NAME

CLIPSeqTools::CompareApp::all - Run all clipseqtools-compare analyses.

SYNOPSIS

clipseqtools-compare all [options/parameters]

DESCRIPTION

Run all clipseqtools-compare analyses.

Takes two libraries (one called input and one called reference) on which all single clipseqtools analyses have ran. Assumes that all single clipseqtools analyses used a common o_prefix for each library.

OPTIONS

  Input options for library.
    --driver <Str>          driver for database connection (eg. mysql,
                            SQLite).
    --database <Str>        database name or path to database file for
                            file based databases (eg. SQLite).
    --table <Str>           database table.
    --host <Str>            hostname for database connection.
    --user <Str>            username for database connection.
    --password <Str>        password for database connection.
    --records_class <Str>   type of records stored in database.
    --filter <Filter>       filter library. May be used multiple times.
                            Syntax: column_name="pattern"
                            e.g. keep reads with deletions AND not repeat
                                masked AND longer than 31
                                --filter deletion="def"
                                --filter rmsk="undef" .
                                --filter query_length=">31".
                            Operators: >, >=, <, <=, =, !=, def, undef
    --res_prefix <Str>      results prefix of clipseqtools analysis.
                            Should match the o_prefix used when running
                            clipseqtools on the library.

  Input options for reference library.
    --r_driver <Str>        driver for database connection (eg. mysql,
                            SQLite).
    --r_database <Str>      database name or path to database file for
                            file based databases (eg. SQLite).
    --r_table <Str>         database table.
    --r_host <Str>          hostname for database connection.
    --r_user <Str>          username for database connection.
    --r_password <Str>      password for database connection.
    --r_records_class <Str> type of records stored in database.
    --r_filter <Filter>     same as filter but for reference library.
    --r_res_prefix <Str>    results prefix of clipseqtools analysis.
                            Should match the o_prefix used when running
                            clipseqtools on the reference library.

  Other input.
    --rname_sizes <Str>     file with sizes for reference alignment
                            sequences (rnames). Must be tab delimited
                            (chromosome\tsize) with one line per rname.

  Output
    --o_prefix <Str>        output path prefix. Script will create and add
                            extension to path. Default: ./

  Other options.
    -v --verbose           print progress lines and extra information.
    -h -? --usage --help   print help message