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jpayne@68
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1 import array
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2 from typing import Optional, Any, Sequence, Iterator
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3
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4 class FastaFile:
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5 def __init__(
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6 self,
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7 filename: str,
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8 filepath_index: Optional[str] = ...,
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9 filepath_index_compressed: Optional[str] = ...,
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10 ) -> None: ...
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11 def is_open(self) -> bool: ...
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12 def __len__(self) -> int: ...
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13 def close(self) -> None: ...
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14 def __enter__(self) -> FastaFile: ...
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15 def __exit__(self, type, value, traceback) -> Any: ...
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16 @property
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17 def closed(self) -> bool: ...
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18 @property
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19 def filename(self) -> str: ...
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20 @property
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21 def references(self) -> Sequence[str]: ...
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22 @property
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23 def nreferences(self) -> Optional[int]: ...
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24 @property
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25 def lengths(self) -> Sequence[int]: ...
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26 def fetch(
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27 self,
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28 reference: Optional[str] = ...,
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29 start: Optional[int] = ...,
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30 end: Optional[int] = ...,
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31 region: Optional[str] = ...,
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32 ) -> str: ...
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33 def get_reference_length(self, reference: str) -> int: ...
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34 def __getitem__(self, reference: str) -> str: ...
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35 def __contains__(self, reference: str) -> bool: ...
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36
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37
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38 class FastqProxy:
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39 @property
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40 def name(self) -> str: ...
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41 @property
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42 def sequence(self) -> str: ...
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43 @property
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44 def comment(self) -> Optional[str]: ...
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45 @property
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46 def quality(self) -> Optional[str]: ...
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47 def to_string(self) -> str: ...
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48 def get_quality_array(self, offset: int = ...) -> Optional[array.array]: ...
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49
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50
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51 class FastxRecord:
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52 comment: Optional[str] = ...
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53 quality: Optional[str] = ...
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54 sequence: Optional[str] = ...
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55 name: Optional[str] = ...
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56 def __init__(
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57 self,
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58 name: Optional[str] = ...,
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59 comment: Optional[str] = ...,
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60 sequence: Optional[str] = ...,
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61 quality: Optional[str] = ...,
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62 ) -> None: ...
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63 def set_name(self, name: str) -> None: ...
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64 def set_comment(self, comment: str) -> None: ...
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65 def set_sequence(self, sequence: str, quality: Optional[str] = ...) -> None: ...
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66 def get_quality_array(self, offset: int = ...) -> array.array: ...
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67
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68 class FastxFile:
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69 def __init__(self, filename: str, persist: bool = ...) -> None: ...
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70 def is_open(self) -> bool: ...
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71 def close(self) -> None: ...
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72 def __enter__(self) -> FastxFile: ...
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73 def __exit__(self, type, value, traceback) -> Any: ...
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74 @property
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75 def closed(self) -> bool: ...
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76 @property
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77 def filename(self) -> str: ...
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78 def __iter__(self) -> Iterator[FastxRecord]: ...
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79 def __next__(self) -> FastxRecord: ...
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80
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81 # deprecated
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82 class FastqFile(FastxFile): ...
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