my $NMB = 1024; # default
-my $status;
+my $status = 0;
my $read_type = 1; # default, single end with qual
my $strand_specific = 0;
+my $mTime = 0;
+my ($time_start, $time_end, $time_alignment, $time_rsem, $time_ci) = (0, 0, 0, 0, 0);
+
GetOptions("keep-intermediate-files" => \$keep_intermediate_files,
"no-qualities" => \$no_qual,
"paired-end" => \$paired_end,
"out-bam" => \$genBamF,
"calc-ci" => \$calcCI,
"ci-memory=i" => \$NMB,
+ "time" => \$mTime,
"q|quiet" => \$quiet,
"h|help" => \$help) or pod2usage(-exitval => 2, -verbose => 2);
if ($is_sam || $is_bam) {
pod2usage(-msg => "Invalid number of arguments!", -exitval => 2, -verbose => 2) if (scalar(@ARGV) != 3);
pod2usage(-msg => "--sam and --bam cannot be active at the same time!", -exitval => 2, -verbose => 2) if ($is_sam == 1&& $is_bam == 1);
- pod2usage(-msg => "--bowtie-path, --bowtie-n, --bowtie-e, --bowtie-m, --phred33-quals, --phred64-quals or --solexa-quals cannot be set if input is SAM/BAM format!", -exitval => 2, -verbose => 2) if ($bowtie_path ne "" || $C != 2 || $E != 999999 || $maxHits != 200 || $phred33 || $phred64 || $solexa);
+ pod2usage(-msg => "--bowtie-path, --bowtie-n, --bowtie-e, --bowtie-m, --phred33-quals, --phred64-quals or --solexa-quals cannot be set if input is SAM/BAM format!", -exitval => 2, -verbose => 2) if ($bowtie_path ne "" || $C != 2 || $E != 99999999 || $maxHits != 200 || $phred33 || $phred64 || $solexa);
}
else {
pod2usage(-msg => "Invalid number of arguments!", -exitval => 2, -verbose => 2) if (!$paired_end && scalar(@ARGV) != 3 || $paired_end && scalar(@ARGV) != 4);
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 .= " | 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;
=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>
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
+
+# LocalWords: usr
projects / rsem.git / blobdiff