Add code

seqreport/SeqCollection.py

@@ -0,0 +1,36 @@
+import dnacauldron
+
+
+class SeqCollection:
+ """Class to store basic properties of a collection of sequences.
+
+
+ **Parameters**
+
+ **fasta**
+ > The FASTA file of the sequences.
+
+ **cost_per_base**
+ > Cost per nucleotide base.
+
+ **cost_per_seq**
+ > Fix overhead cost for each sequence part (cloning, delivery costs etc).
+
+ **currency_symbol**
+ > The currency symbol to display in the report.
+ """
+
+ def __init__(self, fasta, cost_per_base=0.25, cost_per_seq=0, currency_symbol="£"):
+ self.fasta = fasta
+ self.cost_per_base = cost_per_base
+ self.cost_per_seq = cost_per_seq
+ self.currency_symbol = currency_symbol
+ self.sequences = dnacauldron.biotools.load_records_from_files(
+ files=[self.fasta], use_file_names_as_ids=False
+ )
+ self.n_seq = len(self.sequences)
+ n_bp = 0
+ for part in self.sequences:
+ n_bp += len(part.seq)
+ self.n_bp = n_bp
+ self.cost = self.n_seq * self.cost_per_seq + self.n_bp * self.cost_per_base

seqreport/__init__.py

@@ -0,0 +1,2 @@
+from .SeqCollection import SeqCollection
+from .reports import write_pdf_report

seqreport/report_assets/report_style.css

@@ -0,0 +1,29 @@
+.logos {
+ margin: 0 auto;
+}
+
+h1.appendix {
+ page-break-before: always;
+}
+
+h1 {
+ text-align: center;
+}
+
+.ribbon {
+ margin-left: -2.3em !important;
+}
+
+.description {
+ margin-top: 1em;
+}
+
+table {
+ font-size: 0.6em !important;
+}
+
+table img {
+ width: 1.5em;
+ /* height: 1em; */
+ margin-right: 1em
+}

seqreport/report_assets/seq_report.pug

@@ -0,0 +1,45 @@
+#sidebar: p {{sidebar_text}}
+
+.logos
+ img(src="file:https:///{{ egf_logo_url }}" style="height:40px; width: auto")
+
+hr
+h1 Sequence report
+hr
+
+p.
+ This document reports basic sequence statistics.
+p.
+ Number of sequences: <b>{{ seqcollection.n_seq }}</b>
+p.
+ Number of basepairs: <b>{{ seqcollection.n_bp }}</b> bp
+p.
+ Estimated cost: <b>{{ seqcollection.currency_symbol }} {{ seqcollection.cost }}</b>
+
+
+div(style="margin-top:1cm; margin-bottom:1cm;")
+
+<div style = "display:block; clear:both; page-break-after:always;"></div>
+
+p
+ strong Seq Report
+p.
+ The report was generated by <a href="https://edinburgh-genome-foundry.github.io/Ediacara/">Seq Report</a>,
+ a software published by the Edinburgh Genome Foundry (EGF).
+ Seq Report is part of the <a href="https://edinburgh-genome-foundry.github.io/">EGF Codons</a>
+ engineering biology software suite for DNA design, manufacturing and validation.
+
+
+style.
+ .green {
+ color: #86bf86
+ }
+ .grey {
+ color: #a9a9a9
+ }
+ .red {
+ color: #fd5a31
+ }
+ .yellow {
+ color: #f7b500
+ }

seqreport/reports.py

@@ -0,0 +1,47 @@
+from datetime import datetime
+import os
+
+from pdf_reports import (
+ add_css_class,
+ dataframe_to_html,
+ pug_to_html,
+ style_table_rows,
+ write_report,
+)
+import pdf_reports.tools as pdf_tools
+
+from .version import __version__
+
+THIS_PATH = os.path.dirname(os.path.realpath(__file__))
+ASSETS_PATH = os.path.join(THIS_PATH, "report_assets")
+SEQCOLLECTION_REPORT_TEMPLATE = os.path.join(ASSETS_PATH, "seq_report.pug")
+STYLESHEET = os.path.join(ASSETS_PATH, "report_style.css")
+
+
+def end_pug_to_html(template, **context):
+ now = datetime.now().strftime("%Y-%m-%d")
+ defaults = {
+ "sidebar_text": "Generated on %s by Seq Report (version %s)"
+ % (now, __version__),
+ }
+ for k in defaults:
+ if k not in context:
+ context[k] = defaults[k]
+ return pug_to_html(template, **context)
+
+
+def write_pdf_report(target, seqcollection):
+ """Write a sequence collection report with a PDF summary.
+
+
+ **Parameters**
+
+ **target**
+ > Path for PDF file.
+
+ **seqcollection**
+ > `SeqCollection` instance.
+ """
+
+ html = end_pug_to_html(SEQCOLLECTION_REPORT_TEMPLATE, seqcollection=seqcollection)
+ write_report(html, target, extra_stylesheets=(STYLESHEET,))

setup.py

@@ -15,5 +15,5 @@
  keywords="biology dna",
  packages=find_packages(exclude="docs"),
  include_package_data=True,
- install_requires=[],
+ install_requires=["pdf_reports", "dnacauldron"],
 )