From b36c3609a063b3857ab5c23c5c1130c715ab05d0 Mon Sep 17 00:00:00 2001
From: Thomas Faraut <Thomas.Faraut@inra.fr>
Date: Wed, 27 Nov 2019 11:44:53 +0100
Subject: [PATCH] AnnotatedRecord.py becomes Annotate.py
---
svreader/Annotate.py | 2 +
svreader/AnnotatedRecord.py | 130 ------------------------------------
2 files changed, 2 insertions(+), 130 deletions(-)
delete mode 100644 svreader/AnnotatedRecord.py
diff --git a/svreader/Annotate.py b/svreader/Annotate.py
index 5e9d7ec..56fe661 100644
--- a/svreader/Annotate.py
+++ b/svreader/Annotate.py
@@ -1,4 +1,6 @@
+from svreader import SVRecord, SVReader, SVWriter
+
from pysam import VariantFile
HOM_REF = (0, 0)
diff --git a/svreader/AnnotatedRecord.py b/svreader/AnnotatedRecord.py
deleted file mode 100644
index 56fe661..0000000
--- a/svreader/AnnotatedRecord.py
+++ /dev/null
@@ -1,130 +0,0 @@
-
-from svreader import SVRecord, SVReader, SVWriter
-
-from pysam import VariantFile
-
-HOM_REF = (0, 0)
-HET_VAR = (0, 1)
-HOM_VAR = (1, 1)
-
-
-class AnnotatedRecord(object):
- """
- A lightweight object to annotated the final records
- """
- def __init__(self, record):
- """
- A pysam VariantRecord wrapper
- """
- self.__record = record
- if "SVTYPE" in record.info.keys():
- self._sv_type = record.info["SVTYPE"]
- else:
- self._sv_type = record.alts[0][1:-1]
-
- @property
- def record(self):
- return self.__record
-
- @property
- def id(self):
- return self.record.id
-
- @id.setter
- def id(self, id):
- self.__record.id = id
-
- @property
- def pos(self):
- return self.record.pos
-
- @property
- def chrom(self):
- return self.record.chrom
-
- @property
- def stop(self):
- return self.record.stop
-
- @property
- def svtype(self):
- return self._sv_type
-
- @property
- def filter(self):
- return self.record.filter
-
- @property
- def samples(self):
- return self.record.samples
-
-
-class AnnotatedRecordSample(object):
- """
- A lightweight object to VariantRecordSample
- """
- def __init__(self, variantsample):
- self.variantsample = variantsample
-
-
-class VCFReader(SVReader):
-
- def __init__(self, file_name, reference_handle=None, svs_to_report=None):
- super(VCFReader, self).__init__(file_name,
- generic_name,
- reference_handle)
- self.vcf_reader = VariantFile(file_name)
-
- def __iter__(self):
- return self
-
- def __next__(self):
- while True:
- raw_record = next(self.vcf_reader)
- record = AnnotatedRecord(raw_record)
- return record
-
- def getHeader(self):
- return self.vcf_reader.header
-
- def addInfo(self, name, number, type, description):
- self.vcf_reader.header.info.add(id=name,
- number=number,
- type=type,
- description=description)
-
- def addFilter(self, name, description):
- self.vcf_reader.header.filters.add(id=name,
- number=None,
- type=None,
- description=description)
-
- def getOrderedSamples(self):
- samples = self.vcf_reader.header.samples
- sample_names = [sample.rsplit('.')[0] for sample in samples]
- return sample_names
-
- def numSamples(self):
- return len(self.vcf_reader.header.samples)
-
-
-class VCFWriter(SVWriter):
-
- def __init__(self, file_name, template_reader, index=True):
- super(VCFWriter, self).__init__(file_name,
- template_reader.tool_name,
- template_reader)
-
- def _open(self):
- self.vcf_writer = VariantFile(self.filename, 'w',
- header=self.template_reader.getHeader())
- self._isopen = True
-
- def _write(self, record):
- self.vcf_writer.write(record.record)
-
- def _close(self):
- if self._isopen:
- self.vcf_writer.close()
- else: # nothing was written
- self._dumpemptyvcf()
--
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