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Now you can specify '-' instead of input file name, and the script will read from stdin 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1422 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-08-14 20:30:56 +00:00
parent 0ec581080c
commit 843d7e6c8f
1 changed files with 13 additions and 3 deletions
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16
perl/sortByRef.pl
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@ -14,6 +14,10 @@ sub usage {
print " The sort is stable. If -k option is not specified,\n"; print " The sort is stable. If -k option is not specified,\n";
print " it is assumed that the contig name is the first\n"; print " it is assumed that the contig name is the first\n";
print " field in each line.\n\n"; print " field in each line.\n\n";
print " INPUT input file to sort. If '-' is specified, \n";
print " then reads from STDIN.\n";
print " REF_DICT .fai file, or ANY file that has contigs, in the\n";
print " desired soting order, as its first column.\n";
print " --k POS : contig name is in the field POS (1-based)\n"; print " --k POS : contig name is in the field POS (1-based)\n";
print " of input lines.\n\n"; print " of input lines.\n\n";
@ -35,6 +39,7 @@ if ( scalar(@ARGV) != 2 ) {
my $input_file = $ARGV[0]; my $input_file = $ARGV[0];
my $dict_file = $ARGV[1]; my $dict_file = $ARGV[1];
open(DICT, "< $dict_file") or die("Can not open $dict_file: $!"); open(DICT, "< $dict_file") or die("Can not open $dict_file: $!");
my %ref_order; my %ref_order;
@ -52,11 +57,16 @@ while ( <DICT> ) {
close DICT; close DICT;
#we have loaded contig ordering now #we have loaded contig ordering now
open(INPUT, "< $input_file") or die("Can not open $input_file: $!"); my $INPUT;
if ($input_file eq "-" ) {
$INPUT = "STDIN";
} else {
open($INPUT, "< $input_file") or die("Can not open $input_file: $!");
}
my %temp_outputs; my %temp_outputs;
while ( <INPUT> ) { while ( <$INPUT> ) {
my @fields = split '\s'; my @fields = split '\s';
die("Specified field position exceeds the number of fields:\n$_") die("Specified field position exceeds the number of fields:\n$_")
@ -93,7 +103,7 @@ while ( <INPUT> ) {
print $fhandle $_; # send current line to its corresponding temp file print $fhandle $_; # send current line to its corresponding temp file
} }
close INPUT; close $INPUT;
foreach my $f ( values %temp_outputs ) { close $f; } foreach my $f ( values %temp_outputs ) { close $f; }