templates

jeremy/scripts/templates/load_tab_delimited_file.pl

@@ -0,0 +1,139 @@
+#!/usr/bin/perl
+
+=head1
+
+load_tab_delimited_file.pl
+
+=head1 SYNOPSIS
+
+    load_tab_delimited_file.pl -i [input tab-delimited file] -t
+
+=head1 COMMAND-LINE OPTIONS
+
+ -i  tab-delimited data file
+ -n  no header in input file (default: expect header)
+ -h  Help
+
+=cut
+
+use strict;
+use Getopt::Std;
+
+my $file_name;
+my @example_header;
+my @loaded_data;
+my $use_header = 1;
+my @data;
+my $data_row;
+my $cell;
+our ($opt_i, $opt_n, $opt_h);
+
+getopts('hni:');
+if ($opt_h) {
+  help();
+  exit;
+}
+if ($opt_n) {
+  $use_header = 0;
+}
+if (!$opt_i) {
+  print STDERR "\nFilename required\n\n\n";
+  help();
+}
+
+$file_name = $opt_i;
+@example_header = qw(field_a field_b field_c);
+if ($use_header == 1) {
+  @data = load_file($file_name,@example_header);
+}
+else {
+  @data = load_file($file_name);
+}
+foreach $data_row (@data) {
+  my @row = @{$data_row};
+  foreach $cell (@row) {
+    print "$cell\t";
+  }
+  print "\n";
+}
+
+sub load_file {
+  my $name_of_file_to_load = shift;
+  my @expected_header = shift;
+  my @header;
+  my @loaded_data;
+  my %bad_header_fields;
+  my $array_counter = 0;
+  my $current_line = 1;
+  open FILE, "<", $name_of_file_to_load or die $!;
+  @loaded_data = map { chomp; [split /\t/];} <FILE>;
+  if ($expected_header[0]) {
+    @header = @{shift @loaded_data};
+    if (@header < @expected_header) {
+      print STDERR @header;
+      die "Header has too few fields\n";
+    }
+    while ($array_counter < @expected_header) {
+      if ($header[$array_counter] ne $expected_header[$array_counter]) {
+	$bad_header_fields{$expected_header[$array_counter]} = $header[$array_counter];
+      }
+      $array_counter++;
+    }
+    if (%bad_header_fields) {
+      foreach my $bad_field (keys %bad_header_fields) {
+	print STDERR "Header field ".$bad_header_fields{$bad_field}." is incorrect.  Expected ".$bad_field."\n";
+      }
+      die;
+    }
+  }
+  #remove trailing blank lines
+  while (@{$loaded_data[-1]} == 0) {
+      pop (@loaded_data);
+  }
+  #check that each row has the same number of cells
+  foreach my $data_line (@loaded_data) {
+    if (@{$data_line} != @{$loaded_data[0]}) {
+      die "Line $current_line has the wrong number of cells.  Expected ".@{$loaded_data[0]}." and found ".@{$data_line}."\n";
+      $current_line++;
+    }
+  }
+  return @loaded_data;
+}
+
+sub help {
+  print STDERR <<EOF;
+  $0:
+
+    Description:
+
+     This is a template script for loading data from a tab-delimited file.
+
+    Usage:
+     
+      load_tab_delimited_file.pl -i <tab-delimited file name>
+
+    Flags:
+
+      -i <tab-delimited file name>  input data file (mandatory)
+      -n                            no header included in input file
+      -h <help>                     help
+
+EOF
+  exit (1);
+}
+
+=pod
+
+  =back
+
+  =head1 LICENSE
+
+  Same as Perl.
+
+  =head1 AUTHORS
+
+  Jeremy D. Edwards <jde22@cornell.edu>
+
+  =cut
+
+