Add a little tutorial #72
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| The main interface for reading and writing sequence files is the `dnaio.open` function. | ||
| For example, this program reads in a FASTQ file and computes the total number of nucleotides | ||
| it contains:: |
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Does this detect the language automatically? If not the code-block directive does.
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I haven’t seen this file rendered, but the example from the README (which does not use code-block) is syntax highlighted: https://dnaio.readthedocs.io/en/latest/#example-usage
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| As can be seen from the ``.gz`` file extension, | ||
| the input file is gzip-compressed. | ||
| `dnaio.open` detects and handles this automatically by opening the file with |
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Using single backticks creates referencable text, but not code. Double backticks are needed in the latter case.
Do these references reference back to the API documentation?
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Yes, the single backticks were intentional. It worked for dnaio.open in the README, but now I see that it doesn’t work for SequenceRecord and all the other classes where I don’t have a dnaio. prefix.
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Ah, I need to write ~dnaio.SequenceRecord to get what I want.
doc/tutorial.rst
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| `xopen <https://github.com/pycompression/xopen/>`_. | ||
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| Here, the call to `dnaio.open` returns a `FastqReader` object. | ||
| Iterating over it in the ``for`` loop results in `SequenceRecord` objects. |
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On the next line double backticks are used for SequenceRecord. Was this intentional?
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I wanted to create a link only for the first occurrence to avoid too much blue in the text, so this is intentional. (Apart from the fact that it doesn’t work as I discovered now.)
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I fixed the nonworking links. |
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Excellent! |
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