| 160 | best_block = {'start':start,'end':end,'strand':strand,'avg_prob':avg_prob,'start_prob':start_prob,'name':name}
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| 161 | regions.append(chr+"\t"+str(best_block['start'])+"\t"+str(best_block['end'])+"\t"+best_block['name']+"\t"+str(int(best_block['avg_prob']*1000))+"\t"+best_block['strand'])
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| 162 | return regions
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| 163 |
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| 164 | #geneMarkHMM to bed
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| 165 | #converts GeneMarkHMM to bed
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| 166 | #returns an array of bed regions
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| 167 | def get_bed_from_GeneMarkHMM(geneMarkHMM_filename, chr):
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| 168 | orfs = open(geneMarkHMM_filename).readlines()
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| 169 | while True:
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| 170 | line = orfs.pop(0).strip()
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| 171 | if line == "Predicted genes":
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| 172 | orfs.pop(0)
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| 173 | orfs.pop(0)
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| 174 | break
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| 175 | regions = []
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| 176 | for line in orfs:
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| 177 | fields = line.split()
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| 178 | name = "gene_number_"+fields.pop(0)
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| 179 | strand = fields.pop(0)
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| 180 | start = fields.pop(0)
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| 181 | if start.startswith("<"): start = 1
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| 182 | start = int(start)-1
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| 183 | end = fields.pop(0)
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| 184 | if end.startswith(">"): end = end[1:]
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| 185 | end = int(end)
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| 186 | score = 0 # no scores provided
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| 187 | regions.append(chr+"\t"+str(start)+"\t"+str(end)+"\t"+name+"\t"+str(score)+"\t"+strand)
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| 188 | return regions
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| 189 |
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| 190 | #glimmer3 to bed
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| 191 | #converts glimmer3 to bed, doing some linear scaling (probably not correct?) on scores
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| 192 | #returns an array of bed regions
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| 193 | def get_bed_from_glimmer3(glimmer3_filename, chr):
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| 194 | max_score = -sys.maxint
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| 195 | min_score = sys.maxint
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| 196 | orfs = []
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| 197 | for line in open(glimmer3_filename).readlines():
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| 198 | if line.startswith(">"): continue
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| 199 | fields = line.split()
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| 200 | name = fields.pop(0)
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| 201 | start = int(fields.pop(0))
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| 202 | end = int(fields.pop(0))
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| 203 | if int(fields.pop(0))<0:
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| 204 | strand = "-"
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| 205 | temp = start
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| 206 | start = end
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| 207 | end = temp
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| 208 | else:
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| 209 | strand = "+"
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| 210 | start = start - 1
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| 211 | score = (float(fields.pop(0)))
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| 212 | if score > max_score: max_score = score
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| 213 | if score < min_score: min_score = score
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| 214 | orfs.append((chr,start,end,name,score,strand))
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| 215 |
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| 216 | delta = 0
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| 217 | if min_score < 0: delta = min_score * -1
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| 218 | regions = []
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| 219 | for (chr,start,end,name,score,strand) in orfs:
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| 220 | #need to cast to str because was having the case where 1000.0 was rounded to 999 by int, some sort of precision bug?
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| 221 | my_score = int(float(str( ( (score+delta) * (1000-0-(min_score+delta)) ) / ( (max_score + delta) + 0 ))))
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| 222 |
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| 223 | regions.append(chr+"\t"+str(start)+"\t"+str(end)+"\t"+name+"\t"+str(my_score)+"\t"+strand)
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| 224 | return regions
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