Miscellaneous

FileOrSequence

class HTSeq.FileOrSequence(filename_or_sequence)

This class is a a canvenience wrapper around a file.

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.

fos

The argument passed to the constructor, i.e., a filename or a sequence

line_no

The line number (1-based) of the most recently read line. Initially None.

get_line_number_string()

Returns a string describing the position in the file. Useful for error messages.

Version

HTSeq.__version__

a string containing the current version

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