fastseqio 0.0.1__tar.gz

fastseqio-0.0.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: fastseqio
+Version: 0.0.1
+Summary: A package for reading and writing fasta/fastq files
+Author: dwpeng
+Author-email: 1732889554@qq.com

fastseqio-0.0.1/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

fastseqio-0.0.1/setup.py

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+import setuptools
+
+setuptools.setup(
+    name="fastseqio",
+    version="0.0.1",
+    author="dwpeng",
+    author_email="1732889554@qq.com",
+    description="A package for reading and writing fasta/fastq files",
+    packages=setuptools.find_namespace_packages(where="src"),
+    package_dir={"": "src"},
+    package_data={"seqio": ["lib/*.so", "lib/*.dylib", "lib/*.dll"]},
+)

fastseqio-0.0.1/src/fastseqio.egg-info/PKG-INFO

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+Metadata-Version: 2.1
+Name: fastseqio
+Version: 0.0.1
+Summary: A package for reading and writing fasta/fastq files
+Author: dwpeng
+Author-email: 1732889554@qq.com

fastseqio-0.0.1/src/fastseqio.egg-info/SOURCES.txt

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+setup.py
+src/fastseqio.egg-info/PKG-INFO
+src/fastseqio.egg-info/SOURCES.txt
+src/fastseqio.egg-info/dependency_links.txt
+src/fastseqio.egg-info/top_level.txt
+src/seqio/__init__.py
+src/seqio/_seqio.py
+src/seqio/lib/_seqio.cpython-311-x86_64-linux-gnu.so

fastseqio-0.0.1/src/fastseqio.egg-info/dependency_links.txt

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+

fastseqio-0.0.1/src/fastseqio.egg-info/top_level.txt

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+lib
+seqio

fastseqio-0.0.1/src/seqio/__init__.py

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+from . import _seqio
+
+seqioFile = _seqio.seqioFile
+seqioOpenMode = _seqio.seqioOpenMode
+seqioRecord = _seqio.seqioRecord
+
+__all__ = ["seqioFile", "seqioOpenMode", "seqioRecord"]

fastseqio-0.0.1/src/seqio/_seqio.py

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+from .lib._seqio import (
+    seqioFile as _seqioFile,
+    seqOpenMode as _seqOpenMode,
+    seqioRecord as _seqioRecord,
+)
+from typing import Optional
+
+
+class seqioOpenMode:
+    READ = _seqOpenMode.READ
+    WRITE = _seqOpenMode.WRITE
+
+
+class seqioRecord:
+    def __init__(
+        self,
+        name: str,
+        sequence: str,
+        quality: Optional[str] = None,
+        comment: Optional[str] = None,
+    ):
+        self.__record = None
+        self.__length = len(sequence)
+        self.name = name
+        self.sequence = sequence
+        self.quality = quality
+        self.comment = comment
+
+    @classmethod
+    def fromRecord(cls, record: _seqioRecord):
+        self = cls(record.name, record.sequence, record.quality, record.comment)
+        self.__record = record
+        self.__length = record.length()
+        return self
+
+    def length(self):
+        return self.__length
+
+    def upper(self):
+        if self.__record is not None:
+            self.sequence = self.__record.upper()
+        else:
+            self.sequence = self.sequence.upper()
+        return self
+
+    def lower(self):
+        if self.__record is not None:
+            self.sequence = self.__record.lower()
+        else:
+            self.sequence = self.sequence.lower()
+        return self
+
+    def __str__(self):
+        return f"seqioRecord(name={self.name})"
+
+
+class seqioFile:
+    def __init__(
+        self,
+        path: str,
+        mode: seqioOpenMode = seqioOpenMode.READ,
+        compressed: bool = False,
+    ):
+        self.__file = _seqioFile(path, mode, compressed)
+
+    def readOne(self):
+        record = self.__file.readOne()
+        if record is None:
+            return None
+        return seqioRecord.fromRecord(record)
+
+    def readFasta(self):
+        record = self.__file.readFasta()
+        if record is None:
+            return None
+        return seqioRecord.fromRecord(record)
+
+    def readFastq(self):
+        record = self.__file.readFastq()
+        if record is None:
+            return None
+        return seqioRecord.fromRecord(record)
+
+    def __iter__(self):
+        while True:
+            record = self.__file.readOne()
+            if record is None:
+                break
+            yield seqioRecord.fromRecord(record)