/usr/lib/python2.7/dist-packages/pysam/Pileup.py is in python-pysam 0.7.7-1ubuntu1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 | '''Tools for working with files in the samtools pileup -c format.'''
import collections
import pysam
PileupSubstitution = collections.namedtuple( "PileupSubstitution",
" ".join( (\
"chromosome",
"pos",
"reference_base",
"genotype",
"consensus_quality",
"snp_quality",
"mapping_quality",
"coverage",
"read_bases",
"base_qualities" ) ) )
PileupIndel = collections.namedtuple( "PileupIndel",
" ".join( (\
"chromosome",
"pos",
"reference_base",
"genotype",
"consensus_quality",
"snp_quality",
"mapping_quality",
"coverage",
"first_allele",
"second_allele",
"reads_first",
"reads_second",
"reads_diff" ) ) )
def iterate( infile ):
'''iterate over ``samtools pileup -c`` formatted file.
*infile* can be any iterator over a lines.
The function yields named tuples of the type :class:`pysam.Pileup.PileupSubstitution`
or :class:`pysam.Pileup.PileupIndel`.
.. note::
The parser converts to 0-based coordinates
'''
conv_subst = (str,lambda x: int(x)-1,str,str,int,int,int,int,str,str)
conv_indel = (str,lambda x: int(x)-1,str,str,int,int,int,int,str,str,int,int,int)
for line in infile:
d = line[:-1].split()
if d[2] == "*":
try:
yield PileupIndel( *[x(y) for x,y in zip(conv_indel,d) ] )
except TypeError:
raise pysam.SamtoolsError( "parsing error in line: `%s`" % line)
else:
try:
yield PileupSubstitution( *[x(y) for x,y in zip(conv_subst,d) ] )
except TypeError:
raise pysam.SamtoolsError( "parsing error in line: `%s`" % line)
ENCODE_GENOTYPE = {
'A': 'A', 'C': 'C', 'G': 'G', 'T': 'T',
'AA': 'A', 'CC': 'C', 'GG': 'G', 'TT': 'T', 'UU': 'U',
'AG': 'r', 'GA': 'R',
'CT': 'y', 'TC': 'Y',
'AC': 'm', 'CA': 'M',
'GT': 'k', 'TG': 'K',
'CG': 's', 'GC': 'S',
'AT': 'w', 'TA': 'W',
}
DECODE_GENOTYPE = {
'A': 'AA',
'C': 'CC',
'G': 'GG',
'T': 'TT',
'r': 'AG', 'R': 'AG',
'y': 'CT', 'Y': 'CT',
'm': 'AC', 'M': 'AC',
'k': 'GT', 'K': 'GT',
's': 'CG', 'S': 'CG',
'w': 'AT', 'W': 'AT',
}
##------------------------------------------------------------
def encodeGenotype( code ):
'''encode genotypes like GG, GA into a one-letter code.
The returned code is lower case if code[0] < code[1], otherwise
it is uppercase.
'''
return ENCODE_GENOTYPE[ code.upper() ]
def decodeGenotype( code ):
'''decode single letter genotypes like m, M into two letters.
This is the reverse operation to :meth:`encodeGenotype`.
'''
return DECODE_GENOTYPE[ code ]
def translateIndelGenotypeFromVCF( vcf_genotypes, ref ):
'''translate indel from vcf to pileup format.'''
# indels
def getPrefix( s1, s2 ):
'''get common prefix of strings s1 and s2.'''
n = min( len( s1), len( s2 ) )
for x in range( n ):
if s1[x] != s2[x]: return s1[:x]
return s1[:n]
def getSuffix( s1, s2 ):
'''get common sufix of strings s1 and s2.'''
n = min( len( s1), len( s2 ) )
if s1[-1] != s2[-1]: return ""
for x in range( -2, -n - 1, -1 ):
if s1[x] != s2[x]: return s1[x+1:]
return s1[-n:]
def getGenotype( variant, ref ):
if variant == ref: return "*", 0
if len(ref) > len(variant):
# is a deletion
if ref.startswith(variant):
return "-%s" % ref[len(variant):], len(variant) - 1
elif ref.endswith( variant ):
return "-%s" % ref[:-len(variant)], -1
else:
prefix = getPrefix( ref, variant )
suffix = getSuffix( ref, variant )
shared = len(prefix) + len(suffix) - len(variant)
# print "-", prefix, suffix, ref, variant, shared, len(prefix), len(suffix), len(ref)
if shared < 0:
raise ValueError()
return "-%s" % ref[len(prefix):-(len(suffix)-shared)], len(prefix) - 1
elif len(ref) < len(variant):
# is an insertion
if variant.startswith(ref):
return "+%s" % variant[len(ref):], len(ref) - 1
elif variant.endswith(ref):
return "+%s" % variant[:len(ref)], 0
else:
prefix = getPrefix( ref, variant )
suffix = getSuffix( ref, variant )
shared = len(prefix) + len(suffix) - len(ref)
if shared < 0:
raise ValueError()
return "+%s" % variant[len(prefix):-(len(suffix)-shared)], len(prefix)
else:
assert 0, "snp?"
# in pileup, the position refers to the base
# after the coordinate, hence subtract 1
#pos -= 1
genotypes, offsets = [], []
is_error = True
for variant in vcf_genotypes:
try:
g, offset = getGenotype( variant, ref )
except ValueError:
break
genotypes.append( g )
if g != "*": offsets.append( offset )
else:
is_error = False
if is_error:
raise ValueError()
assert len(set(offsets )) == 1, "multiple offsets for indel"
offset = offsets[0]
genotypes = "/".join( genotypes )
return genotypes, offset
def vcf2pileup( vcf, sample ):
'''convert vcf record to pileup record.'''
chromosome = vcf.contig
pos = vcf.pos
reference = vcf.ref
allelles = [reference] + vcf.alt
data = vcf[sample]
# get genotype
genotypes = data["GT"]
if len(genotypes) > 1:
raise ValueError( "only single genotype per position, %s" % (str(vcf)))
genotypes = genotypes[0]
# not a variant
if genotypes[0] == ".": return None
genotypes = [ allelles[int(x)] for x in genotypes if x != "/" ]
# snp_quality is "genotype quality"
snp_quality = consensus_quality = data.get( "GQ", [0])[0]
mapping_quality = vcf.info.get( "MQ", [0])[0]
coverage = data.get( "DP", 0)
if len(reference) > 1 or max([len(x) for x in vcf.alt] ) > 1:
# indel
genotype, offset = translateIndelGenotypeFromVCF( genotypes, reference )
return PileupIndel( chromosome,
pos + offset,
"*",
genotype,
consensus_quality,
snp_quality,
mapping_quality,
coverage,
genotype,
"<" * len(genotype),
0,
0,
0 )
else:
genotype = encodeGenotype( "".join(genotypes) )
read_bases = ""
base_qualities = ""
return PileupSubstitution( chromosome, pos, reference,
genotype,
consensus_quality,
snp_quality,
mapping_quality,
coverage, read_bases, base_qualities )
def iterate_from_vcf( infile, sample ):
'''iterate over a vcf-formatted file.
*infile* can be any iterator over a lines.
The function yields named tuples of the type :class:`pysam.Pileup.PileupSubstitution`
or :class:`pysam.Pileup.PileupIndel`.
Positions without a snp will be skipped.
This method is wasteful and written to support same
legacy code that expects samtools pileup output.
Better use the vcf parser directly.
'''
vcf = pysam.VCF()
vcf.connect( infile )
if sample not in vcf.getsamples():
raise KeyErorr( "sample %s not vcf file" )
for row in vcf.fetch():
result = vcf2pileup( row, sample )
if result: yield result
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