rnazFilter.pl
- Filter output files from rnazCluster.pl
by different criteria.
rnazFilter.pl [options] "filter" [file]
Count the windows/loci instead of printing them.
Prints version information and exits.
Print a short help message and exits.
Prints a detailed manual page and exits.
rnazFilter.pl
reads tab-delimited data files as generated by
rnazCluster.pl
. For each window a filter is applied and if the
filter is passed the window and the corresponding locus are printed
out. Thus, you get all loci with at least one window that fulfills your
filter criteria.
The mandatory filter statement is given within double quotes (" ") and can contain comparison/logical statements and field identifiers as listed below.
Technically, the statement is directly interpreted by Perl, so you can
use anything which works in Perl. The same caveats apply, for example:
If you want compare numbers you must use ==
, if you compare strings
you have to use eq
.
Please note: everything you put in the filter statement is evaluated by Perl. This can be potentially harmful, so take care.
Consecutive numbered ID for each window
The locus which this window belongs to
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 sequence 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 the 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
Specify a particular column by its index #. First column has index 1.
e.g. COL18>0.9
is equivalent to P>0.9
Less than, greater than
Equals numerically
Equals (strings)
Matches regular expression.
Logical operators and grouping
# rnazFilter.pl "P>0.9 and z<-3 and seqID~=/chr13/" results.dat
Gives you all clusters with windows with P>0.9 and z<-3 on chromosome 13.
# rnazFilter.pl -c "P>0.9" results.dat
Counts all windows/loci with P>0.9.
Stefan Washietl <wash@tbi.univie.ac.at>