| 666 |
|
|
| 667 |
=cut |
=cut |
| 668 |
|
|
|
## |
|
| 669 |
sub verify_dir { |
sub verify_dir { |
| 670 |
my($dir) = @_; |
my($dir) = @_; |
| 671 |
|
|
| 696 |
(system($cmd) == 0) || confess "FAILED: $cmd"; |
(system($cmd) == 0) || confess "FAILED: $cmd"; |
| 697 |
} |
} |
| 698 |
|
|
| 699 |
|
|
| 700 |
|
|
| 701 |
|
=pod |
| 702 |
|
|
| 703 |
|
=head1 read_fasta_record(\*FILEHANDLE) |
| 704 |
|
|
| 705 |
|
Usage: ( $seq_id, $sequence, $comment ) = &read_fasta_record(\*FILEHANDLE); |
| 706 |
|
|
| 707 |
|
Function: Reads a FASTA-formatted sequence file one record at a time. |
| 708 |
|
The input filehandle defaults to STDIN if not specified. |
| 709 |
|
Returns a sequence ID, a pointer to the sequence, and an optional |
| 710 |
|
record comment (NOTE: Record comments are deprecated, as some tools |
| 711 |
|
such as BLAST do not handle them gracefully). Returns an empty list |
| 712 |
|
if attempting to read a record results in an undefined value |
| 713 |
|
(e.g., due to reaching the EOF). |
| 714 |
|
|
| 715 |
|
Author: Gordon D. Pusch |
| 716 |
|
|
| 717 |
|
Date: 2004-Feb-18 |
| 718 |
|
|
| 719 |
|
=cut |
| 720 |
|
|
| 721 |
|
sub read_fasta_record |
| 722 |
|
{ |
| 723 |
|
my ($file_handle) = @_; |
| 724 |
|
my ( $old_end_of_record, $fasta_record, @lines, $head, $sequence, @parsed_fasta_record ); |
| 725 |
|
|
| 726 |
|
if (not defined($file_handle)) { $file_handle = \*STDIN; } |
| 727 |
|
|
| 728 |
|
$old_end_of_record = $/; |
| 729 |
|
$/ = "\n>"; |
| 730 |
|
|
| 731 |
|
if (defined($fasta_record = <$file_handle>)) |
| 732 |
|
{ |
| 733 |
|
chomp $fasta_record; |
| 734 |
|
@lines = split( /\n/, $fasta_record ); |
| 735 |
|
$head = shift @lines; |
| 736 |
|
$head =~ s/^>?//; |
| 737 |
|
$head =~ m/^(\S+)/; |
| 738 |
|
$seq_id = $1; |
| 739 |
|
|
| 740 |
|
if ($head =~ m/^\S+\s+(.*)$/) { $comment = $1; } else { $comment = ""; } |
| 741 |
|
|
| 742 |
|
$sequence = join( "", @lines ); |
| 743 |
|
|
| 744 |
|
@parsed_fasta_record = ( $seq_id, \$sequence, $comment ); |
| 745 |
|
} |
| 746 |
|
else |
| 747 |
|
{ |
| 748 |
|
@parsed_fasta_record = (); |
| 749 |
|
} |
| 750 |
|
|
| 751 |
|
$/ = $old_end_of_record; |
| 752 |
|
|
| 753 |
|
return @parsed_fasta_record; |
| 754 |
|
} |
| 755 |
|
|
| 756 |
|
|
| 757 |
=pod |
=pod |
| 758 |
|
|
| 759 |
=head1 display_id_and_seq |
=head1 display_id_and_seq |
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