Bio-SeqAlignment-Applications-SequencingSimulators-RNASeq-Polyester
view release on metacpan or search on metacpan
version 0.02
SYNOPSIS
polyester_polyA.pl [options]
DESCRIPTION
The purpose of the application is to enhance the polyester RNA
sequencing simulation tool by including polyA tails in the reference RNA
being used to generate the simulated sequencing data. The application is
a wrapper around the R package polyester, which only accounts for the
processes of fragmentation, reverse complementation and sequencing when
generating data. Note that the Perl application does not (at this
moment) include the possibility of passing logspline R objects as
parameters to the R script and the the polyester "simulate_experiment"
function. The command line options are the same as the ones in the
polyester R package, with the exception of: * The addition of the
--taildist option, which is mandatory and specifies the tail
distribution to be used. * The addition of the --distparams option,
which is mandatory and specifies the parameters of the distribution. *
The addition of the --maxseqs option, which is optional and specifies
whether to break the single fasta file generated by the application into
--errorrate, -E [FLOAT]
Error probability (optional).
--fastafile, -f [PATH]
Fasta file path (mandatory).
--fcfile, -c [PATH]
Fold change file path (optional).
--fraglen, -F [INTEGER]
Fragment length (average) (optional).
--fragsd, -S [INTEGER]
Fragment length (standard deviation) (optional).
--gcbias, -g [INTEGER]
GC bias (optional).
--modformat, -m [INTEGER]
Case insensitive format for storing modifications (one of JSON,
YAML, or MessagePack) (optional).
--maxseqs, -m [INTEGER]
Strand specificity (optional).
--taildist, -t [STRING]
Tail distribution (mandatory).
--writeinfo, -w [INTEGER]
Save simulation info (optional).
EXAMPLES
polyester_polyA.pl --fastafile myseq.fasta --taildist gamma \
--distparams 125.0 1.0 0.0 250.0 --fraglen 100 --fragsd 10 \
--numreps 1 --strandspec TRUE --readlen 75 --paired F \
--maxseqs 1000 --modformat YAML --outdir /path/to/output
TODO
* Add the possibility of passing logspline R objects as parameters to
the R script and the polyester "simulate_experiment" function.
* Add the possibility of adding UMI tags to sequences.
* Add the possibility of adding sequencing adapters to sequences.
SEE ALSO
* polyester <https://github.com/alyssafrazee/polyester>
Polyester is an R package designed to simulate RNA sequencing
experiments with differential transcript expression.Given a set of
annotated transcripts, Polyester will simulate the steps of an
RNA-seq experiment (fragmentation, reverse-complementing, and
sequencing) and produce files containing simulated RNA-seq reads.
Simulated reads can be analyzed using your choice of downstream
analysis tools. Polyester has a built-in wrapper function to
simulate a case/control experiment with differential transcript
expression and biological replicates. Users are able to set the
levels of differential expression at transcripts of their choosing.
This means they know which transcripts are differentially expressed
in the simulated dataset, so accuracy of statistical methods for
differential expression detection can be analyzed.
bin/polyester.R view on Meta::CPAN
library(utils)
################################################################################
## Specify command line arguments
spec = matrix(c(
## Column 1 : long option name
## Column 2 : short option name
## Column 3 : 0 : no argument, 1 : required argument 2 : optional argument
## Column 4 : one of logical, integer, double, complex, character
'bias' , 'b' , 2, 'character' , ## fragment selection bias
'errormodel' , 'e' , 2 , 'character' , ## error model
'errorrate' , 'E' , 2 , 'double' , ## error probability
'fastafile' , 'f' , 1 , 'character' , ## fasta file (path)
'fcfile' , 'c' , 2 , 'character' , ## fold change (path)
'gcbias' , 'g' , 2 , 'integer' , ## gc bias
'numreps' , 'n' , 2 , 'character' , ## num of replicates in each group
'outdir' , 'o' , 2 , 'character' , ## path to output directory
'paired' , 'p' , 2 , 'logical' , ## paired reads
'readsfile' , 'r' , 1 , 'character' , ## reads_per_transcript (path)
'readlen' , 'R' , 2 , 'integer' , ## read length
'fraglen' , 'F' , 2 , 'integer' , ## fragment length (avg)
'fragsd' , 'S' , 2 , 'integer' , ## fragment length (sd)
'seed' , 'd' , 2 , 'integer' , ## random seed
'strandspec' , 's' , 2 , 'logical' , ## strand specificity
'writeinfo' , 'w' , 2 , 'logical' ## save simulation info?
),byrow=TRUE,ncol = 4)
################################################################################
## process commandline arguments
opt = getopt(spec)
bin/polyester.R view on Meta::CPAN
}
if(is.null(opt$readsfile)) {
cat("No transcript read count file provided. Will exit now.")
quit(save="no",status=1)
}
## (sensible?) default for some optional parameters
if(is.null(opt$bias)) opt$bias <- 'none'
if(is.null(opt$errormodel)) opt$errormodel <- 'uniform'
if(is.null(opt$errorrate)) opt$errorrate <- 0.005
if(is.null(opt$fraglen)) opt$fraglen <-250
if(is.null(opt$fragsd)) opt$fragsd <-25
if(is.null(opt$gcbias)) opt$gcbias <- 0
if(is.null(opt$outdir)) opt$outdir <- '.'
if(is.null(opt$paired)) opt$paired <- FALSE
if(is.null(opt$readlen)) opt$readlen <- 100
if(is.null(opt$seed)) opt$seed <- 12345
if(is.null(opt$strandspec)) opt$strandspec <- FALSE
if(is.null(opt$writeinfo)) opt$writeinfo <- TRUE
## defaults for some options that may be included in the future
if(is.null(opt$distr)) opt$distr <- 'normal'
if(is.null(opt$meanmodel)) opt$meanmodel <- FALSE
bin/polyester.R view on Meta::CPAN
fold_changes = fold_changes,
paired = opt$paired,
error_rate = opt$errorrate,
gcbias = opt$gcbias,
strand_specific = opt$strandspec,
meanmodel = opt$meanmodel,
writeinfo = opt$writeinfo,
seed = opt$seed,
readlen = opt$readlen,
distr = opt$distr,
fraglen = opt$fraglen,
fragsd = opt$fragsd
)
bin/polyester_polyA.pl view on Meta::CPAN
my $fastafile;
my $fcfile;
my $gcbias;
my $max_sequences_per_file = 0; ## default is to not split the files
my $modformat = 'YAML'; ## default format is 'YAML
my @numreps;
my $outdir;
my $paired;
my $readsfile;
my $readlen;
my $fraglen;
my $fragsd;
my $seed;
my $strandspec;
my $taildist;
my $writeinfo;
# Configure Getopt::Long
GetOptions(
'bias|b:s' => \$bias, # fragment selection bias (optional, string)
'distparams|P=f{1,}' => \@distparams
, # distribution parameters (mandatory, list of numeric values)
'errormodel|e:s' => \$errormodel, # error model (optional, string)
'errorrate|E:f' => \$errorrate, # error probability (optional, float)
'fastafile|f=s' => \$fastafile, # fasta file (path) (mandatory, strings)
'fcfile|c:s' => \$fcfile, # fold change (path) (optional, string)
'fraglen|F:i' => \$fraglen, # fragment length (avg) (optional, integer)
'fragsd|S:i' => \$fragsd, # fragment length (sd) (optional, integer)
'gcbias|g:i' => \$gcbias, # gc bias (optional, integer)
'maxseqs|m:i' => \$max_sequences_per_file, # max sequences per file
'modformat|M:s' => \$modformat
, # case insensitive format for storing modifications (one of JSON, YAML, or MessagePack)
'numreps|n:i{,}' =>
\@numreps, # num of replicates in each group (optional, list)
'outdir|o:s' => \$outdir, # path to output directory (optional, string)
'paired|p:s' => \$paired, # paired reads (TRUE or FALSE) (optional, string)
'readlen|R:i' => \$readlen, # read length (optional, integer)
'readsfile|r:s' =>
bin/polyester_polyA.pl view on Meta::CPAN
errormodel => $errormodel,
errorrate => $errorrate,
fastafile => $fastafile,
fcfile => $fcfile,
gcbias => $gcbias,
numreps => \@numreps,
outdir => $outdir,
paired => $paired,
readsfile => $readsfile,
readlen => $readlen,
fraglen => $fraglen,
fragsd => $fragsd,
seed => $seed,
strandspec => $strandspec,
writeinfo => $writeinfo
);
## Pipeline Segment 6 : store the modifications into a file for future use
my $mod_fname = store_modifications(
mods => $modifications_HoH,
bioseq_file => $fastafile,
format => $modformat
bin/polyester_polyA.pl view on Meta::CPAN
my $errormodel = $polyester_params{errormodel};
my $errorrate = $polyester_params{errorrate};
my $fastafile = $polyester_params{fastafile};
my $fcfile = $polyester_params{fcfile};
my $gcbias = $polyester_params{gcbias};
my $numreps = $polyester_params{numreps};
my $outdir = $polyester_params{outdir};
my $paired = $polyester_params{paired};
my $readsfile = $polyester_params{readsfile};
my $readlen = $polyester_params{readlen};
my $fraglen = $polyester_params{fraglen};
my $fragsd = $polyester_params{fragsd};
my $seed = $polyester_params{seed};
my $strandspec = $polyester_params{strandspec};
my $writeinfo = $polyester_params{writeinfo};
my $r_command =
"Rscript --vanilla --slave --default-packages=getopt,polyester,utils "
. File::Spec->catfile( $Bin, "polyester.R" );
## Add the options to the R command
$r_command .= " --bias \"$bias\"" if defined $bias;
$r_command .= " --errormodel \"$errormodel\"" if defined $errormodel;
$r_command .= " --errorrate $errorrate" if defined $errorrate;
$r_command .= " --fastafile \"$fastafile\"";
$r_command .= " --fcfile \"$fcfile\"" if defined $fcfile;
$r_command .= " --gcbias $gcbias" if defined $gcbias;
$r_command .= " --numreps \"@{$numreps}\"" if $numreps;
$r_command .= " --outdir \"$outdir\"" if defined $outdir;
$r_command .= " --paired $paired" if defined $paired;
$r_command .= " --readsfile \"$readsfile\"";
$r_command .= " --readlen $readlen" if defined $readlen;
$r_command .= " --fraglen $fraglen" if defined $fraglen;
$r_command .= " --fragsd $fragsd" if defined $fragsd;
$r_command .= " --seed $seed" if defined $seed;
$r_command .= " --strandspec $strandspec" if defined $strandspec;
$r_command .= " --writeinfo $writeinfo" if defined $writeinfo;
## Execute the R command
system($r_command);
}
__END__
lib/Bio/SeqAlignment/Applications/SequencingSimulators/RNASeq/Polyester.pm view on Meta::CPAN
=head1 SYNOPSIS
polyester_polyA.pl [options]
=head1 DESCRIPTION
The purpose of the application is to enhance the polyester RNA sequencing
simulation tool by including polyA tails in the reference RNA being used to
generate the simulated sequencing data. The application is a wrapper around
the R package polyester, which only accounts for the processes of fragmentation,
reverse complementation and sequencing when generating data.
Note that the Perl application does not (at this moment) include the possibility
of passing logspline R objects as parameters to the R script and the the
polyester "simulate_experiment" function.
The command line options are the same as the ones in the polyester R package,
with the exception of:
* The addition of the --taildist option, which is mandatory and specifies
the tail distribution to be used.
* The addition of the --distparams option, which is mandatory and specifies
the parameters of the distribution.
lib/Bio/SeqAlignment/Applications/SequencingSimulators/RNASeq/Polyester.pm view on Meta::CPAN
Error probability (optional).
=item B<--fastafile, -f> [PATH]
Fasta file path (mandatory).
=item B<--fcfile, -c> [PATH]
Fold change file path (optional).
=item B<--fraglen, -F> [INTEGER]
Fragment length (average) (optional).
=item B<--fragsd, -S> [INTEGER]
Fragment length (standard deviation) (optional).
=item B<--gcbias, -g> [INTEGER]
GC bias (optional).
=item B<--modformat, -m> [INTEGER]
Case insensitive format for storing modifications
lib/Bio/SeqAlignment/Applications/SequencingSimulators/RNASeq/Polyester.pm view on Meta::CPAN
=item B<--writeinfo, -w> [INTEGER]
Save simulation info (optional).
=back
=head1 EXAMPLES
polyester_polyA.pl --fastafile myseq.fasta --taildist gamma \
--distparams 125.0 1.0 0.0 250.0 --fraglen 100 --fragsd 10 \
--numreps 1 --strandspec TRUE --readlen 75 --paired F \
--maxseqs 1000 --modformat YAML --outdir /path/to/output
=head1 TODO
=over 4
=item *
Add the possibility of passing logspline R objects as parameters to the
lib/Bio/SeqAlignment/Applications/SequencingSimulators/RNASeq/Polyester.pm view on Meta::CPAN
=back
=head1 SEE ALSO
=over 4
=item * L<polyester|https://github.com/alyssafrazee/polyester>
Polyester is an R package designed to simulate RNA sequencing experiments with
differential transcript expression.Given a set of annotated transcripts,
Polyester will simulate the steps of an RNA-seq experiment (fragmentation,
reverse-complementing, and sequencing) and produce files containing simulated
RNA-seq reads. Simulated reads can be analyzed using your choice of downstream
analysis tools.
Polyester has a built-in wrapper function to simulate a case/control experiment
with differential transcript expression and biological replicates. Users are
able to set the levels of differential expression at transcripts of their
choosing. This means they know which transcripts are differentially expressed
in the simulated dataset, so accuracy of statistical methods for differential
expression detection can be analyzed.
( run in 1.275 second using v1.01-cache-2.11-cpan-364913b4093 )