Bio-WebService-LANL-SequenceLocator

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app.psgi  view on Meta::CPAN

            return error(406 => "format '$format' is not supported; try one of " . join(", ", @{$self->formats}))
                unless grep { $format eq $_ } @{$self->formats};

            sub (%fasta=) {
                my ($self, $fasta) = @_;
                return $self->locate_sequences_from_fasta($fasta, $base, $format);
            },
            sub (*fasta=) {
                my ($self, $fasta) = @_;
                return error(422 => $fasta->reason)
                    unless $fasta->is_upload;
                return $self->locate_sequences_from_fasta(path($fasta->path)->slurp, $base, $format);
            },
            sub (%@sequence~) {
                my ($self, $sequences) = @_;
                return $self->locate_sequences($sequences, $base, $format);
            },
        },
    },
    sub (GET + /within/hiv) {
        error( 405 => "You must make location requests using POST." )

lib/Bio/WebService/LANL/SequenceLocator/Server.pm  view on Meta::CPAN

            return error(406 => "format '$format' is not supported; try one of " . join(", ", @{$self->formats}))
                unless grep { $format eq $_ } @{$self->formats};

            sub (%fasta=) {
                my ($self, $fasta) = @_;
                return $self->locate_sequences_from_fasta($fasta, $base, $format);
            },
            sub (*fasta=) {
                my ($self, $fasta) = @_;
                return error(422 => $fasta->reason)
                    unless $fasta->is_upload;
                return $self->locate_sequences_from_fasta(path($fasta->path)->slurp, $base, $format);
            },
            sub (%@sequence~) {
                my ($self, $sequences) = @_;
                return $self->locate_sequences($sequences, $base, $format);
            },
        },
    },
    sub (GET + /within/hiv) {
        error( 405 => "You must make location requests using POST." )

share/about.html  view on Meta::CPAN

                    this API.  Get in touch if you need something that's
                    missing!
                </p>

                <h2>Endpoint</h2>
                <h3><code>POST .../within/hiv</code></h3>
                <p>
                    Requires one or more values for the POST parameter
                    <code>sequence</code> <em>or</em> a single-valued
                    <code>fasta</code> parameter as a URL-encoded string or
                    file upload of <a href="https://en.wikipedia.org/wiki/FASTA">FASTA</a>-formatted
                    sequences.
                </p>
                <p>
                    Both protein and nucleotide
                    sequences are accepted, although the data returned varies
                    by type due to what LANL returns.  See the
                    <a href="#curl">curl example</a> which queries a protein
                    sequence and the same sequence as nucleotides.  If you use
                    LANL's tool directly, the reverse complements of your
                    sequences will also be attempted and the best matching

share/about.html  view on Meta::CPAN

                <h2>Quick lookup</h2>
                <p>
                    Submit sequences as a FASTA file and download the location
                    results as a CSV file.  Note that the CSV does not contain
                    all of the information the API can provide since CSV does
                    not have standard support for nested or multi-valued data
                    structures.  This form uses the API described above.
                </p>
                <form action="within/hiv" method="POST" enctype="multipart/form-data" role="form" class="form-inline">
                    <div class="form-group">
                        <label for="fasta-upload">FASTA file</label>
                        <input type="file" id="fasta-upload" name="fasta" style="width: 15em"></label>
                    </div>
                    <div class="form-group">
                        <label><input type="radio" name="base" value="nuc"> Nucleotides</label><br>
                        <label><input type="radio" name="base" value="aa"> Amino acids</label>
                    </div>
                    <input type="hidden" name="format" value="csv">
                    <button type="submit" class="btn btn-default">Submit</button>
                </form>

                <hr>