my $NMB = 1024; # default
-my $status;
+my $status = 0;
my $read_type = 1; # default, single end with qual
my $E = 99999999;
my $L = 25;
my $maxHits = 200;
+my $chunkMbs = 0; # 0 = use bowtie default
my $phred33 = 0;
my $phred64 = 0;
my $solexa = 0;
my $strand_specific = 0;
+my $mTime = 0;
+my ($time_start, $time_end, $time_alignment, $time_rsem, $time_ci) = (0, 0, 0, 0, 0);
+
GetOptions("keep-intermediate-files" => \$keep_intermediate_files,
"no-qualities" => \$no_qual,
"paired-end" => \$paired_end,
"bowtie-n=i" => \$C,
"bowtie-e=i" => \$E,
"bowtie-m=i" => \$maxHits,
+ "bowtie-chunkmbs=i" => \$chunkMbs,
"phred33-quals" => \$phred33,
"phred64-quals" => \$phred64, #solexa1.3-quals" => \$phred64,
"solexa-quals" => \$solexa,
"out-bam" => \$genBamF,
"calc-ci" => \$calcCI,
"ci-memory=i" => \$NMB,
+ "time" => \$mTime,
"q|quiet" => \$quiet,
"h|help" => \$help) or pod2usage(-exitval => 2, -verbose => 2);
pod2usage(-msg => "Min fragment length should be smaller or equal to max fragment length!", -exitval => 2, -verbose => 2) if ($minL > $maxL);
pod2usage(-msg => "The memory allocated for calculating credibility intervals should be at least 1 MB!\n", -exitval => 2, -verbose => 2) if ($NMB < 1);
pod2usage(-msg => "Number of threads should be at least 1!\n", -exitval => 2, -verbose => 2) if ($nThreads < 1);
+pod2usage(-msg => "Seed length should be at least 25!\n", -exitval => 2, -verbose => 2) if ($L < 25);
if ($strand_specific) { $probF = 1.0; }
my $mate2_list = "";
my $inpF = "";
-my ($refName, $taskName, $tmp_dir, $imdName) = ();
+my ($refName, $sampleName, $sampleToken, $temp_dir, $stat_dir, $imdName) = ();
my $gap = 32;
if ($paired_end) {
if ($is_sam || $is_bam) { $inpF = $ARGV[0]; }
else {$mate1_list = $ARGV[0]; }
$refName = $ARGV[1];
- $taskName = $ARGV[2];
+ $sampleName = $ARGV[2];
}
else {
$mate1_list = $ARGV[0];
$mate2_list = $ARGV[1];
$refName = $ARGV[2];
- $taskName = $ARGV[3];
+ $sampleName = $ARGV[3];
}
-$tmp_dir = $taskName.".temp";
-my $pos = rindex($taskName, '/');
-if ($pos < 0) {
- $imdName = "$tmp_dir/$taskName";
-}
-else {
- $imdName = $tmp_dir."/".substr($taskName, $pos + 1);
-}
+my $pos = rindex($sampleName, '/');
+if ($pos < 0) { $sampleToken = $sampleName; }
+else { $sampleToken = substr($sampleName, $pos + 1); }
+
+$temp_dir = "$sampleName.temp";
+$stat_dir = "$sampleName.stat";
+
+if (!(-d $temp_dir) && !mkdir($temp_dir)) { print "Fail to create folder $temp_dir.\n"; exit(-1); }
+if (!(-d $stat_dir) && !mkdir($stat_dir)) { print "Fail to create folder $stat_dir.\n"; exit(-1); }
+
+$imdName = "$temp_dir/$sampleToken";
if (!$is_sam && !$is_bam && $phred33 + $phred64 + $solexa == 0) { $phred33 = 1; }
my ($mate_minL, $mate_maxL) = (1, $maxL);
-if (!(-d $tmp_dir) && !mkdir($tmp_dir)) { print "Fail to create the directory.\n"; exit(-1); }
-
if ($bowtie_path ne "") { $bowtie_path .= "/"; }
my ($fn, $dir, $suf) = fileparse($0);
if ($read_type == 2 || $read_type == 3) { $command .= " -I $minL -X $maxL"; }
if ($strand_specific || $probF == 1.0) { $command .= " --norc"; }
- elsif ($probF = 0.0) { $command .= " --nofw"; }
+ elsif ($probF == 0.0) { $command .= " --nofw"; }
$command .= " -p $nThreads -a -m $maxHits -S";
if ($quiet) { $command .= " --quiet"; }
+ $command .= " --chunkmbs $chunkMbs" if $chunkMbs > 0;
+
$command .= " $refName";
if ($read_type == 0 || $read_type == 1) {
$command .= " $mate1_list";
$command .= " | gzip > $imdName.sam.gz";
print "$command\n";
+
+ if ($mTime) { $time_start = time(); }
+
$status = system($command);
+
+ if ($mTime) { $time_end = time(); $time_alignment = $time_end - $time_start; }
+
if ($status != 0) {
print "bowtie failed! Please check if you provide correct parameters/options for the pipeline!\n";
exit(-1);
$is_sam = 1; # output of bowtie is a sam file
}
-$command = $dir."rsem-parse-alignments $refName $imdName";
+if ($mTime) { $time_start = time(); }
+
+$command = $dir."rsem-parse-alignments $refName $sampleName $sampleToken";
my $samInpType;
if ($is_sam) { $samInpType = "s"; }
}
print "\n";
-$status = open(OUTPUT, ">$imdName.mparams");
-if ($status == 0) { print "Cannot generate $imdName.mparams!\n"; exit(-1); }
+my $doesOpen = open(OUTPUT, ">$imdName.mparams");
+if ($doesOpen == 0) { print "Cannot generate $imdName.mparams!\n"; exit(-1); }
print OUTPUT "$minL $maxL\n";
print OUTPUT "$probF\n";
print OUTPUT "$estRSPD\n";
print OUTPUT "$L\n";
close(OUTPUT);
-$command = $dir."rsem-run-em $refName $read_type $imdName $taskName -p $nThreads";
+$command = $dir."rsem-run-em $refName $read_type $sampleName $sampleToken -p $nThreads";
if ($genBamF) {
$command .= " -b $samInpType $inpF";
if ($fn_list ne "") { $command .= " 1 $fn_list"; }
print "\n";
if ($genBamF) {
- $command = $dir."sam/samtools sort $taskName.bam $taskName.sorted";
+ $command = $dir."sam/samtools sort $sampleName.bam $sampleName.sorted";
print "$command\n";
$status = system($command);
if ($status != 0) {
exit(-1);
}
print "\n";
- $command = $dir."sam/samtools index $taskName.sorted.bam";
+ $command = $dir."sam/samtools index $sampleName.sorted.bam";
print "$command\n";
$status = system($command);
if ($status != 0) {
print "\n";
}
-&collectResults("$imdName.iso_res", "$taskName.isoforms.results"); # isoform level
-&collectResults("$imdName.gene_res", "$taskName.genes.results"); # gene level
+&collectResults("$imdName.iso_res", "$sampleName.isoforms.results"); # isoform level
+&collectResults("$imdName.gene_res", "$sampleName.genes.results"); # gene level
+
+if ($mTime) { $time_end = time(); $time_rsem = $time_end - $time_start; }
+
+if ($mTime) { $time_start = time(); }
if ($calcCI) {
- $command = $dir."rsem-run-gibbs $refName $taskName $imdName $BURNIN $CHAINLEN $SAMPLEGAP";
+ $command = $dir."rsem-run-gibbs $refName $sampleName $sampleToken $BURNIN $CHAINLEN $SAMPLEGAP";
+# $command .= " -p $nThreads";
if ($quiet) { $command .= " -q"; }
print "$command\n";
$status = system($command);
}
print "\n";
- system("mv $taskName.isoforms.results $imdName.isoforms.results.bak1");
- system("mv $taskName.genes.results $imdName.genes.results.bak1");
- &collectResults("$imdName.iso_res", "$taskName.isoforms.results"); # isoform level
- &collectResults("$imdName.gene_res", "$taskName.genes.results"); # gene level
+ system("mv $sampleName.isoforms.results $imdName.isoforms.results.bak1");
+ system("mv $sampleName.genes.results $imdName.genes.results.bak1");
+ &collectResults("$imdName.iso_res", "$sampleName.isoforms.results"); # isoform level
+ &collectResults("$imdName.gene_res", "$sampleName.genes.results"); # gene level
- $command = $dir."rsem-calculate-credibility-intervals $refName $taskName $imdName $CONFIDENCE $NSPC $NMB";
+ $command = $dir."rsem-calculate-credibility-intervals $refName $sampleName $sampleToken $CONFIDENCE $NSPC $NMB";
if ($quiet) { $command .= " -q"; }
print "$command\n";
$status = system($command);
}
print "\n";
- system("mv $taskName.isoforms.results $imdName.isoforms.results.bak2");
- system("mv $taskName.genes.results $imdName.genes.results.bak2");
- &collectResults("$imdName.iso_res", "$taskName.isoforms.results"); # isoform level
- &collectResults("$imdName.gene_res", "$taskName.genes.results"); # gene level
+ system("mv $sampleName.isoforms.results $imdName.isoforms.results.bak2");
+ system("mv $sampleName.genes.results $imdName.genes.results.bak2");
+ &collectResults("$imdName.iso_res", "$sampleName.isoforms.results"); # isoform level
+ &collectResults("$imdName.gene_res", "$sampleName.genes.results"); # gene level
}
+if ($mTime) { $time_end = time(); $time_ci = $time_end - $time_start; }
+
+if ($mTime) { $time_start = time(); }
+
if (!$keep_intermediate_files) {
- $status = system ("rm -rf $tmp_dir");
+ $status = system("rm -rf $temp_dir");
if ($status != 0) {
print "Fail to delete the temporary folder!\n";
exit(-1);
}
}
+if ($mTime) { $time_end = time(); }
+
+if ($mTime) {
+ open(OUTPUT, ">$sampleName.time");
+ print OUTPUT "Alignment: $time_alignment s.\n";
+ print OUTPUT "RSEM: $time_rsem s.\n";
+ print OUTPUT "CI: $time_ci s.\n";
+ my $time_del = $time_end - $time_start;
+ print OUTPUT "Delete: $time_del s.\n";
+ close(OUTPUT);
+}
+
# inpF, outF
sub collectResults {
my $local_status;
++$cnt;
chomp($line);
my @local_arr = split(/\t/, $line);
- if ($cnt == 3) { @comment = @local_arr; }
+ if ($cnt == 4) { @comment = @local_arr; }
else { push(@results, \@local_arr); }
}
=item B<input>
-SAM/BAM formatted input file. If "-" is specified for the filename, SAM/BAM input is instead assumed to come from standard input. SAM/BAM format used is SAM Spec v1.2. RSEM requires all alignments of the same read group together. For paired-end reads, RSEM also requires the two mates of any alignment be adjacent. See Description section for how to make input file obey RSEM's requirements.
+SAM/BAM formatted input file. If "-" is specified for the filename, SAM/BAM input is instead assumed to come from standard input. RSEM requires all alignments of the same read group together. For paired-end reads, RSEM also requires the two mates of any alignment be adjacent. See Description section for how to make input file obey RSEM's requirements.
=item B<reference_name>
=item B<--seed-length> <int>
-Seed length used by the read aligner. Providing the correct value for this parameter is important for RSEM's accuracy if the data are single-end reads. If RSEM runs Bowtie, it uses this value for Bowtie's seed length parameter. (Default: 25)
+Seed length used by the read aligner. Providing the correct value for this parameter is important for RSEM's accuracy if the data are single-end reads. If RSEM runs Bowtie, it uses this value for Bowtie's seed length parameter. The minimum value is 25. Any read with its or at least one of its mates' (for paired-end reads) length less than 25 will be ignored. (Default: 25)
=item B<--tag> <string>
(Bowtie parameter) suppress all alignments for a read if > <int> valid alignments exist. (Default: 200)
+=item B<--bowtie-chunkmbs> <int>
+
+(Bowtie parameter) memory allocated for best first alignment calculation (Default: 0 - use bowtie's default)
+
=item B<--phred33-quals>
Input quality scores are encoded as Phred+33. (Default: on)
sort -k 1,1 -s input.sam > input.sorted.sam
-The SAM/BAM format RSEM uses is v1.2.
+The SAM/BAM format RSEM uses is v1.3. However, it is compatible with old SAM/BAM format.
The user must run 'rsem-prepare-reference' with the appropriate reference before using this program.
'rsem-prepare-reference', there will be no tab after the
tau_value field.
-=item B<sample_name.model> and B<sample_name.theta>
-
-Output files used by RSEM internally for tasks like simulation,
-compute credibility intervals etc.
-
=item B<sample_name.bam, sample_name.sorted.bam and sample_name.sorted.bam.bai>
Only generated when --out-bam is specified.
genomic coordinates. Alignments of reads that have identical genomic
coordinates (i.e., alignments to different isoforms that share the
same genomic region) are collapsed into one alignment. The MAPQ field
-of each alignment is set to max(100, floor(-10 * log10(1.0 - w) +
+of each alignment is set to min(100, floor(-10 * log10(1.0 - w) +
0.5)), where w is the posterior probability of that alignment being
the true mapping of a read. In addition, RSEM pads a new tag
ZW:f:value, where value is a single precision floating number
'sample_name.sorted.bam' and 'sample_name.sorted.bam.bai' are the
sorted BAM file and indices generated by samtools (included in RSEM package).
+=item B<sample_name.stat>
+
+This is a folder instead of a file. All model related statistics are stored in this folder. Use 'rsem-plot-model' can generate plots using this folder.
=back
mmliver_paired_end_quals
=cut
+
projects / rsem.git / blobdiff