v0.1.3-dev (#67)

* Removed unneeded dependency

* Fixed mypy issue

* Corrected test dir path

* Update joblib requirement from >=0.16,<0.18 to >=0.16,<1.1 (#57)

* Update regex requirement from ^2020.7.14 to >=2020.7.14,<2022.0.0 (#65)

* v0.1.3

* Dropped requirements in favor of lock file.

* Dropped codeQL workflow.

* Updated README.

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

.github/workflows/pythonpackage.yml

@@ -39,7 +39,7 @@ jobs:
       fail-fast: true
       matrix:
         os: ["ubuntu-latest"]
-        python-version: [3.6, 3.7, 3.8]
+        python-version: [3.6, 3.7, 3.8, 3.9]
     runs-on: ${{ matrix.os }}
     steps:
     # Checkout repo and setup python
@@ -68,4 +68,4 @@ jobs:
     - name: Test
       run: |
         source .venv/bin/activate
-        pytest radiantkit/tests/
+        pytest fastx_barber/tests/

.gitignore

@@ -8,5 +8,4 @@
 # Python egg metadata, regenerated from source files by setuptools.
 /*.egg-info
 
-poetry.lock
 dummy/*

README.md

@@ -7,7 +7,7 @@
 
 [PyPi](https://pypi.org/project/fastx-barber/) | [docs](https://ggirelli.github.io/fastx-barber/)
 
-A Python3.6.1+ package to trim and extract flags from FASTA  and FASTQ files.
+A Python3.6.13+ package to trim and extract flags from FASTA  and FASTQ files.
 
 ## Features (in short)
 
@@ -23,7 +23,7 @@ For more available features, check out our [docs](https://ggirelli.github.io/fas
 
 ## Requirements
 
-`fastx-barber` has been tested with Python 3.6.1, 3.7, and 3.8. We recommend installing it using `pipx` (see [below](https://github.com/ggirelli/fastx-barber#install)) to avoid dependency conflicts with other packages. The packages it depends on are listed in our [dependency graph](https://github.com/ggirelli/fastx-barber/network/dependencies). We use [`poetry`](https://github.com/python-poetry/poetry) to handle our dependencies.
+`fastx-barber` has been tested with Python 3.6.13, 3.7, 3.8, and 3.9. We recommend installing it using `pipx` (see [below](https://github.com/ggirelli/fastx-barber#install)) to avoid dependency conflicts with other packages. The packages it depends on are listed in our [dependency graph](https://github.com/ggirelli/fastx-barber/network/dependencies). We use [`poetry`](https://github.com/python-poetry/poetry) to handle our dependencies.
 
 ## Install
 

fastx_barber/const.py

@@ -6,7 +6,7 @@
 from enum import Enum
 from typing import DefaultDict, Optional, Tuple
 
-__version__ = "0.1.2"
+__version__ = "0.1.3"
 
 
 BedRecord = Tuple[

fastx_barber/seqio.py

@@ -121,7 +121,7 @@ def __init__(self, path: str, compress_level: int = 6):
         super(ABCSimpleWriter, self).__init__()
         _, _, gzipped = is_gzipped(path)
         if gzipped:
-            self._OH = gzip.open(path, "wt+", compress_level)
+            self._OH = gzip.open(path, "wt", compress_level)
         else:
             self._OH = open(path, "w+")
 
@@ -244,16 +244,16 @@ def open(self, split_value: str) -> IO:
         )
         if self._is_gzipped:
             if self.opened_before(split_value):
-                return gzip.open(path, "at+", self._compress_level)
+                return gzip.open(path, "at", self._compress_level)
             else:
                 self._split_by.add(split_value)
-                return gzip.open(path, "wt+", self._compress_level)
+                return gzip.open(path, "wt", self._compress_level)
         else:
             if self.opened_before(split_value):
-                return open(path, "a+")
+                return open(path, "a")
             else:
                 self._split_by.add(split_value)
-                return open(path, "w+")
+                return open(path, "w")
 
     @abstractmethod
     def write(self, record: Any, flag_data: Dict[str, FlagData], *args) -> None:

fastx_barber/trim.py

@@ -8,7 +8,6 @@
 from fastx_barber.match import ANPMatch
 from fastx_barber.qual import QualityIO
 from fastx_barber.seqio import SimpleFastxRecord, SimpleFastqRecord
-import regex  # type: ignore
 from typing import Any, List, Match, Tuple, Type, Union