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updates to the python snp selector -- now sorts info fields and we stop printing unnecessary debugging info in vcf2table 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2265 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-12-04 22:16:02 +00:00
parent 0f89a38473
commit 0753315156
2 changed files with 6 additions and 5 deletions
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1
python/vcf2table.py
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@ -23,7 +23,6 @@ if __name__ == "__main__":
counter = OPTIONS.skip counter = OPTIONS.skip
fields = OPTIONS.fields.split(',') fields = OPTIONS.fields.split(',')
print sys.stdin
for header, vcf, count in lines2VCF(sys.stdin, extendedOutput = True): for header, vcf, count in lines2VCF(sys.stdin, extendedOutput = True):
#print vcf, count #print vcf, count
if count == 1 and vcf.hasHeader(): if count == 1 and vcf.hasHeader():

10
python/vcfReader.py
View File

@ -1,6 +1,7 @@
import itertools import itertools
VCF_KEYS = "CHROM POS ID REF ALT QUAL FILTER INFO".split() VCF_KEYS = "CHROM POS ID REF ALT QUAL FILTER INFO".split()
VCF_KEYS_FORMAT = "CHROM POS ID REF ALT QUAL FILTER".split()
TRANSITIONS = dict() TRANSITIONS = dict()
for p in ["AG", "CT"]: for p in ["AG", "CT"]:
@ -82,7 +83,7 @@ class VCFRecord:
self.bindings[field] = value self.bindings[field] = value
else: else:
self.info[field] = value self.info[field] = value
self.setField("INFO", self.getInfo()) #self.setField("INFO", self.getInfo())
#print 'getInfo', self.getInfo() #print 'getInfo', self.getInfo()
def getField(self, field, default = None): def getField(self, field, default = None):
@ -100,7 +101,9 @@ class VCFRecord:
return str(x) return str(x)
else: else:
return str(x) + '=' + str(y) return str(x) + '=' + str(y)
return ';'.join(map(lambda x: info2str(*x), self.info.iteritems())) v = ';'.join(map(lambda x: info2str(*x), sorted(self.info.iteritems(), key=lambda x: x[0])))
#print 'V = ', v
return v
def getInfoDict(self): return self.info def getInfoDict(self): return self.info
@ -119,7 +122,7 @@ class VCFRecord:
return ' '.join(['%s=%s' % (x,y) for x,y in self.bindings.iteritems()]) return ' '.join(['%s=%s' % (x,y) for x,y in self.bindings.iteritems()])
def format(self): def format(self):
return '\t'.join([str(self.getField(key)) for key in VCF_KEYS] + self.rest) return '\t'.join([str(self.getField(key)) for key in VCF_KEYS_FORMAT] + [self.getInfo()] + self.rest)
def parseInfo(s): def parseInfo(s):
d = dict() d = dict()
@ -192,7 +195,6 @@ def lines2VCF(lines, extendedOutput = False, decodeAll = True, header=None, colu
yield vcf yield vcf
raise StopIteration() raise StopIteration()
def formatVCF(header, records): def formatVCF(header, records):
#print records #print records
#print records[0] #print records[0]