From 3ab9cd8ef106455c0243b035ad33640d67178101 Mon Sep 17 00:00:00 2001
From: Thomas Faraut <Thomas.Faraut@inra.fr>
Date: Wed, 27 Nov 2019 11:53:52 +0100
Subject: [PATCH] Annotate uses SVReader
---
svreader/Annotate.py | 10 +++++++---
svreader/__init__.py | 2 +-
2 files changed, 8 insertions(+), 4 deletions(-)
diff --git a/svreader/Annotate.py b/svreader/Annotate.py
index 56fe661..d6bb22a 100644
--- a/svreader/Annotate.py
+++ b/svreader/Annotate.py
@@ -1,4 +1,5 @@
+
from svreader import SVRecord, SVReader, SVWriter
from pysam import VariantFile
@@ -7,7 +8,6 @@ HOM_REF = (0, 0)
HET_VAR = (0, 1)
HOM_VAR = (1, 1)
-
class AnnotatedRecord(object):
"""
A lightweight object to annotated the final records
@@ -69,11 +69,14 @@ class AnnotatedRecordSample(object):
class VCFReader(SVReader):
- def __init__(self, file_name, reference_handle=None, svs_to_report=None):
+ def __init__(self, file_name, sv_to_report=None):
super(VCFReader, self).__init__(file_name,
generic_name,
reference_handle)
self.vcf_reader = VariantFile(file_name)
+ self.filename = file_name
+ self.sv_to_report =sv_to_report
+ self.vcf_reader = VariantFile(file_name)
def __iter__(self):
return self
@@ -81,7 +84,7 @@ class VCFReader(SVReader):
def __next__(self):
while True:
raw_record = next(self.vcf_reader)
- record = AnnotatedRecord(raw_record)
+ record = (raw_record)
return record
def getHeader(self):
@@ -111,6 +114,7 @@ class VCFReader(SVReader):
class VCFWriter(SVWriter):
def __init__(self, file_name, template_reader, index=True):
+
super(VCFWriter, self).__init__(file_name,
template_reader.tool_name,
template_reader)
diff --git a/svreader/__init__.py b/svreader/__init__.py
index f9482a5..be3e22c 100644
--- a/svreader/__init__.py
+++ b/svreader/__init__.py
@@ -147,7 +147,7 @@ class SVReader(object):
svs_supported = set(["DEL", "INS", "DUP", "INV"])
- def __init__(self, file_name, tool_name="default", reference_handle=None):
+ def __init__(self, file_name, tool_name="generic", reference_handle=None):
self.file_name = file_name
self.reference_handle = reference_handle
self.__tool_name = tool_name
--
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