rename pRSEm's 'consistency test' to 'testing procedure'

deweylab · Mar 14, 2016 · 12f3e87 · 12f3e87
1 parent 2214a5c
commit 12f3e87
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Showing 3 changed files with 15 additions and 15 deletions.
diff --git a/pRSEM/Param.py b/pRSEM/Param.py
@@ -93,7 +93,7 @@ def __init__(self):
     self.finfo_multi_targets = None
     self.flgt_model_multi_targets = None
 
-    ## for consistency-test
+    ## for testing procedure
     self.targetids = []
 
 

diff --git a/pRSEM/prsem-consistency-test → pRSEM/prsem-testing-procedure b/pRSEM/prsem-consistency-test → pRSEM/prsem-testing-procedure
@@ -4,7 +4,7 @@ __doc__="""
 
   pliu 20150304
 
-  run pRSEM's consistency test to calculate:
+  run pRSEM's testing procedure to calculate:
   1. a p-value on whether external data is informative
   2. a log-likelihood on read counts of partitioned isoforms' fit to DM model
 """
@@ -97,7 +97,7 @@ def writePvalLL(prm):
                                  pvalLL_lines[1]))
   f_fout.close()
 
-  sys.stdout.write("\npRSEM consistency test result is saved in %s\n" %
+  sys.stdout.write("\npRSEM testing procedure result is saved in %s\n" %
                    prm.fall_pvalLL)
 
 if __name__=='__main__':

diff --git a/rsem-run-prsem-consistency-test → rsem-run-prsem-testing-procedure b/rsem-run-prsem-consistency-test → rsem-run-prsem-testing-procedure
@@ -66,7 +66,7 @@ pod2usage(-verbose => 2) if ($help == 1);
          ( $bowtie_path eq '' ) ) &&
        ( $chipseq_bed_files_multi_targets eq '' )
      ) {
-    $msg = "please define one set of the following options to run pRSEM:\n" .
+    $msg = "please define one set of the following options to run pRSEM's testing procedure:\n" .
            "1. --chipseq-peak-file <file>\n" .
            "2. --chipseq-target-read-files <file> and\n" .
            "   --chipseq-control-read-files <file> and\n" .
@@ -103,7 +103,7 @@ pod2usage(-verbose => 2) if ($help == 1);
   } else {
     my $s_prt_mdls = join(', ', @prsem_partition_models);
     $msg = "\n--partition-model <string> must be one of [$s_prt_mdls]\n" .
-           "pRSEM consistency test only supports the above partition models";
+           "pRSEM's testing procedure only supports the above partition models";
   }
 
   if ( $msg ne '' ) {
@@ -141,7 +141,7 @@ if ($bowtie_path ne "") { $bowtie_path .= "/"; }
 my $command = "";
 
 {
-  $command = "$FindBin::RealBin/pRSEM/prsem-consistency-test " .
+  $command = "$FindBin::RealBin/pRSEM/prsem-testing-procedure " .
              " --num-threads $nThreads " .
              " --partition-model $partition_model ";
 
@@ -183,11 +183,11 @@ __END__
 
 =head1 NAME
 
-rsem-run-prsem-consistency-test
+rsem-run-prsem-testing-procedure
 
 =head1 SYNOPSIS
 
-rsem-run-prsem-consistency-test [options] reference_name sample_name
+rsem-run-prsem-testing-procedure [options] reference_name sample_name
 
 =head1 ARGUMENGS
 
@@ -260,7 +260,7 @@ Show help information.
 
 =item B<--keep-intermediate-files>
 
-Keep temporary files generated by RSEM and this consistency test. RSEM creates a temporary directory, 'sample_name.temp', into which it puts all intermediate output files. By default, after consistency test is finished, the temporary directory is deleted.  Set this option to prevent the deletion of this directory and the intermediate files inside of it. (Default: off)
+Keep temporary files generated by RSEM and this testing procedure. RSEM creates a temporary directory, 'sample_name.temp', into which it puts all intermediate output files. By default, after this test is finished, the temporary directory is deleted.  Set this option to prevent the deletion of this directory and the intermediate files inside of it. (Default: off)
 
 =item B<--temporary-folder> <string>
 
@@ -314,11 +314,11 @@ The following output files are the same as the ones generated by 'rsem-calculate
 
 Assuming RSEM reference files are under '/ref' with name 'mouse_125' and expression files are under '/expr' with name 'mouse_125'. Suppose we want to derive prior from four histone modification ChIP-seq read data sets: '/data/H3K27Ac.fastq.gz', '/data/H3K4me1.fastq.gz', '/data/H3K4me2.fastq.gz', and '/data/H3K4me3.fastq.gz'. Also, assuming Bowtie's executables are under '/sw/bowtie/' and we want to use 16 cores:
 
- rsem-run-prsem-consistency-test --partition-model cmb_lgt \
-                                 --chipseq-read-files-multi-targets /data/H3K27Ac.fastq.gz,/data/H3K4me1.fastq.gz,/data/H3K4me2.fastq.gz,/data/H3K4me3.fastq.gz \
-                                 --bowtie-path /sw/bowtie \ 
-                                 --num-threads 16 \
-                                 /ref/mouse_125 \
-                                 /expr/mouse_125
+ rsem-run-prsem-testing-procedure --partition-model cmb_lgt \
+                                  --chipseq-read-files-multi-targets /data/H3K27Ac.fastq.gz,/data/H3K4me1.fastq.gz,/data/H3K4me2.fastq.gz,/data/H3K4me3.fastq.gz \
+                                  --bowtie-path /sw/bowtie \ 
+                                  --num-threads 16 \
+                                  /ref/mouse_125 \
+                                  /expr/mouse_125
 
 =cut