Added posterior standard deviation of counts as output if either '--calc-pme' or...

[rsem.git] / rsem-calculate-expression

diff --git a/rsem-calculate-expression b/rsem-calculate-expression
index d6cb5f2a3f6b989ced2e1f96b3302c8d720ba9b5..ccfc643e1c0cbb2963fcc34159193dd72cd27103 100755 (executable)
--- a/rsem-calculate-expression
+++ b/rsem-calculate-expression
@@ -57,7 +57,6 @@ my $genGenomeBamF = 0;
 my $sampling = 0;
 my $calcPME = 0;
 my $calcCI = 0;
 my $sampling = 0;
 my $calcPME = 0;
 my $calcCI = 0;

-my $var_opt = 0; # temporarily, only for internal use

 my $quiet = 0;
 my $help = 0;
 
 my $quiet = 0;
 my $help = 0;
 


@@ -124,7 +123,6 @@ GetOptions("keep-intermediate-files" => \$keep_intermediate_files,
           "output-genome-bam" => \$genGenomeBamF,
           "sampling-for-bam" => \$sampling,
           "calc-pme" => \$calcPME,
           "output-genome-bam" => \$genGenomeBamF,
           "sampling-for-bam" => \$sampling,
           "calc-pme" => \$calcPME,

-          "var" => \$var_opt,

           "calc-ci" => \$calcCI,
           "ci-memory=i" => \$NMB,
           "samtools-sort-mem=s" => \$SortMem,
           "calc-ci" => \$calcCI,
           "ci-memory=i" => \$NMB,
           "samtools-sort-mem=s" => \$SortMem,


@@ -355,7 +353,7 @@ if ($genBamF) {
     if ($sampling) { $command .= " --sampling"; }
     if ($seed ne "NULL") { $command .= " --seed $seeds[0]"; }
 }
     if ($sampling) { $command .= " --sampling"; }
     if ($seed ne "NULL") { $command .= " --seed $seeds[0]"; }
 }

-if ($calcPME || $var_opt || $calcCI) { $command .= " --gibbs-out"; }
+if ($calcPME || $calcCI) { $command .= " --gibbs-out"; }

 if ($quiet) { $command .= " -q"; }
 
 &runCommand($command);
 if ($quiet) { $command .= " -q"; }
 
 &runCommand($command);


@@ -390,10 +388,9 @@ if ($mTime) { $time_end = time(); $time_rsem = $time_end - $time_start; }
 
 if ($mTime) { $time_start = time(); }
 
 
 if ($mTime) { $time_start = time(); }
 

-if ($calcPME || $var_opt || $calcCI ) {
+if ($calcPME || $calcCI ) {

     $command = "rsem-run-gibbs $refName $imdName $statName $BURNIN $NCV $SAMPLEGAP";
     $command .= " -p $nThreads";
     $command = "rsem-run-gibbs $refName $imdName $statName $BURNIN $NCV $SAMPLEGAP";
     $command .= " -p $nThreads";

-    if ($var_opt) { $command .= " --var"; }

     if ($seed ne "NULL") { $command .= " --seed $seeds[1]"; }
     if ($quiet) { $command .= " -q"; }
     &runCommand($command);
     if ($seed ne "NULL") { $command .= " --seed $seeds[1]"; }
     if ($quiet) { $command .= " -q"; }
     &runCommand($command);


@@ -707,7 +704,7 @@ File containing isoform level expression estimates. The first line
 contains column names separated by the tab character. The format of
 each line in the rest of this file is:
 
 contains column names separated by the tab character. The format of
 each line in the rest of this file is:
 

-transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct [pme_expected_count pme_TPM pme_FPKM IsoPct_from_pme_TPM TPM_ci_lower_bound TPM_ci_upper_bound FPKM_ci_lower_bound FPKM_ci_upper_bound]
+transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct [posterior_mean_count posterior_standard_deviation_of_count pme_TPM pme_FPKM IsoPct_from_pme_TPM TPM_ci_lower_bound TPM_ci_upper_bound FPKM_ci_lower_bound FPKM_ci_upper_bound]

 
 Fields are separated by the tab character. Fields within "[]" are
 optional. They will not be presented if neither '--calc-pme' nor
 
 Fields are separated by the tab character. Fields within "[]" are
 optional. They will not be presented if neither '--calc-pme' nor


@@ -753,9 +750,11 @@ transcript's abandunce over its parent gene's abandunce. If its parent
 gene has only one isoform or the gene information is not provided,
 this field will be set to 100.
 
 gene has only one isoform or the gene information is not provided,
 this field will be set to 100.
 

-'pme_expected_count', 'pme_TPM', 'pme_FPKM' are posterior mean
-estimates calculated by RSEM's Gibbs sampler. 'IsoPct_from_pme_TPM' is
-the isoform percentage calculated from 'pme_TPM' values.
+'posterior_mean_count', 'pme_TPM', 'pme_FPKM' are posterior mean
+estimates calculated by RSEM's Gibbs
+sampler. 'posterior_standard_deviation_of_count' is the posterior
+standard deviation of counts. 'IsoPct_from_pme_TPM' is the isoform
+percentage calculated from 'pme_TPM' values.

 
 'TPM_ci_lower_bound', 'TPM_ci_upper_bound', 'FPKM_ci_lower_bound' and
 'FPKM_ci_upper_bound' are lower(l) and upper(u) bounds of 95%
 
 'TPM_ci_lower_bound', 'TPM_ci_upper_bound', 'FPKM_ci_lower_bound' and
 'FPKM_ci_upper_bound' are lower(l) and upper(u) bounds of 95%


@@ -768,7 +767,7 @@ File containing gene level expression estimates. The first line
 contains column names separated by the tab character. The format of
 each line in the rest of this file is:
 
 contains column names separated by the tab character. The format of
 each line in the rest of this file is:
 

-gene_id transcript_id(s) length effective_length expected_count TPM FPKM [pme_expected_count pme_TPM pme_FPKM TPM_ci_lower_bound TPM_ci_upper_bound FPKM_ci_lower_bound FPKM_ci_upper_bound]
+gene_id transcript_id(s) length effective_length expected_count TPM FPKM [posterior_mean_count posterior_standard_deviation_of_count pme_TPM pme_FPKM TPM_ci_lower_bound TPM_ci_upper_bound FPKM_ci_lower_bound FPKM_ci_upper_bound]

 
 Fields are separated by the tab character. Fields within "[]" are
 optional. They will not be presented if neither '--calc-pme' nor
 
 Fields are separated by the tab character. Fields within "[]" are
 optional. They will not be presented if neither '--calc-pme' nor


@@ -793,7 +792,7 @@ allele-specific expression calculation. The first line
 contains column names separated by the tab character. The format of
 each line in the rest of this file is:
 
 contains column names separated by the tab character. The format of
 each line in the rest of this file is:
 

-allele_id transcript_id gene_id length effective_length expected_count TPM FPKM AlleleIsoPct AlleleGenePct [pme_expected_count pme_TPM pme_FPKM AlleleIsoPct_from_pme_TPM AlleleGenePct_from_pme_TPM TPM_ci_lower_bound TPM_ci_upper_bound FPKM_ci_lower_bound FPKM_ci_upper_bound]
+allele_id transcript_id gene_id length effective_length expected_count TPM FPKM AlleleIsoPct AlleleGenePct [posterior_mean_count posterior_standard_deviation_of_count pme_TPM pme_FPKM AlleleIsoPct_from_pme_TPM AlleleGenePct_from_pme_TPM TPM_ci_lower_bound TPM_ci_upper_bound FPKM_ci_lower_bound FPKM_ci_upper_bound]

 
 Fields are separated by the tab character. Fields within "[]" are
 optional. They will not be presented if neither '--calc-pme' nor
 
 Fields are separated by the tab character. Fields within "[]" are
 optional. They will not be presented if neither '--calc-pme' nor