Moved fiterable table into aplanat and general tidy up
This commit is contained in:
Neil Horner
parent
8b1cc95433
commit
7e33eb2c3b
@ -3,7 +3,6 @@
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import argparse
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from collections import Counter, defaultdict, OrderedDict
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from functools import reduce
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import math
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from pathlib import Path
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@ -19,7 +18,6 @@ from bokeh.palettes import Category10_10
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from bokeh.plotting import figure
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from bokeh.transform import dodge
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import gffutils
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from jinja2 import Template
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import numpy as np
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import pandas as pd
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import sigfig
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@ -50,30 +48,6 @@ def _hbar(y, right, title='', fig_height=300, fig_width=300,
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return fig
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class Table:
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"""A table report component.
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Adapted from aplanat
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"""
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def __init__(self, template, data_frame, index, table_id, **kwargs):
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"""Initialize table component.
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:param dataframe: dataframe to turn in to simple table.
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"""
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template = Template(template)
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for key, val in kwargs.items():
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if isinstance(val, bool):
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kwargs[key] = str(val).lower()
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self.div = template.render(dataframe=data_frame.to_html(
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table_id=table_id,
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index=index),
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table_id=table_id,
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kwargs=kwargs)
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def simple_hbar(df, y, right, title="", color=Colors.cerulean,
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fig_kwargs={}, plot_kwargs={}):
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"""Create a simple barplot.
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@ -461,33 +435,22 @@ def gff_compare_plots(report, gffcompare_outdirs: Path, sample_ids):
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tracking['Overlaps'].values.tolist(),
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tracking['Percent'].values.tolist(), title="{}".format(id_))
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# Edit for creating unified table
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tracking.rename(columns={'sample_id': id_ + ' count'}, inplace=True)
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tracking.drop(columns=['Count'], inplace=True)
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tracking.drop(columns=['sample_id'], inplace=True)
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tracking_dfs.append(tracking)
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# section.plot(grid)
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# Tracking table
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df_class_table = reduce(
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lambda left, right: pd.merge(left, right), tracking_dfs)
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desc = pd.Series(df_class_table.Overlaps.apply(
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tracking['description'] = pd.Series(tracking.Overlaps.apply(
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lambda x: x.split(':')[0]))
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df_class_table.insert(0, 'description', desc)
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code = pd.Series(df_class_table.Overlaps.apply(
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tracking['code'] = pd.Series(tracking.Overlaps.apply(
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lambda x: x.split(':')[1]))
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df_class_table.insert(0, 'code', code)
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cols = [TableColumn(field=Ci, title=Ci, width=100)
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for Ci in df_class_table.columns]
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for Ci in tracking.columns]
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track_table = DataTable(columns=cols,
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source=ColumnDataSource(df_class_table),
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source=ColumnDataSource(tracking),
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index_position=None,
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width=500)
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df_class_table.drop(columns=['Overlaps'], inplace=True)
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tabs.append(Panel(
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child=gridplot([track_bar, track_table], ncols=2), title=id_)
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)
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@ -654,7 +617,7 @@ def cluster_quality(cluster_qc_dir, report, sample_ids):
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section.plot(cover_panel)
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def transcript_table(report, df_tmaps, covr_threshold, table_template):
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def transcript_table(report, df_tmaps, covr_threshold):
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"""Create searchable table of transcripts."""
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section = report.add_section()
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@ -701,11 +664,7 @@ def transcript_table(report, df_tmaps, covr_threshold, table_template):
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df.sort_values('parent gene iso num', inplace=True, ascending=True)
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with open(table_template, 'r') as fh:
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tabletempl = fh.read()
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bigtable = Table(tabletempl, df, index=False, table_id='bigtable')
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section._add_item(bigtable.div)
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section.table(df, index=False)
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def tanscriptome_summary(report, gffs, sample_ids, denovo=False):
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@ -868,12 +827,6 @@ def main():
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parser.add_argument(
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"--sample_ids", required=True, nargs='+',
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help="List of sample ids")
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parser.add_argument(
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"--report_template", required=True,
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help="Jinja template")
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parser.add_argument(
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"--table_template", required=True,
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help="Template for big transcript table")
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parser.add_argument(
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"--transcript_table_cov_thresh", required=False, type=int, default=50,
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help="Isoforms without this support will be excluded from the table")
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@ -932,14 +885,8 @@ def main():
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if len(pc_df) > 0:
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pychopper_plots(report, pc_df)
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with open(args.report_template, "r") as fh:
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reptempl = fh.read()
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report.template = Template(reptempl)
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if df_tmaps is not None:
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transcript_table(report, df_tmaps, args.transcript_table_cov_thresh,
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args.table_template)
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transcript_table(report, df_tmaps, args.transcript_table_cov_thresh)
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if args.cluster_qc_dirs is not None:
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cluster_quality(args.cluster_qc_dirs, report, sample_ids)
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@ -1,42 +0,0 @@
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<!doctype html>
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<html lang="en" xmlns="http://www.w3.org/1999/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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<meta name="viewport" content="width=device-width, initial-scale=1">
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<title>wf-isoforms report</title>
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<link rel="stylesheet"
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href="https://stackpath.bootstrapcdn.com/bootstrap/3.4.1/css/bootstrap.min.css"
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integrity="sha384-HSMxcRTRxnN+Bdg0JdbxYKrThecOKuH5zCYotlSAcp1+c8xmyTe9GYg1l9a69psu"
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crossorigin="anonymous">
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<link href="https://cdn.jsdelivr.net/npm/simple-datatables@latest/dist/style.css"
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rel="stylesheet" type="text/css">
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<script src="https://cdn.jsdelivr.net/npm/simple-datatables@latest"
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type="text/javascript"></script>
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<link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet"/>
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<script
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src="https://code.jquery.com/jquery-3.6.0.slim.min.js"
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integrity="sha256-u7e5khyithlIdTpu22PHhENmPcRdFiHRjhAuHcs05RI="
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crossorigin="anonymous"></script>
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<script src="https://cdn.datatables.net/1.11.3/js/jquery.dataTables.min.js"
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type="text/javascript"></script>
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<link rel="stylesheet"
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href="https://cdn.datatables.net/1.11.3/css/jquery.dataTables.min.css"
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type="text/css">
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{{ resources }}
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{{ script }}
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<!-- delete?-->
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{{ bigtable_js }}
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</head>
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<body>
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<div class="container">
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<h1>{{ title }}</h1>
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<p class="lead">{{ lead }}
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{{ div }}
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<div class="container" id="bigtable">
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{{ big_table }}
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</div>
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</body>
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</html>
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@ -1,106 +0,0 @@
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<script type="text/javascript">
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$(document).ready(function(){
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$("#load_msg").hide();
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$("#{{ table_id }}").show();
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});
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</script>
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<style>
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table{
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table-layout: fixed;
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word-wrap: break-word;
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}
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#{{ table_id }}{
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<!-- To make the column widths smaller -->
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font-family: Arial, Helvetica, sans-serif;
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border-collapse: collapse;
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width: 100%;
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display: none;
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}
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#{{ table_id }} td, #{{ table_id }} th {
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border: 1px solid #ddd;
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padding: 4px;
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}
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#{{ table_id }} tr:nth-child(even){background-color: #f2f2f2;}
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#{{ table_id }} tr:hover {background-color: #90C5E7;}
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#{{ table_id }} th {
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padding-top: 4px;
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padding-bottom: 4px;
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text-align: left;
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background-color: #0084A9;
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}
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</style>
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<body>
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<div id='load_msg'>Table loading</div>
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{{ dataframe }}
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</body>
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<script type="text/javascript">
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$(document).ready(function () {
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// Setup - add a text input to each footer cell
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$('#{{ table_id }} thead tr')
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.clone(true)
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.addClass('filters')
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.appendTo('#{{ table_id }} thead');
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var table = $('#{{ table_id }}').DataTable({
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"columnDefs": [
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{ "width": "5%", "targets": [2, 4] }],
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sDom: 'lrtip', // removes search box while still allowing search
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searching: true,
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pageLength: 30,
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orderCellsTop: true,
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fixedHeader: true,
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initComplete: function () {
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var api = this.api();
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// For each column
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api
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.columns()
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.eq(0)
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.each(function (colIdx) {
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// Set the header cell to contain the input element
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var cell = $('.filters th').eq(
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$(api.column(colIdx).header()).index()
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);
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var title = $(cell).text();
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$(cell).html('<input type="text" placeholder=" Search" style="font-family:Arial, FontAwesome; width:100%" />');
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// On every keypress in this input
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$(
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'input',
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$('.filters th').eq($(api.column(colIdx).header()).index())
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)
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.off('keyup change')
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.on('keyup change', function (e) {
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e.stopPropagation();
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// Get the search value
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$(this).attr('title', $(this).val());
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var regexr = '({search})'; //$(this).parents('th').find('select').val();
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var cursorPosition = this.selectionStart;
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// Search the column for that value
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api
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.column(colIdx)
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.search(
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this.value != ''
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? regexr.replace('{search}', '(((' + this.value + ')))')
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: '',
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this.value != '',
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this.value == ''
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)
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.draw();
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$(this)
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.focus()[0]
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.setSelectionRange(cursorPosition, cursorPosition);
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});
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});
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},
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});
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});
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</script>
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1
evaluation/tests.sh
Normal file → Executable file
1
evaluation/tests.sh
Normal file → Executable file
@ -26,7 +26,6 @@ multisampledir="test_data/demultiplexed_fastq"
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#"--minimap2_opts '-uf --splice-flank=no'"
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results=()
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OUTPUT=$1/denovo_multi_sample_no_ref_genome;
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nextflow run . --fastq $multisampledir $config --denovo --ref_genome test_data/SIRV_150601a.fasta -profile local --out_dir ${OUTPUT} -w ${OUTPUT}/workspace \
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--sample_sheet test_data/sample_sheet -resume;
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76
main.nf
76
main.nf
@ -42,7 +42,6 @@ process getVersions {
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python -c "import pysam; print(f'pysam,{pysam.__version__}')" >> versions.txt
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python -c "import aplanat; print(f'aplanat,{aplanat.__version__}')" >> versions.txt
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python -c "import pandas; print(f'pandas,{pandas.__version__}')" >> versions.txt
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python -c "import sklearn; print(f'scikit-learn,{sklearn.__version__}')" >> versions.txt
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fastcat --version | sed 's/^/fastcat,/' >> versions.txt
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minimap2 --version | sed 's/^/minimap2,/' >> versions.txt
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samtools --version | head -n 1 | sed 's/ /,/' >> versions.txt
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@ -87,15 +86,9 @@ process preprocess_reads {
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tuple val(sample_id), path('*.tsv'), emit: report
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script:
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"""
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if [[ ${params.use_pychopper} == true ]];
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then
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cdna_classifier.py -t ${params.threads} ${params.pychopper_opts} ${input_reads} ${sample_id}_full_length_reads.fq
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mv cdna_classifier_report.tsv ${sample_id}_cdna_classifier_report.tsv
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generate_pychopper_stats.py --data ${sample_id}_cdna_classifier_report.tsv --output .
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else
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ln -s `realpath $input_reads` "${sample_id}_full_length_reads.fq"
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touch $sample_id}_cdna_classifier_report.tsv
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fi
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cdna_classifier.py -t ${params.threads} ${params.pychopper_opts} ${input_reads} ${sample_id}_full_length_reads.fq
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mv cdna_classifier_report.tsv ${sample_id}_cdna_classifier_report.tsv
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generate_pychopper_stats.py --data ${sample_id}_cdna_classifier_report.tsv --output .
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"""
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}
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@ -267,8 +260,6 @@ process makeReport {
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label "isoforms"
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input:
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path report_template
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path table_template
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path versions
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path "params.json"
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val denovo
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@ -289,8 +280,6 @@ process makeReport {
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def OPT_DENOVO = denovo ? "--denovo" : ''
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"""
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report.py --report $report_name \
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--report_template $report_template \
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--table_template $table_template \
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--versions $versions \
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--params params.json \
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$OPT_ALN \
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@ -301,8 +290,6 @@ process makeReport {
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--gff_annotation $gff_annotation \
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--transcript_table_cov_thresh $params.transcript_table_cov_thresh \
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$OPT_DENOVO
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"""
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}
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@ -311,43 +298,24 @@ process makeReport {
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// decoupling the publish from the process steps.
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process output {
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// publish inputs to output directory
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label "isoforms"
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publishDir "${params.results_dir}/${sample_id}", mode: 'copy', pattern: "*"
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publishDir "${params.out_dir}", mode: 'copy', pattern: "*"
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input:
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tuple val(sample_id), path(fname)
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path fname
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output:
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path fname
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"""
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echo "Writing output files"
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echo $fname
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"""
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}
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process output_report {
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publishDir "${params.results_dir}", mode: 'copy', pattern: "*report.html"
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input:
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path fname
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output:
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path fname
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"""
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echo "Copying report"
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"""
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}
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// workflow module
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workflow pipeline {
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take:
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reads
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ref_genome
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ref_annotation
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report_template
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table_template
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main:
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map_sample_ids_cls = {it ->
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map_sample_ids_cls = {it ->
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/* Harmonize tuples
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output:
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tuple val(sample_id), path('*.gff')
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@ -405,9 +373,7 @@ workflow pipeline {
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seq_for_transcriptome_build = sample_ids.flatten().combine(Channel.fromPath(params.ref_genome))
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}
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makeReport(report_template,
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table_template,
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software_versions,
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makeReport(software_versions,
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workflow_params,
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params.denovo,
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summariseConcatReads.out.summary
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@ -424,18 +390,22 @@ workflow pipeline {
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.join(run_gffcompare.out.gffcmp_dir)
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.join(seq_for_transcriptome_build))
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if (use_ref_ann){
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if (use_ref_ann){
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results = preprocess_reads.out.report
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.concat(run_gffcompare.output.gffcmp_dir,
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m.stats,
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get_transcriptome.out.flatMap(map_sample_ids_cls),
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)
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}
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get_transcriptome.out.flatMap(map_sample_ids_cls))
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.map {it -> it[1]}
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.concat(makeReport.out.report)
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}
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if (!use_ref_ann && !params.denovo){
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results = preprocess_reads.out.report
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.concat(m.stats,
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get_transcriptome.out.flatMap(map_sample_ids_cls),
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)
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get_transcriptome.out.flatMap(map_sample_ids_cls))
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.map {it -> it[1]}
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.concat(makeReport.out.report)
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}
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if (params.denovo){
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results = m.cds
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@ -443,18 +413,19 @@ workflow pipeline {
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seq_for_transcriptome_build,
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get_transcriptome.out.flatMap(map_sample_ids_cls),
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merge_gff_bundles.out.gff,
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m.opt_qual_ch.flatMap {it ->
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m.opt_qual_ch.flatMap {it ->
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l = []
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for (x in it[1..-1]){
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l.add(tuple(it[0], x))
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}
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return l
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})
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.map {it -> it[1]}
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.concat(makeReport.out.report)
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}
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emit:
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results
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report
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telemetry = workflow_params
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}
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@ -463,10 +434,6 @@ WorkflowMain.initialise(workflow, params, log)
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workflow {
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start_ping()
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params.results_dir = "${params.out_dir}/output"
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||||
|
||||
report_template = file("$projectDir/bin/report_template.html")
|
||||
table_template = file("$projectDir/bin/table_template.html")
|
||||
|
||||
fastq = file(params.fastq, type: "file")
|
||||
|
||||
@ -510,10 +477,9 @@ workflow {
|
||||
params.fastq, params.out_dir, params.sample, params.sample_sheet, params.sanitize_fastq
|
||||
)
|
||||
|
||||
pipeline(reads, ref_genome, ref_annotation, report_template, table_template)
|
||||
pipeline(reads, ref_genome, ref_annotation)
|
||||
|
||||
output(pipeline.out.results)
|
||||
output_report(pipeline.out.report)
|
||||
|
||||
end_ping(pipeline.out.telemetry)
|
||||
}
|
||||
|
||||
@ -15,17 +15,15 @@ params {
|
||||
fastq = null
|
||||
ref_genome = false
|
||||
ref_annotation = null
|
||||
// Process cDNA reads using pychopper, turn off for direct RNA:
|
||||
use_pychopper = true
|
||||
threads = 4
|
||||
// Thresholds for viewing isoforms in report table
|
||||
transcript_table_cov_thresh = 50
|
||||
|
||||
out_dir = null
|
||||
out_dir = "output"
|
||||
sample = null
|
||||
sample_sheet = null
|
||||
sanitize_fastq = false
|
||||
wfversion = "v0.1.0"
|
||||
wfversion = "v0.1.1"
|
||||
aws_image_prefix = null
|
||||
aws_queue = null
|
||||
report_name = "report"
|
||||
|
||||
@ -61,11 +61,6 @@
|
||||
"type": "integer",
|
||||
"default": 4
|
||||
},
|
||||
"use_pychopper": {
|
||||
"type": "boolean",
|
||||
"description": "Use pychopper to preprcess reads",
|
||||
"default": true
|
||||
},
|
||||
"pychopper_opts": {
|
||||
"type": "string",
|
||||
"description": "Extra pychopper opts",
|
||||
|
||||
@ -24,8 +24,8 @@ process map_reads{
|
||||
minimap2 -t ${params.threads} -ax splice ${params.minimap2_opts} ${index} "reads.fa"\
|
||||
| samtools view -q ${params.minimum_mapping_quality} -F 2304 -Sb -\
|
||||
| seqkit bam -j ${params.threads} -x -T '${ContextFilter}' -\
|
||||
| samtools sort -@ ${params.threads} -o "${sample_id}_reads_aln_sorted.bam" - \
|
||||
| ((seqkit bam -s -j ${params.threads} - 2>&1) | tee ${sample_id}_read_aln_stats.tsv ) || true
|
||||
| samtools sort -@ ${params.threads} -o "${sample_id}_reads_aln_sorted.bam" - ;
|
||||
((cat "${sample_id}_reads_aln_sorted.bam" | seqkit bam -s -j ${params.threads} - 2>&1) | tee ${sample_id}_read_aln_stats.tsv ) || true
|
||||
|
||||
if [[ -s "internal_priming_fail.tsv" ]];
|
||||
then
|
||||
|
||||
Loading…
Reference in New Issue
Block a user