USeqInfo.pl
A script to collect basic information about a USeq archive.
USeqInfo.pl [--options...] <file1.useq> <file2.useq ...>
Options: -c | --chrom -s | --stat -v | --version -h | --help
The command line flags and descriptions:
Print each of the chromosome names and their lengths.
Print statistics for the scores across the genome, including mean, standard deviation, minimum, and maximum values. If the chromosomes are printed also, then chromosome level statistics are printed as well.
Print the version number.
Display this POD documentation.
This program will present basic information about a USeq archive. Basic metadata from the internal archiveReadMe.txt is listed, including genome version, data type, graph type, description, source data, and date, as well as additional information about the chromosomes, slices, observations, and content.
If desired, chromosome information, including name and length, may also be presented.
If the archive includes score data, it may also optionally present basic statistics across the genome, including mean, standard deviation, minimum, and maximum values. If chromosome information is also presented, then chromosome level statistics are included as well. Note that this may take extra time to calculate, as the entire file must be read. If the archive file is writable by the user, then chromosome and genome statistics are automatically updated in the archiveReadMe.txt file, avoiding future calculations.
Timothy J. Parnell, PhD Dept of Oncological Sciences Huntsman Cancer Institute University of Utah Salt Lake City, UT, 84112
This package is free software; you can redistribute it and/or modify it under the terms of the Artistic License 2.0.
To install Bio::DB::USeq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::DB::USeq
CPAN shell
perl -MCPAN -e shell install Bio::DB::USeq
For more information on module installation, please visit the detailed CPAN module installation guide.