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<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>
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<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>
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<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: kbrinda@hsph.harvard.edu
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 <karel.brinda@gmail.com>
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 <kamil.salikhov@univ-mlv.fr>
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>
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