HTSeq 2.0.7__cp312-cp312-macosx_10_9_x86_64.whl

HTSeq/utils.py

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+import itertools
+import warnings
+import os
+import shlex
+import sys
+
+import HTSeq
+from HTSeq._HTSeq import *
+from HTSeq._version import __version__
+
+
+class FileOrSequence:
+    """ The construcutor takes one argument, which may either be a string,
+    which is interpreted as a file name (possibly with path), or a
+    connection, by which we mean a text file opened for reading, or
+    any other object that can provide an iterator over strings
+    (lines of the file).
+
+    The advantage of passing a file name instead of an already opened file
+    is that if an iterator is requested several times, the file will be
+    re-opened each time. If the file is already open, its lines can be read
+    only once, and then, the iterator stays exhausted.
+
+    Furthermore, if a file name is passed that end in ".gz" or ".gzip"
+    (case insensitive), it is transparently gunzipped.
+    """
+
+    def __init__(self, filename_or_sequence):
+        self.fos = filename_or_sequence
+        self.should_close = False
+        self.line_no = None
+        self.lines = None
+
+        try:
+            os.fspath(self.fos)
+            self.fos_is_path = True
+        except TypeError:
+            # assumed to be a file handle
+            self.fos_is_path = False
+
+    def __enter__(self):
+        if self.fos_is_path:
+            fos = os.fspath(self.fos)
+            self.should_close = True
+            if fos.lower().endswith((".gz", ".gzip")):
+                lines = gzip.open(self.fos, 'rt')
+            else:
+                lines = open(self.fos)
+        else:
+            lines = self.fos
+
+        self.lines = lines
+        return self
+
+    def __exit__(self, type, value, traceback):
+        if self.should_close:
+            self.lines.close()
+        self.lines = None
+
+    def __iter__(self):
+        self.line_no = 1
+        if self.lines is None:
+            call_exit = True
+            self.__enter__()
+        else:
+            call_exit = False
+        lines = self.lines
+
+        try:
+            for line in lines:
+                yield line
+                self.line_no += 1
+        finally:
+            if call_exit:
+                self.__exit__(None, None, None)
+        self.line_no = None
+
+    def __repr__(self):
+        if isinstance(self.fos, str):
+            return "<%s object, connected to file name '%s'>" % (
+                self.__class__.__name__, self.fos)
+        else:
+            return "<%s object, connected to %s >" % (
+                self.__class__.__name__, repr(self.fos))
+
+    def get_line_number_string(self):
+        if self.line_no is None:
+            if isinstance(self.fos, str):
+                return "file %s closed" % self.fos
+            else:
+                return "file closed"
+        if isinstance(self.fos, str):
+            return "line %d of file %s" % (self.line_no, self.fos)
+        else:
+            return "line %d" % self.line_no

HTSeq-2.0.7.data/scripts/htseq-count

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+#!python
+
+import HTSeq.scripts.count
+
+HTSeq.scripts.count.main()

HTSeq-2.0.7.data/scripts/htseq-count-barcodes

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+#!python
+
+import HTSeq.scripts.count_with_barcodes
+
+HTSeq.scripts.count_with_barcodes.main()

HTSeq-2.0.7.data/scripts/htseq-qa

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+#!python
+
+import HTSeq.scripts.qa
+
+HTSeq.scripts.qa.main()