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| 1 : | parrello | 1.1 | =head1 Return Data From Contigs in PATRIC |
| 2 : | |||
| 3 : | p3-get-genome-contigs [options] | ||
| 4 : | |||
| 5 : | This script returns data about the contigs for the genomes identified in the standard input. It supports standard filtering | ||
| 6 : | parameters and the specification of additional columns if desired. | ||
| 7 : | |||
| 8 : | =head2 Parameters | ||
| 9 : | |||
| 10 : | There are no positional parameters. | ||
| 11 : | |||
| 12 : | parrello | 1.2 | The standard input can be overriddn using the options in L<P3Utils/ih_options>. |
| 13 : | parrello | 1.1 | |
| 14 : | parrello | 1.2 | Additional command-line options are those given in L<P3Utils/data_options> and L<P3Utils/col_options> plus the following. |
| 15 : | |||
| 16 : | =over 4 | ||
| 17 : | |||
| 18 : | =item fields | ||
| 19 : | |||
| 20 : | Display the available field names. | ||
| 21 : | |||
| 22 : | =back | ||
| 23 : | parrello | 1.1 | |
| 24 : | =cut | ||
| 25 : | |||
| 26 : | use strict; | ||
| 27 : | use P3DataAPI; | ||
| 28 : | use P3Utils; | ||
| 29 : | |||
| 30 : | # Get the command-line options. | ||
| 31 : | my $opt = P3Utils::script_opts('', P3Utils::data_options(), P3Utils::col_options(), P3Utils::ih_options(), | ||
| 32 : | ['fields|f', 'Show available fields']); | ||
| 33 : | |||
| 34 : | parrello | 1.5 | # Get access to PATRIC. |
| 35 : | my $p3 = P3DataAPI->new(); | ||
| 36 : | parrello | 1.1 | my $fields = ($opt->fields ? 1 : 0); |
| 37 : | if ($fields) { | ||
| 38 : | print_usage(); | ||
| 39 : | exit(); | ||
| 40 : | } | ||
| 41 : | # Compute the output columns. | ||
| 42 : | parrello | 1.3 | my ($selectList, $newHeaders) = P3Utils::select_clause($p3, contig => $opt); |
| 43 : | parrello | 1.1 | # Compute the filter. |
| 44 : | my $filterList = P3Utils::form_filter($opt); | ||
| 45 : | # Open the input file. | ||
| 46 : | my $ih = P3Utils::ih($opt); | ||
| 47 : | # Read the incoming headers. | ||
| 48 : | my ($outHeaders, $keyCol) = P3Utils::process_headers($ih, $opt); | ||
| 49 : | # Form the full header set and write it out. | ||
| 50 : | parrello | 1.2 | if (! $opt->nohead) { |
| 51 : | push @$outHeaders, @$newHeaders; | ||
| 52 : | P3Utils::print_cols($outHeaders); | ||
| 53 : | } | ||
| 54 : | parrello | 1.1 | # Loop through the input. |
| 55 : | while (! eof $ih) { | ||
| 56 : | my $couplets = P3Utils::get_couplets($ih, $keyCol, $opt); | ||
| 57 : | # Get the output rows for these input couplets. | ||
| 58 : | my $resultList = P3Utils::get_data($p3, contig => $filterList, $selectList, genome_id => $couplets); | ||
| 59 : | # Print them. | ||
| 60 : | for my $result (@$resultList) { | ||
| 61 : | P3Utils::print_cols($result); | ||
| 62 : | } | ||
| 63 : | } | ||
| 64 : | |||
| 65 : | sub print_usage { | ||
| 66 : | parrello | 1.4 | my $fieldList = P3Utils::list_object_fields($p3, 'contig'); |
| 67 : | parrello | 1.1 | print join("\n", @$fieldList, ""); |
| 68 : | } |
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