[Bio] / FigKernelScripts / p3-get-genome-contigs.pl Repository:
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revision 1.1, Tue Jul 11 18:15:43 2017 UTC revision 1.2, Tue Aug 8 19:18:41 2017 UTC
# Line 9  Line 9 
9    
10  There are no positional parameters.  There are no positional parameters.
11    
12  The standard input can be overwritten using the options in L<P3Utils/ih_options>.  The standard input can be overriddn using the options in L<P3Utils/ih_options>.
13    
14  Additional command-line options are those given in L<P3Utils/data_options> and L<P3Utils/col_options>.  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    
24  =cut  =cut
25    
# Line 39  Line 47 
47  # Read the incoming headers.  # Read the incoming headers.
48  my ($outHeaders, $keyCol) = P3Utils::process_headers($ih, $opt);  my ($outHeaders, $keyCol) = P3Utils::process_headers($ih, $opt);
49  # Form the full header set and write it out.  # Form the full header set and write it out.
50    if (! $opt->nohead) {
51  push @$outHeaders, @$newHeaders;  push @$outHeaders, @$newHeaders;
52  P3Utils::print_cols($outHeaders);  P3Utils::print_cols($outHeaders);
53    }
54  # Loop through the input.  # Loop through the input.
55  while (! eof $ih) {  while (! eof $ih) {
56      my $couplets = P3Utils::get_couplets($ih, $keyCol, $opt);      my $couplets = P3Utils::get_couplets($ih, $keyCol, $opt);

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