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08f34f748b
* Apply prettier to css, js, html, md, ts, and yml As a followup I will add prettier to the .pre-commit config. This patch is 100% generated by prettier. I used a forked version of prettier that understands the py-script tag. See https://github.com/hoodmane/pyscript-prettier-precommit for more info. * Apply old pre-commit * Revert some problems * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Revert some changes * More changes * Fix pre-commit * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
173 lines
5.4 KiB
HTML
173 lines
5.4 KiB
HTML
<!doctype html>
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<html>
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<head>
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<meta charset="utf-8" />
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<meta http-equiv="X-UA-Compatible" content="IE=edge" />
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<title>PyScript — Simple Bioinformatics Example</title>
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<link rel="icon" type="image/x-icon" href="./favicon.png" />
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<link
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rel="stylesheet"
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type="text/css"
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media="screen"
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href="https://cdn.jsdelivr.net/npm/bulma@0.9.3/css/bulma.min.css"
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/>
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<link
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rel="icon"
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type="image/png"
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href="https://user-images.githubusercontent.com/49681382/166738771-d0c26557-426c-4688-9641-8db5e6b08348.png"
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/>
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<script defer src="https://pyscript.net/latest/pyscript.js"></script>
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</head>
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<body>
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<!-- Header -->
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<section class="hero is-primary is-small">
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<div class="hero-body">
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<p class="title is-3">
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PyScript — Simple Bioinformatics Example
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<span class="tag is-white">v.1</span>
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</p>
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<p class="subtitle is-6">
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Demonstrates the simple use of
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<a href="https://pyscript.net/" target="_blank"
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><code>PyScript</code></a
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>
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in <strong>Bioinformatics/Computational Biology</strong> fields!
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</p>
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</div>
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</section>
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<!-- Main Content -->
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<div class="container is-white is-fluid" style="margin-top: 45px">
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<p class="title is-3">🧬 DNA Sequence Tool</p>
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<!--- DNA Sequence Input -->
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<div class="field">
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<label class="label">Input DNA Sequence</label>
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<div class="control">
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<textarea
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class="textarea"
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placeholder="GATTACA"
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id="dna_seq"
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></textarea>
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</div>
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</div>
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<!-- Operation Selection -->
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<label class="label">Pick the operation to be applied</label>
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<div class="field has-addons">
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<div class="control is-expanded">
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<div class="select is-fullwidth">
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<select name="operation" id="operation">
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<option value="Reverse">Compute the reverse counterpart</option>
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<option value="Complement">
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Compute the complement counterpart
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</option>
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<option value="ReverseComplement">
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Compute the reverse complement counterpart
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</option>
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</select>
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</div>
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</div>
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<div class="control">
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<button
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id="run"
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type="button"
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class="button is-primary"
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py-onClick="run()"
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>
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Run!
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</button>
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<button
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id="clear"
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type="button"
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class="button is-danger"
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py-onClick="clear()"
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>
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Clear
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</button>
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</div>
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</div>
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<hr />
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<!--- DNA Sequence Output -->
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<label class="label"
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>Output for the
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<code id="operation_name_output">given operation</code></label
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>
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<div id="output"></div>
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</div>
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<br /><br />
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<!-- Footer -->
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<footer class="footer">
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<div class="content has-text-centered">
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<p>
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Developed by
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<a href="mailto:furkanmtorun@gmail.com"
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><strong>Furkan M. Torun (@furkanmtorun)</strong></a
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>
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<br />
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<a href="https://github.com/furkanmtorun">GitHub</a>
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<a href="https://scholar.google.com/citations?user=d5ZyOZ4AAAAJ"
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>Google Scholar</a
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>
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| <a href="https://twitter.com/furkanmtorun">Twitter</a> |
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<a href="https://www.linkedin.com/in/furkanmtorun/">LinkedIn</a>
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</p>
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</div>
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</footer>
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<py-script>
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# Define HTML elements and inputs
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dna_alphabet = "ATGC"
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output = Element("output")
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dna_seq_element = Element("dna_seq")
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operation_element = Element("operation")
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operation_name_output_element = Element("operation_name_output")
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# DNA Sequene Operations
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def return_reverse(dna_seq):
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return dna_seq[::-1]
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def return_complement(dna_seq):
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return dna_seq.translate(str.maketrans("ATCG", "TAGC"))
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def return_reverse_complement(dna_seq):
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return dna_seq.translate(str.maketrans("ATCG", "TAGC"))[::-1]
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# Check DNA seq is valid
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def check_dna_seq(dna_seq):
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return all(letter in dna_alphabet for letter in dna_seq.upper())
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# Clear the form and output
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def clear(*args, **kwargs):
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dna_seq_element.clear()
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output.clear()
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# Run
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def run(*args, **kwargs):
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dna_seq = dna_seq_element.value
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is_dna_seq_valid = check_dna_seq(dna_seq)
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if is_dna_seq_valid:
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operation_name = operation_element.value
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operation_name_output_element.write(operation_name)
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# Compute the desired outputs
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if operation_name == "Reverse":
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output_dna_seq = return_reverse(dna_seq)
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elif operation_name == "Complement":
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output_dna_seq = return_complement(dna_seq)
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elif operation_name == "ReverseComplement":
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output_dna_seq = return_reverse_complement(dna_seq)
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# Output the result
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output.write(output_dna_seq)
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elif (dna_seq.strip() == "") or (dna_seq is None):
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output.write("No DNA sequence provided")
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else:
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output.write("Invalid DNA sequence entered")
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</py-script>
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</body>
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</html>
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