08-13-2013
Hello to all,
If there is an option extract the sequences directly from the binary file would be better and faster I think,
I'm not sure if it is possible with bash or Perl or another option you can suggest me.
Hello Jotne,
Thanks for your help. Your script detects the position of the sequences but I would like to
extract those sequences to a new file having in the output file one line per information of each block
in binary.
Hello wisecracker,
I'll check the option you mention, but it is possible with your script to extract the complete byte sequence?
Thanks again for the help.
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LEARN ABOUT DEBIAN
rnacalibrate
RNACALIBRATE(1) General Commands Manual RNACALIBRATE(1)
NAME
RNAcalibrate - calibrate statistics of secondary structure hybridisations of RNAs
SYNOPSIS
RNAcalibrate [-h] [-d frequency_file] [-f from,to] [-k sample_size] [-l mean,std] [-m max_target_length] [-n max_query_length] [-u
iloop_upper_limit] [-v bloop_upper_limit] [-s] [-t target_file] [-q query_file] [target] [query]
DESCRIPTION
RNAcalibrate is a tool for calibrating minimum free energy (mfe) hybridisations performed with RNAhybrid. It searches a random database
that can be given on the command line or otherwise generates random sequences according to given sample size, length distribution parame-
ters and dinucleotide frequencies. To the empirical distribution of length normalised minimum free energies, parameters of an extreme value
distribution (evd) are fitted. The output gives for each miRNA its name (or "command_line" if it was submitted on the command line), the
number of data points the evd fit was done on, the location and the scale parameter. The location and scale parameters of the evd can then
be given to RNAhybrid for the calculation of mfe p-values.
OPTIONS
-h Give a short summary of command line options.
-d frequency_file
Generate random sequences according to dinucleotide frequencies given in frequency_file. See example directory for example files.
-f from,to
Forces all structures to have a helix from position from to position to with respect to the query. The first base has position 1.
-k sample_size
Generate sample_size random sequences. Default value is 5000.
-l mean,std
Generate random sequences with a normal length distribution of mean mean and standard deviation std. Default values are 500 and 300,
respectively.
-m max_target_length
The maximum allowed length of a target sequence. The default value is 2000. This option only has an effect if a target file is given
with the -t option (see below).
-n max_query_length
The maximum allowed length of a query sequence. The default value is 30. This option only has an effect if a query file is given
with the -q option (see below).
-u iloop_upper_limit
The maximally allowed number of unpaired nucleotides in either side of an internal loop.
-v bloop_upper_limit
The maximally allowed number of unpaired nucleotides in a bulge loop.
-s Generate random sequences according to the dinucleotide distribution of given targets (either with the -t option or on command line.
If no -t is given, either the last argument (if a -q is given) or the second last argument (if no -q is given) to RNAcalibrate is
taken as a target). See -t option.
-t target_file
Without the -s option, each of the target sequences in target_file is subject to hybridisation with each of the queries (which
either are from the query_file or is the one query given on command line; see -q below). The sequences in the target_file have to be
in FASTA format, ie. one line starting with a > and directly followed by a name, then one or more following lines with the sequence
itself. Each individual sequence line must not have more than 1000 characters.
With the -s option, the target (or target file) dinucleotide distribution is counted, and random sequences are generated according
to this distribution.
If no -t is given, random sequences are generated as described above (see -d option).
-q query_file
See -t option above. If no -q is given, the last argument to RNAcalibrate is taken as a query.
REFERENCES
The energy parameters are taken from:
Mathews DH, Sabina J, Zuker M, Turner DH. "Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary
structure" J Mol Biol., 288 (5), pp 911-940, 1999
VERSION
This man page documents version 2.0 of RNAcalibrate.
AUTHORS
Marc Rehmsmeier, Peter Steffen, Matthias Hoechsmann.
LIMITATIONS
Character dependent energy values are only defined for [acgtuACGTU]. All other characters lead to values of zero in these cases.
SEE ALSO
RNAhybrid, RNAeffective
RNACALIBRATE(1)