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-<title>Jalview Command Line Arguments (next generation)</title>
-<body>
-
- <h1>Jalview Command Line Arguments (next generation)</h1>
-
- <p>
- For a summary of Jalview command line arguments see <a href="clarguments-ng-summary.html">Summary
- of Command Line Arguments</a>.
- </p>
-
- <p>
- From version 2.11.3.0 Jalview processes a new set of command line arguments
- which allow more powerful and flexible combinations of arguments, though can
- also be used for very simple use cases too.
- </p>
-
- <p>
- These new arguments are all accessed with a <code>--doubledash</code> form of
- command line argument (with the one exception where simply opening one or more
- files can be performed without any arguments other than the filenames).
- </p>
-
- <p>
- The old command line arguments can still be used (see
- <a href="clarguments.html">the old page on command line arguments</a>) so
- existing scripts utilising them should not break. <strong>These will be removed</strong> in a future version of Jalview.
- </p>
-
- <p>
- However, you cannot mix old and new style arguments, so if you use any
- <code>-singledash</code> arguments, they will all be interpreted as
- old style arguments with the new <code>--doubledash</code>
- arguments being ignored. If you have a script
- that uses the old arguments without any dashes, and uses the bare-word
- <code>open</code> then these will also be interpreted as old style arguments.
- <br/>
- <strong>Note!</strong> If you use command line arguments without any dashes and
- <em>don't</em> use the bare-word argument <code>open</code> then all
- your arguments will be interpreted as alignment files to be opened by the
- new command line argument process!
- </p>
-
- <p>
- Not everything that can be done with the old arguments is currently implemented in the new arguments but functionality of the new command line arguments will increase over releases. Significant new functionality, particularly allowing batch processing of files, is available in the new arguments.
- </p>
-
- <p>
- To launch Jalview from the command line, see
- <a href="commandline.html">running Jalview from the command line</a>.
- </p>
-
-
- <h2>Processing command line arguments</h2>
-
- <p>
- Jalview no longer necessarily processes arguments sequentially, although
- in typical use cases you may still want to think of it as doing so.
- <br/>
- For more advanced use please see
- <!--<a href="advancedclarguments.html">Advanced Command Line Arguments</a>.-->
- </p>
-
-
- <h3>Typical Use Cases</h3>
-
- <h4 name="opening_files">Opening files (<code>--open</code>, <code>--append</code>, <code>--new</code>)</h4>
-
- <p>
- To simply open one or more alignment files in different windows just put the filenames as the first arguments:
- <pre>
- jalview filename1 filename2 ...
- </pre>
- </p>
-
- <p>
- You can use shell-expanded wildcards:
- <pre>
- jalview this/filename* that/filename* other/filename*
- </pre>
- and URLs:
- <pre>
- jalview https://rest.uniprot.org/uniprotkb/P00221.fasta
- </pre>
- </p>
-
- <p>
- (Using initial filenames is the same as using the <code>--open</code> argument, and further arguments can be used
- after the initial filenames.)
- </p>
-
- <h5 name="open"><code>--open</code></h5>
-
- <p>
- Use the <code>--open</code> argument to open alignment files each in their own window.
- </p>
-
- <p>
- The following are equivalent:
- <pre>
- jalview --open filename1 filename2 ...
-
- jalview --open filename*
-
- jalview --open filename1 --open filename2 --open ...
-
- jalview filename1 filename2 ...
- </pre>
- </p>
-
- <p>
- Similarly you can open URLs:
- <pre>
- jalview --open https://rest.uniprot.org/uniprotkb/P00221.fasta
- </pre>
- </p>
-
- <h5 name="append"><code>--append</code></h5>
-
- <p>
- To append several alignment files together use:
- <pre>
- jalview --open filename1.fa --append filename2.fa filename3.fa
- </pre>
- or, if you haven't previously used <code>--open</code> then you can use --append to open one new window and keep appending each set of alignments:
- <pre>
- jalview --append these/filename*.fa --append more/filename*.fa
-
- jalview --append https://rest.uniprot.org/uniprotkb/P00221.fasta https://www.uniprot.org/uniprotkb/A0A0K9QVB3/entry
- </pre>
- </p>
-
- <p>
- <strong>Note</strong> that whilst you can include a Jalview Project File (<code>.jvp</code>) as an <code>--append</code> value, the items in the file will always open in their original windows and not append to another.
- </p>
-
- <h5 name="new"><code>--new</code></h5>
-
- <p>
- To append different sets of alignment files in different windows, use <code>--new</code> to move on to a new alignment window:
- <pre>
- jalview --append these/filename*.fa --new --append other/filename*.fa
- </pre>
- </p>
-
- <p>
- <code>--open</code> is like using <code>--new --append</code> applied to every filename/URL given to <code>--open</code>
- </p>
-
-
- <h4 name="alignmentoptions">Alignment options (<code>--colour, --wrap</code>)</h4>
-
- <h5 name="colour"><code>--colour</code></h5>
-
- <p>
- You can specify a residue/base colouring for the alignment using the <code>--colour</code> option (note spelling -- Jalview is made in Scotland!):
- <pre>
- jalview --open examples/uniref50.fa --colour gecos-flower
- </pre>
- There are several colour schemes that you can use. See the <a href="../colourSchemes/index.html">page on Colour Schemes</a> for details.
- The names to use on the command line for colour schemes are:
- </p>
- <p>
- <code>clustal</code>,
- <br/>
- <code>blosum62</code>,
- <br/>
- <code>pc-identity</code>,
- <br/>
- <code>zappo</code>,
- <br/>
- <code>taylor</code>,
- <br/>
- <code>gecos-flower</code>,
- <br/>
- <code>gecos-blossom</code>,
- <br/>
- <code>gecos-sunset</code>,
- <br/>
- <code>gecos-ocean</code>,
- <br/>
- <code>hydrophobic</code>,
- <br/>
- <code>helix-propensity</code>,
- <br/>
- <code>strand-propensity</code>,
- <br/>
- <code>turn-propensity</code>,
- <br/>
- <code>buried-index</code>,
- <br/>
- <code>nucleotide</code>,
- <br/>
- <code>nucleotide-ambiguity</code>,
- <br/>
- <code>purine-pyrimidine</code>,
- <br/>
- <code>rna-helices</code>,
- <br/>
- <code>t-coffee-scores</code>,
- <br/>
- <code>sequence-id</code>
- </p>
-
- <h5 name="wrap"><code>--wrap</code></h5>
- <p>
- An alignment should open with your usual preferences stored in the <code>.jalview_properties</code> file. To open an alignment with the sequences (definitely) wrapped, following your <code>--open</code> (or first <code>--append</code>) argument use the argument <code>--wrap</code>:
- <pre>
- jalview --open examples/uniref50.fa --wrap
- </pre>
- To ensure an alignment is not wrapped use <code>--nowrap</code>:
- <pre>
- jalview --open examples/uniref50.fa --nowrap
- </pre>
- </p>
-
- <h5 name="annotations"><code>--annotations</code></h5>
-
- <p>
- You can specify whether the currently opened alignment window should show alignment annotations (e.g. Conservation, Quality, Consensus...) or not with either <code>--annotations</code> or <code>--noannotations</code>. If you don't specify then your saved preference will be used.
- <pre>
- jalview --open examples/uniref50.fa --noannotations
- </pre>
- </p>
-
- <h5 name="title"><code>--title</code></h5>
-
- <p>
- If you would like to give the alignment window a specific title you can do so with the <code>--title</code> option:
- <pre>
- jalview --open examples/uniref50.fa --title "My example alignment"
- </pre>
- </p>
-
- <h5 name=""><code>--structure</code></h5>
-
- <p>
- You can add a 3D structure file to a sequence in the current alignment window with the <code>--structure</code> option:
- <pre>
- jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb
- </pre>
- </p>
-
-
- <p>
- <code>seqid</code>:
- By default this attaches to the first sequence in the alignment but most likely you will want to attach it to another sequence.
- To do this you can specify a <em>sub-value</em> with the sequence ID, by preceding the value with square brackets and <code>seqid=SequenceId</code>
- like this:
- <pre>
- jalview --open examples/uniref50.fa --structure [seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
- </pre>
-
- Remember that you might need to escape any spaces in the sequence ID or enclose the ID in quotation marks.
- </p>
-
- <p>
- <em><code>index</code></em>:
- You can alternatively specify the (zero-indexed) index of the sequence within the alignment, although this is less precise. So to attach the structure to the 8th sequence use:
- <pre>
- jalview --open examples/uniref50.fa --structure [7]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
- </pre>
- </p>
-
- <p>
- <code>structureviewer</code>:
- You can specify which structure viewer (or not) to use to open the structure using the <code>structureviewer</code> sub-value. Multiple sub-values can be specified, separated by a comma ','. Possible values for the <code>structureviewer</code> sub-value are:
- <br/>
- <code>none</code>,
- <br/>
- <code>jmol</code>,
- <br/>
- <code>chimera</code>,
- <br/>
- <code>chimerax</code>,
- <br/>
- <code>pymol</code>.
- </p>
- <p>
- <code>none</code> and <code>jmol</code> will always be available, but to use the others you must have the appropriate software already set up on your computer and in Jalview. See the page <a href="../features/viewingpdbs.html">Discovering and Viewing PDB and 3D-Beacons structures</a> for more details.
- <pre>
- jalview --open examples/uniref50.fa --structure [seqid=FER1_SPIOL,structureviewer=none]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
- </pre>
- </p>
-
-
- <h4 name="">(<code></code>)</h4>
-
- <p>
- </p>
-
- <h5 name=""><code>--</code></h5>
-
- <p>
- <pre>
- </pre>
- </p>
-
-
-
-
-
-
-</body>
-</html>
git://source.jalview.org / jalview.git / blobdiff