Bio-ToolBox

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scripts/bam2wig.pl  view on Meta::CPAN

# Command line options
GetOptions(
	'i|in=s'            => \@bamfiles,           # one or more bam files
	'o|out=s'           => \$outfile,            # name of output file
	's|start!'          => \$use_start,          # record start point
	'd|mid!'            => \$use_mid,            # record mid point
	'a|span!'           => \$use_span,           # record span
	'cspan!'            => \$use_cspan,          # record center span
	'e|extend!'         => \$use_extend,         # extend read
	'smartcov!'         => \$use_smartpe,        # smart paired coverage
	'ends!'             => \$use_ends,           # record paired-end endpoints
	'coverage!'         => \$use_coverage,       # calculate coverage
	'position=s'        => \$position,           # legacy option
	'l|splice|split!'   => \$splice,             # split splices
	'p|pe!'             => \$paired,             # paired-end alignments
	'P|fastpe!'         => \$fastpaired,         # fast paired-end alignments
	'I|shift!'          => \$shift,              # shift coordinates 3'
	'H|shiftval=i'      => \$shift_value,        # value to shift coordinates
	'x|extval=i'        => \$extend_value,       # value to extend reads
	'chrom=i'           => \$chr_number,         # number of chromosomes to sample
	'minr=f'            => \$correlation_min,    # R minimum value for shift

scripts/bam2wig.pl  view on Meta::CPAN

	if ( $shift and $splice ) {
		print
" WARNING: enabling both shift and splices is currently not allowed. Pick one.\n";
		exit 1;
	}
	if ( $shift and $paired ) {
		print " WARNING: disabling shift with paired reads\n";
		undef $shift;
	}
	if ( $use_ends and $shift ) {
		print " WARNING: disabling shift when recording paired endpoints\n";
		undef $shift;
	}
	if ( $use_ends and $splice ) {
		print " WARNING: disabling splices when recording paired endpoints\n";
		undef $splice;
	}

	# check to shift position or not
	if ( $shift or $use_extend ) {

		# set parameters for calculating shift value
		unless ( $shift_value or $extend_value ) {

			# not provided by user, empirical calculation required

scripts/bam2wig.pl  view on Meta::CPAN

	elsif ( $paired and not $do_strand and $use_smartpe ) {
		$callback = \&smart_pe;
		print " Recording smart paired-end coverage\n";
	}
	elsif ( $paired and $do_strand and $use_smartpe ) {
		$callback = \&smart_stranded_pe;
		print " Recording stranded, smart paired-end coverage\n";
	}
	elsif ( $paired and not $do_strand and $use_ends ) {
		$callback = \&pe_ends;
		print " Recording paired-end fragment endpoints\n";
	}
	elsif ( $paired and $do_strand and $use_ends ) {
		$callback = \&pe_strand_ends;
		print " Recording stranded, paired-end fragment endpoints\n";
	}
	else {
		die "programmer error!\n" unless $shift;    # special exception
	}

	# summary of wig file being written
	if ($do_bedgraph) {
		print " Writing bedGraph format in $bin_size bp increments\n";
	}
	elsif ($do_varstep) {

scripts/bam2wig.pl  view on Meta::CPAN

		# we continue but this will silently fail the low level fetch below
		# but at least an empty temp file will be written allowing program to finish
	}
	my $seq_length = $seq_name2length{$seq_id};

	# walk through the chromosome in 1 kb increments
	my $chrom_data;
	for ( my $start = 0; $start < $seq_length; $start += $coverage_dump ) {

		# set endpoint
		my $end = $start + $coverage_dump;
		$end = $seq_length if $end > $seq_length;

		# using the low level interface for a little more performance
		my $coverage = low_level_bam_coverage( $sam, $tid, $start, $end );

		# record the coverage
		&{$coverage_sub}( $coverage, \$chrom_data );
	}

scripts/bam2wig.pl  view on Meta::CPAN

 Required options:
  -i --in <filename.bam>        repeat if multiple bams, or comma-delimited list
 
 Reporting options (pick one):
  -s --start                    record at 5' position
  -d --mid                      record at midpoint of alignment or pair
  -a --span                     record across entire alignment or pair
  -e --extend                   extend alignment (record predicted fragment)
  --cspan                       record a span centered on midpoint
  --smartcov                    record paired coverage without overlaps, splices
  --ends                        record paired endpoints
  --coverage                    raw alignment coverage
 
 Alignment reporting options:
  -l --splice                   split alignment at N splices
  -t --strand                   record separate strands as two wig files
  --flip                        flip the strands for convenience
  
 Paired-end alignments:
  -p --pe                       process paired-end alignments, both are checked
  -P --fastpe                   process paired-end alignments, only F are checked

scripts/bam2wig.pl  view on Meta::CPAN

or fragment (paired-end) midpoint will be recorded in the wig file.
The span is defined by the extension value.

=item --smartcov

Smart alignment coverage of paired-end alignments without 
double-counting overlaps or recording gaps (intron splices). 

=item --ends

Record both endpoints of paired-end fragments, i.e. the outermost 
or 5' ends of properly paired fragments. This may be useful with 
ATAC-Seq, Cut&Run-Seq, or other cleavage experiments where you want 
to record the locations of cutting yet retain the ability to filter 
paired-end fragment sizes.

=item --coverage

Specify that the raw alignment coverage be calculated and reported 
in the wig file. This utilizes a special low-level operation and 
precludes any alignment filtering or post-normalization methods. 

scripts/get_gene_regions.pl  view on Meta::CPAN

=item --stop E<lt>integerE<gt>

=item --end E<lt>integerE<gt>

Optionally specify adjustment values to adjust the reported start and 
end coordinates of the collected regions. A negative value is shifted 
upstream (5' direction), and a positive value is shifted downstream.
Adjustments are made relative to the feature's strand, such that 
a start adjustment will always modify the feature's 5'end, either 
the feature startpoint or endpoint, depending on its orientation. 

=back

=head2 General options

=over 4

=item --bed

Automatically convert the output file to a BED file.