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<div class="section" id="ggd-search">
<span id="id1"></span><h1>ggd search<a class="headerlink" href="#ggd-search" title="Permalink to this headline">¶</a></h1>
<p>[<a class="reference internal" href="index.html#home-page"><span class="std std-ref">Click here to return to the home page</span></a>]</p>
<p>ggd search is used to search for a data package stored within the ggd ecosystem. It is dependent on the ggd channel
provided.</p>
<div class="section" id="using-ggd-search">
<h2>Using ggd search<a class="headerlink" href="#using-ggd-search" title="Permalink to this headline">¶</a></h2>
<p>Once ggd is installed on your system you can run <code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">search</span></code> to search for available data packages.
Running <code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">search</span> <span class="pre">-h</span></code> will give you the a similar help message as below:</p>
<p>Search arguments:</p>
<table class="docutils align-default">
<colgroup>
<col style="width: 26%" />
<col style="width: 74%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>ggd search</p></th>
<th class="head"><p>Search for available ggd data packages. Results are filtered by match score from high to low.
(Only 5 results will be reported unless the -dn flag is changed)</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">-h</span></code>, <code class="docutils literal notranslate"><span class="pre">--help</span></code></p></td>
<td><p>show this help message and exit</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">search_term</span></code></p></td>
<td><p><strong>Required</strong> The term(s) to search for. Multiple terms can be used. Example:
‘ggd search reference genome’, where “reference” and “genome” are the search terms</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--search-type</span></code></p></td>
<td><p>(Optional) How to search for data packages with the search terms provided. Options =
‘combined-only’, ‘non-combined-only’, and ‘both’. ‘combined-only’ will use the provided search
terms as a single search term. ‘non-combined-only’ will use the provided search terms to search
for data package that match each search term separately. ‘both’ will use the search terms combined
and each search term separately to search for data packages. Default = ‘both’</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">-g</span></code>, <code class="docutils literal notranslate"><span class="pre">--genome_build</span></code></p></td>
<td><p>(Optional) Filter results by the genome build of the desired recipe</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">-s</span></code>, <code class="docutils literal notranslate"><span class="pre">--species</span></code></p></td>
<td><p>(Optional) Filter results by the species for the desired recipe</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">-dn</span></code>, <code class="docutils literal notranslate"><span class="pre">--display-number</span></code></p></td>
<td><p>(Optional) The number of search results to display. (Default = 5)</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">-m</span></code>, <code class="docutils literal notranslate"><span class="pre">--match_score</span></code></p></td>
<td><p>(Optional) A score between 0 and 100 to use to filter the results by. (Default = 75).
The lower the number the more results will be output”</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">-c</span></code>, <code class="docutils literal notranslate"><span class="pre">--channel</span></code></p></td>
<td><p>(Optional) The ggd channel to search. (Default = genomics)</p></td>
</tr>
</tbody>
</table>
<p>Any combination of search terms can be used to search for a package.</p>
<div class="section" id="additional-argument-explanation">
<h3>Additional argument explanation:<a class="headerlink" href="#additional-argument-explanation" title="Permalink to this headline">¶</a></h3>
<p>Required arguments:</p>
<ul class="simple">
<li><p><em>search_term:</em> The <code class="code docutils literal notranslate"><span class="pre">search_term</span></code> is a positional argument that represents the “terms” to search for. At least one search term is required, but multiple can be provided
<strong>NOTE: You do not need to add the keyword</strong> <code class="code docutils literal notranslate"><span class="pre">search_term</span></code>.</p></li>
</ul>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>If the genome build or the species is added to the search terms the results will be filtered based on the species and/or genome build provided. (The genome build and/or species
need to be spelled the same as the choices for the <code class="code docutils literal notranslate"><span class="pre">-g</span></code> or <code class="code docutils literal notranslate"><span class="pre">-s</span></code> flags</p>
</div>
<p>Optional arguments:</p>
<ul>
<li><p><em>–search-type</em> The <code class="code docutils literal notranslate"><span class="pre">--search-type</span></code> flag is used to set search term combination filtering. There are three options. (1) Search
for <code class="code docutils literal notranslate"><span class="pre">combined-only</span></code> matches, meaning search for packages when the search terms are combined as a single search term. (2) Search
for <code class="code docutils literal notranslate"><span class="pre">non-combined-only</span></code> matches, meaning search for packages where each term is used as a separate search term. (3) Search for
<code class="code docutils literal notranslate"><span class="pre">both</span></code> combined and non-combined matches, meaning do both (1) and (2). The default behavior is set to <code class="code docutils literal notranslate"><span class="pre">both</span></code>.</p></li>
<li><p><em>-g:</em> The <code class="code docutils literal notranslate"><span class="pre">-g</span></code> flag is used to filter the search results on a specific “genome build”. This flag is not required, however, if
provided the resulting search will be filtered to only include data packages with that genome build.</p></li>
<li><p><em>-s:</em> The <code class="code docutils literal notranslate"><span class="pre">-s</span></code> flag is used to filter the search results on a specific “species”. Only data packages for that specific species
will be displayed.</p></li>
<li><p><em>-dn:</em> The <code class="code docutils literal notranslate"><span class="pre">-dn</span></code> flag is used to filter the search results based on the number of results to display. Default = 5. If more than
5 results are available and you don’t see the desired package in the results list, add the <code class="code docutils literal notranslate"><span class="pre">-dn</span> <span class="pre">{N}</span></code> flag where <em>N</em> is the number
of results to show.</p></li>
<li><p><em>-m:</em> The <code class="code docutils literal notranslate"><span class="pre">-m</span></code> flag represents the “match” score to use for searching. A fuzzy word match is used to identify similar packages
to the terms search for, and the match score defines which packages will be displayed based on a cutoff. A default match score
cutoff is provided, but this flag can be used to provide more strict or more lenient search results. (Default = 75)</p></li>
<li><p><em>-c:</em> The <code class="code docutils literal notranslate"><span class="pre">-c</span></code> flag is used to set the ggd channel to search in. The <em>genomics</em> channel is set by default.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>There is no limit to the number of search terms you can use. However, the more search terms used will result in an increase in the number of results returned.</p>
<p>Additionally, the genome build or species can be used as a search term. If they are spelled correctly, regardless of case, the results will be filtered by that genome
build and/or species. If a genome build or species is added as a search term and is not spelled correctly the results will NOT be filtered by the intended genome build
and/or species.</p>
</div>
</li>
</ul>
</div>
</div>
<div class="section" id="example">
<h2>Example<a class="headerlink" href="#example" title="Permalink to this headline">¶</a></h2>
<p>Some examples of using the <cite>ggd search</cite> tool:</p>
<div class="section" id="simple-example-with-one-search-term">
<h3>1. Simple example with one search term:<a class="headerlink" href="#simple-example-with-one-search-term" title="Permalink to this headline">¶</a></h3>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ggd search reference
----------------------------------------------------------------------------------------------------
mm10-reference-ucsc-v1
<span class="o">======================</span>
Summary: Reference genome <span class="k">for</span> mouse from UCSC
Species: Mus_musculus
Genome Build: mm10
Keywords: reference, ucsc, mouse, mm10, reference-genome, fasta-file
Data Version: <span class="m">07</span>-Feb-2012
To install run:
ggd install mm10-reference-ucsc-v1
----------------------------------------------------------------------------------------------------
hg19-reference-genome-ucsc-v1
<span class="o">=============================</span>
Summary: The hg19 soft masked genomic DNA seqeunce reference genome from UCSC <span class="o">(</span>patch <span class="m">13</span><span class="o">)</span>. Repeats found by <span class="s1">'RepeatMasker'</span> and <span class="s1">'Tandem Repeat Finder'</span> are shown as lower <span class="k">case</span>. Non repeating seqeunce are shown as upper <span class="k">case</span>.
Species: Homo_sapiens
Genome Build: hg19
Keywords: ref, reference-genome, fasta-file, soft-masked
Data Provider: UCSC
Data Version: <span class="m">17</span>-Jan-2020
File type<span class="o">(</span>s<span class="o">)</span>: fa
Data file coordinate base: NA
Included Data Files:
hg19-reference-genome-ucsc-v1.fa.gz
hg19-reference-genome-ucsc-v1.fa.gz.fai
hg19-reference-genome-ucsc-v1.fa.gz.gzi
Approximate Data File Sizes:
hg19-reference-genome-ucsc-v1.fa.gz: <span class="m">997</span>.23M
hg19-reference-genome-ucsc-v1.fa.gz.fai: <span class="m">12</span>.23K
hg19-reference-genome-ucsc-v1.fa.gz.gzi: <span class="m">808</span>.71K
To install run:
ggd install hg19-reference-genome-ucsc-v1
----------------------------------------------------------------------------------------------------
hg38-reference-genome-ucsc-v1
<span class="o">=============================</span>
Summary: The hg38 soft masked genomic DNA seqeunce reference genome from UCSC <span class="o">(</span>patch <span class="m">12</span><span class="o">)</span>. Repeats found by <span class="s1">'RepeatMasker'</span> and <span class="s1">'Tandem Repeat Finder'</span> are shown as lower <span class="k">case</span>. Non repeating seqeunce are shown as upper <span class="k">case</span>.
Species: Homo_sapiens
Genome Build: hg38
Keywords: ref, reference-genome, fasta-file, soft-masked
Data Provider: UCSC
Data Version: <span class="m">10</span>-Aug-2018
File type<span class="o">(</span>s<span class="o">)</span>: fa
Data file coordinate base: NA
Included Data Files:
hg38-reference-genome-ucsc-v1.fa.gz
hg38-reference-genome-ucsc-v1.fa.gz.fai
hg38-reference-genome-ucsc-v1.fa.gz.gzi
Approximate Data File Sizes:
hg38-reference-genome-ucsc-v1.fa.gz: <span class="m">1</span>.02G
hg38-reference-genome-ucsc-v1.fa.gz.fai: <span class="m">25</span>.61K
hg38-reference-genome-ucsc-v1.fa.gz.gzi: <span class="m">814</span>.34K
To install run:
ggd install hg38-reference-genome-ucsc-v1
----------------------------------------------------------------------------------------------------
grch37-reference-genome-1000g-v1
<span class="o">================================</span>
Summary: GRCh37 reference genome from <span class="m">1000</span> genomes
Species: Homo_sapiens
Genome Build: GRCh37
Keywords: ref, reference, fasta-file
Data Version: phase2_reference
To install run:
ggd install grch37-reference-genome-1000g-v1
----------------------------------------------------------------------------------------------------
hg19-reference-genome-gencode-v1
<span class="o">================================</span>
Summary: The GRCh37 DNA nucleotide sequence primary assembly. Sequence regions include reference chromosomes and scaffoldings. Mapped to hg19
Species: Homo_sapiens
Genome Build: hg19
Keywords: Reference-Genome, Fasta, DNA-Sequence, GENCODE-34, Fasta-sequence, primary-assembly
Data Provider: GENCODE
Data Version: release-34
File type<span class="o">(</span>s<span class="o">)</span>: fa
Data file coordinate base: NA
Included Data Files:
hg19-reference-genome-gencode-v1.fa.gz
hg19-reference-genome-gencode-v1.fa.gz.fai
hg19-reference-genome-gencode-v1.fa.gz.gzi
Approximate Data File Sizes:
hg19-reference-genome-gencode-v1.fa.gz: <span class="m">881</span>.99M
hg19-reference-genome-gencode-v1.fa.gz.fai: <span class="m">2</span>.82K
hg19-reference-genome-gencode-v1.fa.gz.gzi: <span class="m">772</span>.92K
To install run:
ggd install hg19-reference-genome-gencode-v1
----------------------------------------------------------------------------------------------------
>>> Scroll up to see package details and install info <span class="o"><<<</span>
************************************
Package Name <span class="nv">Results</span>
<span class="o">====================</span>
mm10-reference-ucsc-v1
hg19-reference-genome-ucsc-v1
hg38-reference-genome-ucsc-v1
grch37-reference-genome-1000g-v1
hg19-reference-genome-gencode-v1
grch37-reference-genome-gencode-v1
NOTE: Name order matches order of packages in detailed section above
************************************
:ggd:search: NOTE Only showing results <span class="k">for</span> top <span class="m">5</span> of <span class="m">30</span> matches.
:ggd:search: To display all matches append your search <span class="nb">command</span> with <span class="s1">'-dn 30'</span>
ggd search reference -dn <span class="m">30</span>
</pre></div>
</div>
</div>
<div class="section" id="simple-example-with-two-search-terms">
<h3>2. Simple example with two search terms:<a class="headerlink" href="#simple-example-with-two-search-terms" title="Permalink to this headline">¶</a></h3>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ggd search chrom sizes
----------------------------------------------------------------------------------------------------
hg19-chromsizes-ggd-v1
<span class="o">======================</span>
Summary: Chromosome lengths <span class="k">for</span> hg19
Species: Homo_sapiens
Genome Build: hg19
Keywords: genome, chromosome, lengths, sizes
Data Provider: GGD
Data Version: <span class="m">16</span>-Apirl-2020
File type<span class="o">(</span>s<span class="o">)</span>: txt
Data file coordinate base: NA
Included Data Files:
hg19-chromsizes-ggd-v1.txt
Approximate Data File Sizes:
hg19-chromsizes-ggd-v1.txt: <span class="m">1</span>.99K
To install run:
ggd install hg19-chromsizes-ggd-v1
----------------------------------------------------------------------------------------------------
hg38-chromsizes-ggd-v1
<span class="o">======================</span>
Summary: Chromosome lengths <span class="k">for</span> hg38
Species: Homo_sapiens
Genome Build: hg38
Keywords: genome, chromosome, lengths, sizes
Data Provider: GGD
Data Version: <span class="m">16</span>-Apirl-2020
File type<span class="o">(</span>s<span class="o">)</span>: txt
Data file coordinate base: NA
Included Data Files:
hg38-chromsizes-ggd-v1.txt
Approximate Data File Sizes:
hg38-chromsizes-ggd-v1.txt: <span class="m">15</span>.53K
To install run:
ggd install hg38-chromsizes-ggd-v1
----------------------------------------------------------------------------------------------------
grch37-chromsizes-ggd-v1
<span class="o">========================</span>
Summary: Chromosome lengths <span class="k">for</span> GRCh37
Species: Homo_sapiens
Genome Build: GRCh37
Keywords: genome, chromosome, lengths, sizes
Data Provider: GGD
Data Version: <span class="m">16</span>-Apirl-2020
File type<span class="o">(</span>s<span class="o">)</span>: txt
Data file coordinate base: NA
Included Data Files:
grch37-chromsizes-ggd-v1.txt
Approximate Data File Sizes:
grch37-chromsizes-ggd-v1.txt: <span class="m">5</span>.17K
To install run:
ggd install grch37-chromsizes-ggd-v1
----------------------------------------------------------------------------------------------------
grch38-chromsizes-ggd-v1
<span class="o">========================</span>
Summary: Chromosome lengths <span class="k">for</span> GRCh38
Species: Homo_sapiens
Genome Build: GRCh38
Keywords: genome, chromosome, lengths, sizes
Data Provider: GGD
Data Version: <span class="m">16</span>-April-2020
File type<span class="o">(</span>s<span class="o">)</span>: txt
Data file coordinate base: NA
Included Data Files:
grch38-chromsizes-ggd-v1.txt
Approximate Data File Sizes:
grch38-chromsizes-ggd-v1.txt: <span class="m">11</span>.14K
To install run:
ggd install grch38-chromsizes-ggd-v1
----------------------------------------------------------------------------------------------------
>>> Scroll up to see package details and install info <span class="o"><<<</span>
***************************
Package Name <span class="nv">Results</span>
<span class="o">====================</span>
hg19-chromsizes-ggd-v1
hg38-chromsizes-ggd-v1
grch37-chromsizes-ggd-v1
grch38-chromsizes-ggd-v1
NOTE: Name order matches order of packages in detailed section above
***************************
:ggd:search: NOTE: Only showing results <span class="k">for</span> top <span class="m">5</span> of <span class="m">22</span> matches.
:ggd:search: To display all matches append your search <span class="nb">command</span> with <span class="s1">'-dn 22'</span>
ggd search chrom sizes -dn <span class="m">22</span>
</pre></div>
</div>
</div>
<div class="section" id="simple-example-with-the-genome-build-as-a-search-term">
<h3>3. Simple example with the genome build as a search term:<a class="headerlink" href="#simple-example-with-the-genome-build-as-a-search-term" title="Permalink to this headline">¶</a></h3>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ggd search repeat masker hg19
----------------------------------------------------------------------------------------------------
hg19-repeatmasker-ucsc-v1
<span class="o">=========================</span>
Summary: RepeatMasker track from UCSC in bed format. Interspersed repeats and low complexity sequences identified using the RepeatMasker program. Scaffoldings missing from the GGD hg19.genome file are removed.
Species: Homo_sapiens
Genome Build: hg19
Keywords: rmsk, region, low-complexity-repeats, SINE, ALUs, LINE, LTR, DNA-repeat-elements, simple-repeats, RNA-repeats
Data Provider: UCSC
Data Version: <span class="m">22</span>-Mar-2020
File type<span class="o">(</span>s<span class="o">)</span>: bed
Data file coordinate base: <span class="m">0</span>-based-inclusive
Included Data Files:
hg19-repeatmasker-ucsc-v1.bed.gz
hg19-repeatmasker-ucsc-v1.bed.gz.tbi
Approximate Data File Sizes:
hg19-repeatmasker-ucsc-v1.bed.gz: <span class="m">114</span>.62M
hg19-repeatmasker-ucsc-v1.bed.gz.tbi: <span class="m">526</span>.98K
To install run:
ggd install hg19-repeatmasker-ucsc-v1
----------------------------------------------------------------------------------------------------
hg19-simple-repeats-ucsc-v1
<span class="o">===========================</span>
Summary: Simple repeats track from UCSC. Simple tandem repeats and imperfect repeats identified by the Tandem Repeats Finder <span class="o">(</span>TRF<span class="o">)</span> algorithm. Any scaffoldings not in the hg19.genome file are removed from the final file
Species: Homo_sapiens
Genome Build: hg19
Keywords: simrep, simple-repeats, repeats, tandem-repeats, simple-tandem-repeats
Data Provider: UCSC
Data Version: <span class="m">22</span>-Mar-2020
File type<span class="o">(</span>s<span class="o">)</span>: bed
Data file coordinate base: <span class="m">0</span>-based-inclusive
Included Data Files:
hg19-simple-repeats-ucsc-v1.bed.gz
hg19-simple-repeats-ucsc-v1.bed.gz.tbi
Approximate Data File Sizes:
hg19-simple-repeats-ucsc-v1.bed.gz: <span class="m">25</span>.58M
hg19-simple-repeats-ucsc-v1.bed.gz.tbi: <span class="m">1</span>.35M
To install run:
ggd install hg19-simple-repeats-ucsc-v1
----------------------------------------------------------------------------------------------------
hg19-microsatellites-ucsc-v1
<span class="o">============================</span>
Summary: Microsatellites from UCSC. Region which tend to be highly polymorphic and with at least <span class="m">15</span> di- or tri-nucletodie repeats
Species: Homo_sapiens
Genome Build: hg19
Keywords: microsatellites, microsats, STR, STRs, short-tandem-repeat, repeats, repeat-regions
Data Provider: UCSC
Data Version: <span class="m">28</span>-Nov-2010
File type<span class="o">(</span>s<span class="o">)</span>: bed
Data file coordinate base: <span class="m">0</span>-based-inclusive
Included Data Files:
hg19-microsatellites-ucsc-v1.bed.gz
hg19-microsatellites-ucsc-v1.bed.gz.tbi
Approximate Data File Sizes:
hg19-microsatellites-ucsc-v1.bed.gz: <span class="m">401</span>.08K
hg19-microsatellites-ucsc-v1.bed.gz.tbi: <span class="m">298</span>.03K
To install run:
ggd install hg19-microsatellites-ucsc-v1
----------------------------------------------------------------------------------------------------
hg19-self-chain-ucsc-v1
<span class="o">=======================</span>
Summary: Self chain alignemnts of the human genome with an improved gap scoring system. Alignemtns point out areas of duplication wihtin the human genome, with the exception of the pseudoautosomal regions on X and Y. From the Human Chained Self Alignemnts track on UCSC.
Species: Homo_sapiens
Genome Build: hg19
Keywords: Self-Chain, Self-Alignment, Repeats, low-copy-repeats
Data Provider: UCSC
Data Version: <span class="m">27</span>-Apr-2009
File type<span class="o">(</span>s<span class="o">)</span>: bed
Data file coordinate base: <span class="m">0</span>-based-inclusive
Included Data Files:
hg19-self-chain-ucsc-v1.bed.gz
hg19-self-chain-ucsc-v1.bed.gz.tbi
Approximate Data File Sizes:
hg19-self-chain-ucsc-v1.bed.gz: <span class="m">21</span>.74M
hg19-self-chain-ucsc-v1.bed.gz.tbi: <span class="m">201</span>.69K
To install run:
ggd install hg19-self-chain-ucsc-v1
----------------------------------------------------------------------------------------------------
>>> Scroll up to see package details and install info <span class="o"><<<</span>
******************************
Package Name <span class="nv">Results</span>
<span class="o">====================</span>
hg19-repeatmasker-ucsc-v1
hg19-simple-repeats-ucsc-v1
hg19-microsatellites-ucsc-v1
hg19-self-chain-ucsc-v1
NOTE: Name order matches order of
******************************
</pre></div>
</div>
</div>
<div class="section" id="example-using-g-and-s-flags-to-filter-the-results">
<h3>4. Example using <code class="docutils literal notranslate"><span class="pre">-g</span></code> and <code class="docutils literal notranslate"><span class="pre">-s</span></code> flags to filter the results:<a class="headerlink" href="#example-using-g-and-s-flags-to-filter-the-results" title="Permalink to this headline">¶</a></h3>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ggd search autosomal-dominant -g GRCh37 -s Homo_sapiens
----------------------------------------------------------------------------------------------------
grch37-autosomal-dominant-genes-berg-v1
=======================================
Summary: CDS region genomic coordinates, along with the compliment coordinates, for OMIM disease genes (as of June 2011) deemed to follow autosomal dominant inheritance. (Assembled by Macarthur Lab). Berg et al, 2013: (https://www.ncbi.nlm.nih.gov/pubmed/22995991).
Species: Homo_sapiens
Genome Build: GRCh37
Keywords: genes, autosomal-dominant, disease, Berg_et_al, AD, OMIM, gene_coordinates, CDS-regions
Data Provider: berg
Data Version: 1-15-2013
File type(s): bed
Data file coordinate base: 0-based-inclusive
Included Data Files:
grch37-autosomal-dominant-genes-berg-v1.bed.gz
grch37-autosomal-dominant-genes-berg-v1.bed.gz.tbi
grch37-autosomal-dominant-genes-berg-v1.compliment.bed.gz
grch37-autosomal-dominant-genes-berg-v1.compliment.bed.gz.tbi
Approximate Data File Sizes:
grch37-autosomal-dominant-genes-berg-v1.bed.gz: 119.97K
grch37-autosomal-dominant-genes-berg-v1.bed.gz.tbi: 27.12K
grch37-autosomal-dominant-genes-berg-v1.compliment.bed.gz: 73.13K
grch37-autosomal-dominant-genes-berg-v1.compliment.bed.gz.tbi: 20.39K
To install run:
ggd install grch37-autosomal-dominant-genes-berg-v1
----------------------------------------------------------------------------------------------------
grch37-autosomal-dominant-genes-blekhman-v1
===========================================
Summary: CDS region genomic coordinates, along with the compliment coordinates, for OMIM disease genes deemed to follow autosomal dominant inheritance according to extensive manual curation by Molly Przeworski's group.(https://www.ncbi.nlm.nih.gov/pubmed/18571414).
Species: Homo_sapiens
Genome Build: GRCh37
Keywords: genes, autosomal-dominant, disease, Blekhman_et_al, AD, OMIM, gene_coordinates, CDS-regions
Data Provider: blekhman
Data Version: 6-24-2008
File type(s): bed
Data file coordinate base: 0-based-inclusive
Included Data Files:
grch37-autosomal-dominant-genes-blekhman-v1.bed.gz
grch37-autosomal-dominant-genes-blekhman-v1.bed.gz.tbi
grch37-autosomal-dominant-genes-blekhman-v1.compliment.bed.gz
grch37-autosomal-dominant-genes-blekhman-v1.compliment.bed.gz.tbi
Approximate Data File Sizes:
grch37-autosomal-dominant-genes-blekhman-v1.bed.gz: 59.94K
grch37-autosomal-dominant-genes-blekhman-v1.bed.gz.tbi: 15.15K
grch37-autosomal-dominant-genes-blekhman-v1.compliment.bed.gz: 38.45K
grch37-autosomal-dominant-genes-blekhman-v1.compliment.bed.gz.tbi: 15.37K
To install run:
ggd install grch37-autosomal-dominant-genes-blekhman-v1
----------------------------------------------------------------------------------------------------
grch37-autosomal-dominant-genes-berg-blekhman-v1
================================================
Summary: CDS region genomic coordinates, along with the compliment coordinates, for combined set of OMIM disease genes deemed to follow autosomal dominant inheritance. (Assembled by Macarthur Lab). Gene sets from: Berg et al, 2013: (https://www.ncbi.nlm.nih.gov/pubmed/22995991). Blekham et al, 2008: (https://www.ncbi.nlm.nih.gov/pubmed/18571414)
Species: Homo_sapiens
Genome Build: GRCh37
Keywords: genes, autosomal-dominant, disease, Berg_et_al, Blekhman_et_al, AD, OMIM, gene_coordinates, CDS-regions
Data Provider: berg-blekhman
Data Version: 1-15-2013_6-24-2008
File type(s): bed
Data file coordinate base: 0-based-inclusive
Included Data Files:
grch37-autosomal-dominant-genes-berg-blekhman-v1.bed.gz
grch37-autosomal-dominant-genes-berg-blekhman-v1.bed.gz.tbi
grch37-autosomal-dominant-genes-berg-blekhman-v1.compliment.bed.gz
grch37-autosomal-dominant-genes-berg-blekhman-v1.compliment.bed.gz.tbi
Approximate Data File Sizes:
grch37-autosomal-dominant-genes-berg-blekhman-v1.bed.gz: 135.22K
grch37-autosomal-dominant-genes-berg-blekhman-v1.bed.gz.tbi: 29.55K
grch37-autosomal-dominant-genes-berg-blekhman-v1.compliment.bed.gz: 83.03K
grch37-autosomal-dominant-genes-berg-blekhman-v1.compliment.bed.gz.tbi: 21.44K
To install run:
ggd install grch37-autosomal-dominant-genes-berg-blekhman-v1
----------------------------------------------------------------------------------------------------
>>> Scroll up to see package details and install info <<<
**************************************************
Package Name Results
====================
grch37-autosomal-dominant-genes-berg-v1
grch37-autosomal-dominant-genes-blekhman-v1
grch37-autosomal-dominant-genes-berg-blekhman-v1
NOTE: Name order matches order of packages in detailed section above
**************************************************
</pre></div>
</div>
</div>
<div class="section" id="example-of-searching-for-two-different-data-packages-at-the-same-time-for-a-specific-genome-build">
<h3>5. Example of searching for two different data packages at the same time for a specific genome build<a class="headerlink" href="#example-of-searching-for-two-different-data-packages-at-the-same-time-for-a-specific-genome-build" title="Permalink to this headline">¶</a></h3>
<p>The default behavior is to search for terms both combine and separately. Therefore, one does noes need
to set the <code class="code docutils literal notranslate"><span class="pre">--search-type</span></code> unless they would like to refine the results. The example below can also
be done with setting search-type flag as such: <code class="code docutils literal notranslate"><span class="pre">--search</span> <span class="pre">type</span> <span class="pre">non-combined-only</span></code></p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ggd search pfam cpg hg19
----------------------------------------------------------------------------------------------------
hg19-pfam-domains-ucsc-v1
<span class="o">=========================</span>
Summary: High quality, manually curated Pfam domain annotation in bed12 format from UCSC
Species: Homo_sapiens
Genome Build: hg19
Keywords: pfam, domains, protein, protein-domains, UCSC
Data Provider: UCSC
Data Version: <span class="m">16</span>-Apr-2017
File type<span class="o">(</span>s<span class="o">)</span>: bed
Data file coordinate base: <span class="m">0</span>-based-inclusive
Included Data Files:
hg19-pfam-domains-ucsc-v1.bed12.bed.gz
hg19-pfam-domains-ucsc-v1.bed12.bed.gz.tbi
Approximate Data File Sizes:
hg19-pfam-domains-ucsc-v1.bed12.bed.gz: <span class="m">1</span>.41M
hg19-pfam-domains-ucsc-v1.bed12.bed.gz.tbi: <span class="m">143</span>.50K
To install run:
ggd install hg19-pfam-domains-ucsc-v1
----------------------------------------------------------------------------------------------------
hg19-cpg-islands-ucsc-v1
<span class="o">========================</span>
Summary: cpg islands from UCSC in bed format. Scaffoldings that are not contained in the hg19.genome file are removed
Species: Homo_sapiens
Genome Build: hg19
Keywords: CpG, region, bed-file, cpg-islands, islands
Data Provider: UCSC
Data Version: <span class="m">22</span>-Mar-2020
File type<span class="o">(</span>s<span class="o">)</span>: bed
Data file coordinate base: <span class="m">0</span>-based-inclusive
Included Data Files:
hg19-cpg-islands-ucsc-v1.bed.gz
hg19-cpg-islands-ucsc-v1.bed.gz.tbi
Approximate Data File Sizes:
hg19-cpg-islands-ucsc-v1.bed.gz: <span class="m">621</span>.35K
hg19-cpg-islands-ucsc-v1.bed.gz.tbi: <span class="m">186</span>.06K
To install run:
ggd install hg19-cpg-islands-ucsc-v1
----------------------------------------------------------------------------------------------------
>>> Scroll up to see package details and install info <span class="o"><<<</span>
***************************
Package Name <span class="nv">Results</span>
<span class="o">====================</span>
hg19-pfam-domains-ucsc-v1
hg19-cpg-islands-ucsc-v1
NOTE: Name order matches order of packages in detailed section above
***************************
</pre></div>
</div>
</div>
<div class="section" id="example-refining-search-results-based-on-combined-terms">
<h3>6. Example refining search results based on combined terms<a class="headerlink" href="#example-refining-search-results-based-on-combined-terms" title="Permalink to this headline">¶</a></h3>
<p>In this example the <code class="code docutils literal notranslate"><span class="pre">--search-term</span></code> flag is set to <cite>combined-only</cite>. This is often done when you know which
package you want but don’t know the exact package name. This will refine the results to those based on a combination
of the terms provided.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>ggd search chrom sizes --search-type combined-only -dn <span class="m">8</span>
----------------------------------------------------------------------------------------------------
grch37-chromsizes-ggd-v1
<span class="o">========================</span>
Summary: Chromosome lengths <span class="k">for</span> GRCh37
Species: Homo_sapiens
Genome Build: GRCh37
Keywords: genome, chromosome, lengths, sizes
Data Provider: GGD
Data Version: <span class="m">16</span>-Apirl-2020
File type<span class="o">(</span>s<span class="o">)</span>: txt
Data file coordinate base: NA
Included Data Files:
grch37-chromsizes-ggd-v1.txt
Approximate Data File Sizes:
grch37-chromsizes-ggd-v1.txt: <span class="m">5</span>.17K
To install run:
ggd install grch37-chromsizes-ggd-v1
----------------------------------------------------------------------------------------------------
grch37-chromsizes-ncbi-v1
<span class="o">=========================</span>
Summary: Chromosome lengths <span class="k">for</span> the GRCh37 genome build from NCBI. <span class="o">(</span>Used to create the Go Get Data <span class="o">(</span>GGD<span class="o">)</span> GRCh37.genome file<span class="o">)</span>
Species: Homo_sapiens
Genome Build: GRCh37
Keywords: genome, chromosome, lengths, sizes, chrom-lengths
Data Provider: NCBI
Data Version: <span class="m">12</span>-October-2016-<span class="o">(</span>patch13<span class="o">)</span>
File type<span class="o">(</span>s<span class="o">)</span>: genome
Data file coordinate base: NA
Included Data Files:
grch37-chromsizes-ncbi-v1.genome
Approximate Data File Sizes:
grch37-chromsizes-ncbi-v1.genome: <span class="m">5</span>.17K
To install run:
ggd install grch37-chromsizes-ncbi-v1
----------------------------------------------------------------------------------------------------
grch38-chromsizes-ggd-v1
<span class="o">========================</span>
Summary: Chromosome lengths <span class="k">for</span> GRCh38
Species: Homo_sapiens
Genome Build: GRCh38
Keywords: genome, chromosome, lengths, sizes
Data Provider: GGD
Data Version: <span class="m">16</span>-April-2020
File type<span class="o">(</span>s<span class="o">)</span>: txt
Data file coordinate base: NA