-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathcli.html
576 lines (500 loc) · 27.9 KB
/
cli.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
<!DOCTYPE html>
<html lang="en" data-content_root="./">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
<title>9. Command-line interface — ProPhyle 0.3.3.2 documentation</title>
<link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
<link rel="stylesheet" type="text/css" href="_static/sphinx13.css?v=ec60a4c3" />
<script src="_static/documentation_options.js?v=e7e3125d"></script>
<script src="_static/doctools.js?v=9a2dae69"></script>
<script src="_static/sphinx_highlight.js?v=dc90522c"></script>
<link rel="search" type="application/opensearchdescription+xml"
title="Search within ProPhyle 0.3.3.2 documentation"
href="_static/opensearch.xml"/>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="prev" title="8. File formats" href="formats.html" />
<link href='https://fonts.googleapis.com/css?family=Open+Sans:300,400,700'
rel='stylesheet' type='text/css' />
<style type="text/css">
table.right { float: right; margin-left: 20px; }
table.right td { border: 1px solid #ccc; }
</style>
<script type="text/javascript">
// intelligent scrolling of the sidebar content
$(window).scroll(function() {
var sb = $('.sphinxsidebarwrapper');
var win = $(window);
var sbh = sb.height();
var offset = $('.sphinxsidebar').position()['top'];
var wintop = win.scrollTop();
var winbot = wintop + win.innerHeight();
var curtop = sb.position()['top'];
var curbot = curtop + sbh;
// does sidebar fit in window?
if (sbh < win.innerHeight()) {
// yes: easy case -- always keep at the top
sb.css('top', $u.min([$u.max([0, wintop - offset - 10]),
$(document).height() - sbh - 200]));
} else {
// no: only scroll if top/bottom edge of sidebar is at
// top/bottom edge of window
if (curtop > wintop && curbot > winbot) {
sb.css('top', $u.max([wintop - offset - 10, 0]));
} else if (curtop < wintop && curbot < winbot) {
sb.css('top', $u.min([winbot - sbh - offset - 20,
$(document).height() - sbh - 200]));
}
}
});
</script>
</head><body>
<div class="pageheader">
<ul>
<li><a href="index.html">Home</a></li>
<li><a href="install.html">Get it</a></li>
<li><a href="contents.html">Docs</a></li>
<li><a href="http://github.com/prophyle/prophyle">Extend/Develop</a></li>
</ul>
<div>
<a href="index.html">
<!--
<img src="_static/sphinxheader.png" alt="SPHINX" />
-->
<div style="color:white;font-size:240%">ProPhyle</div>
<div style="color:white;font-size:140%">DNA sequence classification</div>
</a>
</div>
</div>
<div class="related" role="navigation" aria-label="Related">
<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
<a href="genindex.html" title="General Index"
accesskey="I">index</a></li>
<li class="right" >
<a href="formats.html" title="8. File formats"
accesskey="P">previous</a> |</li>
<li><a href="index.html">ProPhyle home</a> |</li>
<li><a href="contents.html">Documentation</a> »</li>
<li class="nav-item nav-item-this"><a href=""><span class="section-number">9. </span>Command-line interface</a></li>
</ul>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="Main">
<div class="sphinxsidebarwrapper">
<div>
<h3><a href="contents.html">Table of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">9. Command-line interface</a><ul>
<li><a class="reference internal" href="#prophyle-the-main-program">9.1. ProPhyle – the main program</a><ul>
<li><a class="reference internal" href="#prophyle"><code class="docutils literal notranslate"><span class="pre">prophyle</span></code></a></li>
<li><a class="reference internal" href="#prophyle-download"><code class="docutils literal notranslate"><span class="pre">prophyle</span> <span class="pre">download</span></code></a></li>
<li><a class="reference internal" href="#prophyle-index"><code class="docutils literal notranslate"><span class="pre">prophyle</span> <span class="pre">index</span></code></a></li>
<li><a class="reference internal" href="#prophyle-classify"><code class="docutils literal notranslate"><span class="pre">prophyle</span> <span class="pre">classify</span></code></a></li>
<li><a class="reference internal" href="#prophyle-compress"><code class="docutils literal notranslate"><span class="pre">prophyle</span> <span class="pre">compress</span></code></a></li>
<li><a class="reference internal" href="#prophyle-decompress"><code class="docutils literal notranslate"><span class="pre">prophyle</span> <span class="pre">decompress</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#prophyle-assembler">9.2. <code class="docutils literal notranslate"><span class="pre">prophyle_assembler</span></code></a></li>
<li><a class="reference internal" href="#id1">9.3. <code class="docutils literal notranslate"><span class="pre">prophyle_index</span></code></a></li>
<li><a class="reference internal" href="#prophyle-assignment">9.4. <code class="docutils literal notranslate"><span class="pre">prophyle_assignment</span></code></a></li>
<li><a class="reference internal" href="#prophyle-propagation-makefile-py">9.5. <code class="docutils literal notranslate"><span class="pre">prophyle_propagation_makefile.py</span></code></a></li>
<li><a class="reference internal" href="#prophyle-propagation-preprocessing-py">9.6. <code class="docutils literal notranslate"><span class="pre">prophyle_propagation_preprocessing.py</span></code></a></li>
<li><a class="reference internal" href="#prophyle-propagation-postprocessing-py">9.7. <code class="docutils literal notranslate"><span class="pre">prophyle_propagation_postprocessing.py</span></code></a></li>
<li><a class="reference internal" href="#prophyle-validate-tree-py">9.8. <code class="docutils literal notranslate"><span class="pre">prophyle_validate_tree.py</span></code></a></li>
</ul>
</li>
</ul>
</div>
<div>
<h4>Previous topic</h4>
<p class="topless"><a href="formats.html"
title="previous chapter"><span class="section-number">8. </span>File formats</a></p>
</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
<li><a href="_sources/cli.rst.txt"
rel="nofollow">Show Source</a></li>
</ul>
</div>
<search id="searchbox" style="display: none" role="search">
<h3 id="searchlabel">Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="search.html" method="get">
<input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
<input type="submit" value="Go" />
</form>
</div>
</search>
<script>document.getElementById('searchbox').style.display = "block"</script>
</div>
</div>
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
<div class="body" role="main">
<section id="command-line-interface">
<span id="cli"></span><h1><span class="section-number">9. </span>Command-line interface<a class="headerlink" href="#command-line-interface" title="Link to this heading">¶</a></h1>
<nav class="contents local" id="contents">
<ul class="simple">
<li><p><a class="reference internal" href="#prophyle-the-main-program" id="id2">ProPhyle – the main program</a></p>
<ul>
<li><p><a class="reference internal" href="#prophyle" id="id3"><code class="docutils literal notranslate"><span class="pre">prophyle</span></code></a></p></li>
<li><p><a class="reference internal" href="#prophyle-download" id="id4"><code class="docutils literal notranslate"><span class="pre">prophyle</span> <span class="pre">download</span></code></a></p></li>
<li><p><a class="reference internal" href="#prophyle-index" id="id5"><code class="docutils literal notranslate"><span class="pre">prophyle</span> <span class="pre">index</span></code></a></p></li>
<li><p><a class="reference internal" href="#prophyle-classify" id="id6"><code class="docutils literal notranslate"><span class="pre">prophyle</span> <span class="pre">classify</span></code></a></p></li>
<li><p><a class="reference internal" href="#prophyle-compress" id="id7"><code class="docutils literal notranslate"><span class="pre">prophyle</span> <span class="pre">compress</span></code></a></p></li>
<li><p><a class="reference internal" href="#prophyle-decompress" id="id8"><code class="docutils literal notranslate"><span class="pre">prophyle</span> <span class="pre">decompress</span></code></a></p></li>
</ul>
</li>
<li><p><a class="reference internal" href="#prophyle-assembler" id="id9"><code class="docutils literal notranslate"><span class="pre">prophyle_assembler</span></code></a></p></li>
<li><p><a class="reference internal" href="#id1" id="id10"><code class="docutils literal notranslate"><span class="pre">prophyle_index</span></code></a></p></li>
<li><p><a class="reference internal" href="#prophyle-assignment" id="id11"><code class="docutils literal notranslate"><span class="pre">prophyle_assignment</span></code></a></p></li>
<li><p><a class="reference internal" href="#prophyle-propagation-makefile-py" id="id12"><code class="docutils literal notranslate"><span class="pre">prophyle_propagation_makefile.py</span></code></a></p></li>
<li><p><a class="reference internal" href="#prophyle-propagation-preprocessing-py" id="id13"><code class="docutils literal notranslate"><span class="pre">prophyle_propagation_preprocessing.py</span></code></a></p></li>
<li><p><a class="reference internal" href="#prophyle-propagation-postprocessing-py" id="id14"><code class="docutils literal notranslate"><span class="pre">prophyle_propagation_postprocessing.py</span></code></a></p></li>
<li><p><a class="reference internal" href="#prophyle-validate-tree-py" id="id15"><code class="docutils literal notranslate"><span class="pre">prophyle_validate_tree.py</span></code></a></p></li>
</ul>
</nav>
<section id="prophyle-the-main-program">
<h2><span class="section-number">9.1. </span>ProPhyle – the main program<a class="headerlink" href="#prophyle-the-main-program" title="Link to this heading">¶</a></h2>
<section id="prophyle">
<h3><code class="docutils literal notranslate"><span class="pre">prophyle</span></code><a class="headerlink" href="#prophyle" title="Link to this heading">¶</a></h3>
<blockquote>
<div><div class="code text highlight-default notranslate"><div class="highlight"><pre><span></span>$ prophyle -h
usage: prophyle.py [-h] [-v] ...
Program: prophyle (phylogeny-based metagenomic classification)
Version: 0.3.1.0
Authors: Karel Brinda, Kamil Salikhov, Simone Pignotti, Gregory Kucherov
Contact: [email protected]
Usage: prophyle <command> [options]
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
subcommands:
download download a genomic database
index build index
classify classify reads
analyze analyze results (experimental)
compress compress a ProPhyle index
decompress decompress a compressed ProPhyle index
compile compile auxiliary ProPhyle programs
</pre></div>
</div>
</div></blockquote>
</section>
<section id="prophyle-download">
<h3><code class="docutils literal notranslate"><span class="pre">prophyle</span> <span class="pre">download</span></code><a class="headerlink" href="#prophyle-download" title="Link to this heading">¶</a></h3>
<blockquote>
<div><div class="code text highlight-default notranslate"><div class="highlight"><pre><span></span>$ prophyle download -h
usage: prophyle.py download [-h] [-d DIR] [-l STR] [-F] [-c [STR [STR ...]]]
<library> [<library> ...]
positional arguments:
<library> genomic library ['bacteria', 'viruses', 'plasmids',
'hmp', 'all']
optional arguments:
-h, --help show this help message and exit
-d DIR directory for the tree and the sequences [~/prophyle]
-l STR log file
-F rewrite library files if they already exist
-c [STR [STR ...]] advanced configuration (a JSON dictionary)
</pre></div>
</div>
</div></blockquote>
</section>
<section id="prophyle-index">
<h3><code class="docutils literal notranslate"><span class="pre">prophyle</span> <span class="pre">index</span></code><a class="headerlink" href="#prophyle-index" title="Link to this heading">¶</a></h3>
<blockquote>
<div><div class="code text highlight-default notranslate"><div class="highlight"><pre><span></span>$ prophyle index -h
usage: prophyle.py index [-h] [-g DIR] [-j INT] [-k INT] [-l STR] [-s FLOAT]
[-F] [-M] [-P] [-K] [-T] [-A] [-c [STR [STR ...]]]
<tree.nw> [<tree.nw> ...] <index.dir>
positional arguments:
<tree.nw> phylogenetic tree (in Newick/NHX)
<index.dir> index directory (will be created)
optional arguments:
-h, --help show this help message and exit
-g DIR directory with the library sequences [dir. of the first
tree]
-j INT number of threads [auto (4)]
-k INT k-mer length [31]
-l STR log file [<index.dir>/log.txt]
-s FLOAT rate of sampling of the tree [no sampling]
-F rewrite index files if they already exist
-M mask repeats/low complexity regions (using DustMasker)
-P do not add prefixes to node names when multiple trees
are used
-K skip k-LCP construction (then restarted search only)
-T keep temporary files from k-mer propagation
-A autocomplete tree (names of internal nodes and FASTA
paths)
-c [STR [STR ...]] advanced configuration (a JSON dictionary)
</pre></div>
</div>
</div></blockquote>
</section>
<section id="prophyle-classify">
<h3><code class="docutils literal notranslate"><span class="pre">prophyle</span> <span class="pre">classify</span></code><a class="headerlink" href="#prophyle-classify" title="Link to this heading">¶</a></h3>
<blockquote>
<div><div class="code text highlight-default notranslate"><div class="highlight"><pre><span></span>$ prophyle classify -h
usage: prophyle.py classify [-h] [-k INT] [-m {h1,c1,h2,c2}] [-f {kraken,sam}]
[-l STR] [-P] [-A] [-L] [-X] [-M] [-C] [-K]
[-c [STR [STR ...]]]
<index.dir> <reads1.fq> [<reads2.fq>]
positional arguments:
<index.dir> index directory
<reads1.fq> first file with reads in FASTA/FASTQ (- for standard
input)
<reads2.fq> second file with reads in FASTA/FASTQ
optional arguments:
-h, --help show this help message and exit
-k INT k-mer length [detect automatically from the index]
-m {h1,c1,h2,c2} measure: h1=hit count, c1=coverage, h2=norm.hit count,
c2=norm.coverage [h1]
-f {kraken,sam} output format [sam]
-l STR log file
-P incorporate sequences and qualities into SAM records
-A annotate assignments (using tax. information from NHX)
-L replace read assignments by their LCA
-X replace k-mer matches by their LCA
-M mimic Kraken (equivalent to "-m h1 -f kraken -L -X")
-C use C++ impl. of the assignment algorithm (experimental)
-K force restarted search mode
-c [STR [STR ...]] advanced configuration (a JSON dictionary)
</pre></div>
</div>
</div></blockquote>
</section>
<section id="prophyle-compress">
<h3><code class="docutils literal notranslate"><span class="pre">prophyle</span> <span class="pre">compress</span></code><a class="headerlink" href="#prophyle-compress" title="Link to this heading">¶</a></h3>
<blockquote>
<div><div class="code text highlight-default notranslate"><div class="highlight"><pre><span></span>$ prophyle compress -h
usage: prophyle.py compress [-h] [-c [STR [STR ...]]]
<index.dir> [<archive.tar.gz>]
positional arguments:
<index.dir> index directory
<archive.tar.gz> output archive [<index.dir>.tar.gz]
optional arguments:
-h, --help show this help message and exit
-c [STR [STR ...]] advanced configuration (a JSON dictionary)
</pre></div>
</div>
</div></blockquote>
</section>
<section id="prophyle-decompress">
<h3><code class="docutils literal notranslate"><span class="pre">prophyle</span> <span class="pre">decompress</span></code><a class="headerlink" href="#prophyle-decompress" title="Link to this heading">¶</a></h3>
<blockquote>
<div><div class="code text highlight-default notranslate"><div class="highlight"><pre><span></span>$ prophyle decompress -h
usage: prophyle.py decompress [-h] [-K] [-c [STR [STR ...]]]
<archive.tar.gz> [<output.dir>]
positional arguments:
<archive.tar.gz> output archive
<output.dir> output directory [./]
optional arguments:
-h, --help show this help message and exit
-K skip k-LCP construction
-c [STR [STR ...]] advanced configuration (a JSON dictionary)
</pre></div>
</div>
</div></blockquote>
</section>
</section>
<section id="prophyle-assembler">
<h2><span class="section-number">9.2. </span><code class="docutils literal notranslate"><span class="pre">prophyle_assembler</span></code><a class="headerlink" href="#prophyle-assembler" title="Link to this heading">¶</a></h2>
<blockquote>
<div><div class="code text highlight-default notranslate"><div class="highlight"><pre><span></span>$ prophyle_assembler -h
Program: prophyle_assembler (greedy assembler for ProPhyle)
Contact: Karel Brinda <[email protected]>
Usage: prophyle_assembler [options]
Examples: prophyle_assembler -k 15 -i f1.fa -i f2.fa -x fx.fa
- compute intersection of f1 and f2
prophyle_assembler -k 15 -i f1.fa -i f2.fa -x fx.fa -o g1.fa -o g2.fa
- compute intersection of f1 and f2, and subtract it from them
prophyle_assembler -k 15 -i f1.fa -o g1.fa
- re-assemble f1 to g1
Command-line parameters:
-k INT K-mer size.
-i FILE Input FASTA file (can be used multiple times).
-o FILE Output FASTA file (if used, must be used as many times as -i).
-x FILE Compute intersection, subtract it, save it.
-s FILE Output file with k-mer statistics.
-S Silent mode.
Note that '-' can be used for standard input/output.
</pre></div>
</div>
</div></blockquote>
</section>
<section id="id1">
<h2><span class="section-number">9.3. </span><code class="docutils literal notranslate"><span class="pre">prophyle_index</span></code><a class="headerlink" href="#id1" title="Link to this heading">¶</a></h2>
<blockquote>
<div><div class="code text highlight-default notranslate"><div class="highlight"><pre><span></span>$ prophyle_index -h
Program: prophyle_index (alignment of k-mers)
Contact: Kamil Salikhov <[email protected]>
Usage: prophyle_index command [options]
Command: build construct index
query query reads against index
</pre></div>
</div>
<div class="code text highlight-default notranslate"><div class="highlight"><pre><span></span>$ prophyle_index build -h
Usage: prophyle_index build <prefix>
Options: -k INT length of k-mer
-s construct k-LCP and SA in parallel
-i sampling distance for SA
</pre></div>
</div>
<div class="code text highlight-default notranslate"><div class="highlight"><pre><span></span>$ prophyle_index query -h
Usage: prophyle_index query [options] <prefix> <in.fq>
Options: -k INT length of k-mer
-u use k-LCP for querying
-v output set of chromosomes for every k-mer
-p do not check whether k-mer is on border of two contigs, and show such k-mers in output
-b print sequences and base qualities
-l STR log file name to output statistics
-t INT number of threads [1]
</pre></div>
</div>
</div></blockquote>
</section>
<section id="prophyle-assignment">
<h2><span class="section-number">9.4. </span><code class="docutils literal notranslate"><span class="pre">prophyle_assignment</span></code><a class="headerlink" href="#prophyle-assignment" title="Link to this heading">¶</a></h2>
<blockquote>
<div><div class="code text highlight-default notranslate"><div class="highlight"><pre><span></span>$ prophyle_assignment.py -h
usage: prophyle_assignment.py [-h] [-f {kraken,sam}] [-m {h1,c1,c2,h2}] [-A]
[-L] [-X] [-c [STR [STR ...]]]
<tree.nhx> <k> <assignments.txt>
Implementation of assignment algorithm
positional arguments:
<tree.nhx> phylogenetic tree (Newick/NHX)
<k> k-mer length
<assignments.txt> assignments in generalized Kraken format
optional arguments:
-h, --help show this help message and exit
-f {kraken,sam} format of output [sam]
-m {h1,c1,c2,h2} measure: h1=hit count, c1=coverage, h2=norm.hit count,
c2=norm.coverage [h1]
-A annotate assignments
-L use LCA when tie (multiple assignments with the same
score)
-X use LCA for k-mers (multiple hits of a k-mer)
-c [STR [STR ...]] configuration (a JSON dictionary)
</pre></div>
</div>
</div></blockquote>
</section>
<section id="prophyle-propagation-makefile-py">
<h2><span class="section-number">9.5. </span><code class="docutils literal notranslate"><span class="pre">prophyle_propagation_makefile.py</span></code><a class="headerlink" href="#prophyle-propagation-makefile-py" title="Link to this heading">¶</a></h2>
<blockquote>
<div><div class="code text highlight-default notranslate"><div class="highlight"><pre><span></span>$ prophyle_propagation_makefile.py -h
usage: prophyle_propagation_makefile.py [-h] -k int
<tree.nw> <library.dir> <output.dir>
<Makefile>
Create Makefile for parallelized ProPhyle k-mer propagation.
positional arguments:
<tree.nw> phylogenetic tree (in Newick/NHX).
<library.dir> directory with the library
<output.dir> output directory for the index
<Makefile> output Makefile
optional arguments:
-h, --help show this help message and exit
-k int k-mer length
</pre></div>
</div>
</div></blockquote>
</section>
<section id="prophyle-propagation-preprocessing-py">
<h2><span class="section-number">9.6. </span><code class="docutils literal notranslate"><span class="pre">prophyle_propagation_preprocessing.py</span></code><a class="headerlink" href="#prophyle-propagation-preprocessing-py" title="Link to this heading">¶</a></h2>
<blockquote>
<div><div class="code text highlight-default notranslate"><div class="highlight"><pre><span></span>$ prophyle_propagation_preprocessing.py -h
usage: prophyle_propagation_preprocessing.py [-h] [-s FLOAT] [-A] [-V] [-P]
<in_tree.nw{@node_name}>
[<in_tree.nw{@node_name}> ...]
<out_tree.nw>
Merge multiple ProPhyle trees. Specific subtrees might be extracted before merging. Examples:
$ prophyle_merge_trees.py ~/prophyle/bacteria.nw ~/prophyle/viruses.nw bv.nw
$ prophyle_merge_trees.py ~/prophyle/bacteria.nw@562 ecoli.nw
positional arguments:
<in_tree.nw{@node_name}>
input tree
<out_tree.nw> output tree
optional arguments:
-h, --help show this help message and exit
-s FLOAT rate of sampling the tree [no sampling]
-A autocomplete tree (names of internal nodes and FASTA paths)
-V verbose
-P do not add prefixes to node names
</pre></div>
</div>
</div></blockquote>
</section>
<section id="prophyle-propagation-postprocessing-py">
<h2><span class="section-number">9.7. </span><code class="docutils literal notranslate"><span class="pre">prophyle_propagation_postprocessing.py</span></code><a class="headerlink" href="#prophyle-propagation-postprocessing-py" title="Link to this heading">¶</a></h2>
<blockquote>
<div><div class="code text highlight-default notranslate"><div class="highlight"><pre><span></span>$ prophyle_propagation_postprocessing.py -h
usage: prophyle_propagation_postprocessing.py [-h]
<propagation.dir> <index.fa>
<in.tree.nw> <counts.tsv>
<out.tree.nw>
K-mer propagation postprocessing: merging FASTA files and k-mer annotation.
positional arguments:
<propagation.dir> directory with FASTA files
<index.fa> output fast file
<in.tree.nw> input phylogenetic tree
<counts.tsv> input phylogenetic tree
<out.tree.nw> output phylogenetic tree
optional arguments:
-h, --help show this help message and exit
</pre></div>
</div>
</div></blockquote>
</section>
<section id="prophyle-validate-tree-py">
<h2><span class="section-number">9.8. </span><code class="docutils literal notranslate"><span class="pre">prophyle_validate_tree.py</span></code><a class="headerlink" href="#prophyle-validate-tree-py" title="Link to this heading">¶</a></h2>
<blockquote>
<div><div class="code text highlight-default notranslate"><div class="highlight"><pre><span></span>$ prophyle_validate_tree.py -h
usage: prophyle_validate_tree.py [-h] <tree.nw> [<tree.nw> ...]
Verify a Newick/NHX tree
positional arguments:
<tree.nw> phylogenetic tree (in Newick/NHX)
optional arguments:
-h, --help show this help message and exit
</pre></div>
</div>
</div></blockquote>
</section>
</section>
<div class="clearer"></div>
</div>
</div>
</div>
<div class="clearer"></div>
</div>
<div class="related" role="navigation" aria-label="Related">
<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
<a href="genindex.html" title="General Index"
>index</a></li>
<li class="right" >
<a href="formats.html" title="8. File formats"
>previous</a> |</li>
<li><a href="index.html">ProPhyle home</a> |</li>
<li><a href="contents.html">Documentation</a> »</li>
<li class="nav-item nav-item-this"><a href=""><span class="section-number">9. </span>Command-line interface</a></li>
</ul>
</div>
<div class="footer" role="contentinfo">
© Copyright 2015-2024, Karel Břinda, Kamil Salikhov, Simone Pignotti, Gregory Kucherov.
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 8.0.2.
</div>
<!-- Global site tag (gtag.js) - Google Analytics -->
<script async src="https://www.googletagmanager.com/gtag/js?id=UA-112241191-1"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'UA-112241191-1');
</script>
</body>
</html>