rnazSort.pl
- Sorts output files from rnazCluster.pl
by different criteria
rnazSort.pl [options] key [file]
Sort in reverse order.
Do not preserve the locus grouping but simply sort the windows.
Prints version information and exits.
Prints a short help message and exits.
Prints a detailed manual page and exits.
rnazSort.pl
reads tab-delimited data files as generated by
rnazCluster.pl
. The files are sorted according to a key which is
given at the command line as a mandatory argument. See below for a
list of possible keys. By default ``better" hits are listed first
(e.g. lower z-score or higher P). This can be changed by using the
--reverse
option. By default, the grouping in loci is preserved
during sorting. For example if you sort by z-score, you get first the
locus first whicht contains the window with the lowest z-score. If you
simply want all windows sorted without considering the grouping use
the --no-loci
option.
Consecutive numbered ID for each window. BUG: currently window10 comes before window9 because it is sorted alphabetically.
The locus which this window belongs to. BUG: currently locus10 comes before locus9 because it is sorted alphabetically.
Identifier of the sequence (e.g. human.chr1 or contig42)
Start position of the reference sequence in the window
End position of the reference sequence in the window
Indicates if the reference seqeunce is from the positive or negative strand
Number of sequences in the alignment
Number of columns in the alignment
Mean pairwise identity of the alignment
Mean minimum free energy of the single sequences as calculated by the RNAfold algorithm
``Consensus MFE" for the alignment as calculated by RNAalifold algorithm
Contribution to the consensus MFE which comes from the energy part of the RNAalifold algorithm
Contribution to the consensus MFE which comes from the covariance part of the RNAalifold algorithm
Number of different base combinations per predicted pair in the consensus seconary structure
Mean z-score of the sequences in the alignment
Structure conservation index for the alignment
Support vector machine decision value
RNA class probability as calculated by the SVM
# rnazSort.pl combPerPair results.dat
Sort by ``combinations per pair" value, i.e. gives you the hits with the most compensatory mutations.
Stefan Washietl <wash@tbi.univie.ac.at>