++ed by:
ZMUGHAL

1 PAUSE user(s)

Emmanouil "Manolis" Maragkakis
and 1 contributors

NAME

CLIPSeqTools::PreprocessApp::annotate_with_file - Annotate alignments in a database table with regions from a BED/SAM file.

SYNOPSIS

clipseqtools-preprocess annotate_with_file [options/parameters]

DESCRIPTION

Annotate alignments in a database table with regions from a BED/SAM file. Adds a user defined column that will be NOT NULL if an alignment is contained within a region from the file and NULL otherwise.

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

  Other input
    --a_type <Str>         type of file with annotation regions (i.e. BED,
                           SAM).
    --a_file <Str>         file with annotation regions.

  Database options.
    --drop                 drop column if it already exists (not
                           supported in SQlite).

  Other options.
    --column <Str>         name for the new annotation column.
    --both_strands         annotate both strands irrespective of the
                           region strand specified in the file. May be
                           useful for repeats where only one strand is
                           usually provided.
    -v --verbose           print progress lines and extra information.
    -h -? --usage --help   print help message