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| 1 : | overbeek | 1.1 | use strict; |
| 2 : | use Data::Dumper; | ||
| 3 : | use Carp; | ||
| 4 : | |||
| 5 : | # | ||
| 6 : | # This is a SAS Component | ||
| 7 : | # | ||
| 8 : | |||
| 9 : | |||
| 10 : | =head1 svr_is_hypo [-c N] [-v] | ||
| 11 : | |||
| 12 : | Keep just hypotheticals | ||
| 13 : | |||
| 14 : | ------ | ||
| 15 : | |||
| 16 : | Example: | ||
| 17 : | |||
| 18 : | svr_all_features 3702.1 peg | svr_is_hypo | ||
| 19 : | |||
| 20 : | would produce a 1-column table containing the hypotheticals in 3702.1 | ||
| 21 : | |||
| 22 : | overbeek | 1.3 | Normally, a stream of feature IDs (PEGs) is used as input. If the things you send |
| 23 : | through do not look like PEGs, then they are treated as functional roles. | ||
| 24 : | |||
| 25 : | overbeek | 1.1 | ------ |
| 26 : | |||
| 27 : | The standard input should be a tab-separated table (i.e., each line | ||
| 28 : | is a tab-separated set of fields). Normally, the last field in each | ||
| 29 : | line would contain the PEG . If some other column contains the PEGs, use | ||
| 30 : | |||
| 31 : | -c N | ||
| 32 : | |||
| 33 : | where N is the column (from 1) that contains the PEG in each case. | ||
| 34 : | |||
| 35 : | This is a pipe command. The input is taken from the standard input, and the | ||
| 36 : | output is to the standard output. | ||
| 37 : | |||
| 38 : | =head2 Command-Line Options | ||
| 39 : | |||
| 40 : | =over 4 | ||
| 41 : | |||
| 42 : | =item -c Column | ||
| 43 : | |||
| 44 : | This is used only if the column containing PEGs is not the last. | ||
| 45 : | |||
| 46 : | parrello | 1.2 | =item -v [keep only non-hypotheticals] |
| 47 : | overbeek | 1.1 | |
| 48 : | =back | ||
| 49 : | |||
| 50 : | =head2 Output Format | ||
| 51 : | |||
| 52 : | This is a filter producing a subset of the input lines. | ||
| 53 : | |||
| 54 : | =cut | ||
| 55 : | |||
| 56 : | use SeedUtils; | ||
| 57 : | use SAPserver; | ||
| 58 : | my $sapObject = SAPserver->new(); | ||
| 59 : | use Getopt::Long; | ||
| 60 : | |||
| 61 : | my $usage = "usage: svr_is_hypo [-c column] [-v]"; | ||
| 62 : | |||
| 63 : | my $column; | ||
| 64 : | my $v; | ||
| 65 : | my $rc = GetOptions('c=i' => \$column, | ||
| 66 : | 'v' => \$v); | ||
| 67 : | if (! $rc) { print STDERR $usage; exit } | ||
| 68 : | |||
| 69 : | my @lines = map { chomp; [split(/\t/,$_)] } <STDIN>; | ||
| 70 : | (@lines > 0) || exit; | ||
| 71 : | if (! $column) { $column = @{$lines[0]} } | ||
| 72 : | overbeek | 1.3 | my @fids = grep { $_ =~ /^fig\|/ } map { $_->[$column-1] } @lines; |
| 73 : | overbeek | 1.1 | |
| 74 : | my $functions = $sapObject->ids_to_functions(-ids => \@fids); | ||
| 75 : | foreach $_ (@lines) | ||
| 76 : | { | ||
| 77 : | overbeek | 1.3 | my $thing = $_->[$column-1]; |
| 78 : | my $func; | ||
| 79 : | if ($thing =~ /^fig\|/) | ||
| 80 : | { | ||
| 81 : | $func = $functions->{$thing}; | ||
| 82 : | } | ||
| 83 : | else | ||
| 84 : | { | ||
| 85 : | $func = $thing; | ||
| 86 : | } | ||
| 87 : | overbeek | 1.1 | my $hypo = &SeedUtils::hypo($func); |
| 88 : | if (((! $v) && $hypo) || ($v && (! $hypo))) | ||
| 89 : | { | ||
| 90 : | print join("\t",@$_),"\n"; | ||
| 91 : | } | ||
| 92 : | } |
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