# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+use warnings;
use strict;
use vars qw ( @ISA @EXPORT );
}
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSL format <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-sub psl_get_entry
-{
- # Martin A. Hansen, August 2008.
-
- # Reads PSL next entry from a PSL file and returns a record.
-
- my ( $fh, # file handle of PSL filefull path to PSL file
- ) = @_;
-
- # Returns hashref.
-
- my ( $line, @fields, %record );
-
- while ( $line = <$fh> )
- {
- chomp $line;
-
- @fields = split "\t", $line;
-
- if ( scalar @fields == 21 )
- {
- %record = (
- REC_TYPE => "PSL",
- MATCHES => $fields[ 0 ],
- MISMATCHES => $fields[ 1 ],
- REPMATCHES => $fields[ 2 ],
- NCOUNT => $fields[ 3 ],
- QNUMINSERT => $fields[ 4 ],
- QBASEINSERT => $fields[ 5 ],
- SNUMINSERT => $fields[ 6 ],
- SBASEINSERT => $fields[ 7 ],
- STRAND => $fields[ 8 ],
- Q_ID => $fields[ 9 ],
- Q_LEN => $fields[ 10 ],
- Q_BEG => $fields[ 11 ],
- Q_END => $fields[ 12 ] - 1,
- S_ID => $fields[ 13 ],
- S_LEN => $fields[ 14 ],
- S_BEG => $fields[ 15 ],
- S_END => $fields[ 16 ] - 1,
- BLOCK_COUNT => $fields[ 17 ],
- BLOCK_LENS => $fields[ 18 ],
- Q_BEGS => $fields[ 19 ],
- S_BEGS => $fields[ 20 ],
- );
-
- $record{ "SCORE" } = $record{ "MATCHES" } + int( $record{ "REPMATCHES" } / 2 ) - $record{ "MISMATCHES" } - $record{ "QNUMINSERT" } - $record{ "SNUMINSERT" };
- $record{ "Q_SPAN" } = $fields[ 12 ] - $fields[ 11 ];
- $record{ "S_SPAN" } = $fields[ 16 ] - $fields[ 15 ];
-
- return wantarray ? %record : \%record;
- }
- }
-
- return undef;
-}
-
-
-sub psl_get_entries
-{
- # Martin A. Hansen, February 2008.
-
- # Reads PSL entries and returns a list of records.
-
- my ( $path, # full path to PSL file
- ) = @_;
-
- # Returns hashref.
-
- my ( $fh, @lines, @fields, $i, %record, @records );
-
- $fh = Maasha::Common::read_open( $path );
-
- @lines = <$fh>;
-
- close $fh;
-
- chomp @lines;
-
- for ( $i = 5; $i < @lines; $i++ )
- {
- @fields = split "\t", $lines[ $i ];
-
- Maasha::Common::error( qq(Bad PSL format in file "$path") ) if not @fields == 21;
-
- undef %record;
-
- %record = (
- REC_TYPE => "PSL",
- MATCHES => $fields[ 0 ],
- MISMATCHES => $fields[ 1 ],
- REPMATCHES => $fields[ 2 ],
- NCOUNT => $fields[ 3 ],
- QNUMINSERT => $fields[ 4 ],
- QBASEINSERT => $fields[ 5 ],
- SNUMINSERT => $fields[ 6 ],
- SBASEINSERT => $fields[ 7 ],
- STRAND => $fields[ 8 ],
- Q_ID => $fields[ 9 ],
- Q_LEN => $fields[ 10 ],
- Q_BEG => $fields[ 11 ],
- Q_END => $fields[ 12 ] - 1,
- S_ID => $fields[ 13 ],
- S_LEN => $fields[ 14 ],
- S_BEG => $fields[ 15 ],
- S_END => $fields[ 16 ] - 1,
- BLOCK_COUNT => $fields[ 17 ],
- BLOCK_LENS => $fields[ 18 ],
- Q_BEGS => $fields[ 19 ],
- S_BEGS => $fields[ 20 ],
- );
-
- $record{ "SCORE" } = $record{ "MATCHES" } + int( $record{ "REPMATCHES" } / 2 ) - $record{ "MISMATCHES" } - $record{ "QNUMINSERT" } - $record{ "SNUMINSERT" };
-
- push @records, { %record };
- }
-
- return wantarray ? @records : \@records;
-}
-
-
-sub psl_put_header
-{
- # Martin A. Hansen, September 2007.
-
- # Write a PSL header to file.
-
- my ( $fh, # file handle - OPTIONAL
- ) = @_;
-
- # Returns nothing.
-
- $fh = \*STDOUT if not $fh;
-
- print $fh qq(psLayout version 3
-match mis- rep. N's Q gap Q gap T gap T gap strand Q Q Q Q T T T T block blockSizes qStart match match count bases count bases name size start end name size start end count
----------------------------------------------------------------------------------------------------------------------------------------------------------------
-);
-}
-
-
-sub psl_put_entry
-{
- # Martin A. Hansen, September 2007.
-
- # Write a PSL entry to file.
-
- my ( $record, # hashref
- $fh, # file handle - OPTIONAL
- ) = @_;
-
- # Returns nothing.
-
- $fh = \*STDOUT if not $fh;
-
- my @output;
-
- push @output, $record->{ "MATCHES" };
- push @output, $record->{ "MISMATCHES" };
- push @output, $record->{ "REPMATCHES" };
- push @output, $record->{ "NCOUNT" };
- push @output, $record->{ "QNUMINSERT" };
- push @output, $record->{ "QBASEINSERT" };
- push @output, $record->{ "SNUMINSERT" };
- push @output, $record->{ "SBASEINSERT" };
- push @output, $record->{ "STRAND" };
- push @output, $record->{ "Q_ID" };
- push @output, $record->{ "Q_LEN" };
- push @output, $record->{ "Q_BEG" };
- push @output, $record->{ "Q_END" } + 1;
- push @output, $record->{ "S_ID" };
- push @output, $record->{ "S_LEN" };
- push @output, $record->{ "S_BEG" };
- push @output, $record->{ "S_END" } + 1;
- push @output, $record->{ "BLOCK_COUNT" };
- push @output, $record->{ "BLOCK_LENS" };
- push @output, $record->{ "Q_BEGS" };
- push @output, $record->{ "S_BEGS" };
-
- print $fh join( "\t", @output ), "\n";
-}
-
-
sub psl_upload_to_ucsc
{
# Martin A. Hansen, September 2007.
# Given a PhastCons entry converts this to a
# list of super blocks.
+# $options->{ "min" } ||= 10;
+# $options->{ "dist" } ||= 25;
+# $options->{ "threshold" } ||= 0.8;
+# $options->{ "gap" } ||= 5;
+
my ( $lines, # list of lines
$args, # argument hash
) = @_;
# Normalizes a list of lists with PhastCons scores,
# in such a way that each list contains the same number
- # or PhastCons scores.
+ # of PhastCons scores.
my ( $AoA, # AoA with PhastCons scores
) = @_;
# splice @{ $list }, $pos, 0, "X";
}
- die qq(ERROR: bad inflate\n) if scalar @{ $list } != $len + $diff;
+ die qq(ERROR: Bad inflate\n) if scalar @{ $list } != $len + $diff;
}
splice @{ $list }, $pos, 1;
}
- die qq(ERROR: bad deflate\n) if scalar @{ $list } != $len - $diff;
+ die qq(ERROR: Dad deflate\n) if scalar @{ $list } != $len - $diff;
}
# Returns a string.
- my ( $fh, $line, $user );
+ my ( $file, $fh, $line, $user );
- $fh = Maasha::Common::read_open( "$ENV{ 'HOME' }/.hg.conf" );
+ $file = "$ENV{ 'HOME' }/.hg.conf";
+
+ return if not -f $file;
+
+ $fh = Maasha::Common::read_open( $file );
while ( $line = <$fh> )
{
# Returns a string.
- my ( $fh, $line, $password );
+ my ( $file, $fh, $line, $password );
+
+ $file = "$ENV{ 'HOME' }/.hg.conf";
+
+ return if not -f $file;
- $fh = Maasha::Common::read_open( "$ENV{ 'HOME' }/.hg.conf" );
+ $fh = Maasha::Common::read_open( $file );
while ( $line = <$fh> )
{
projects / biopieces.git / blobdiff