Source Command

NOR

The NOR command reads non-ordered relations from a single file or a nested source. File sources are assumed to be tab-separated (.tsv, .rep, or .map) and with # as the first symbol in the first line to indicate that it is a header. Comma-separated files can also be used if they are named .csv. Likewise, .gor and .gorz files can be read, but are treated as unordered relations.

The -h option can be used to instruct the query to read the first line as a header, but this option is not necessary if the first line starts with a # symbol.

It is important to note that NOR queries on very large files can be memory intensive.

Usage

nor file.tsv | ...

Options

-h

Instructs the query to read the first line as a header.

-asdict

Tells the query to return the metadata content of the dictionary table.

-i

Ignore empty lines in the input stream.

-f A[,B]*

List of tags to filter files and file contents on. Used with .nord and .gord files.

-ff File

Read tags from a tag file and filter files and file contents on. Also accepts a nested query. Used with .nord and .gord files.

-fs

Silent filter, filter tags don’t need to be in the dictionary table. Only applicable with the -f or -ff options.

-s [name]

Write source name into output (alias if present in dictionary table, else filename). Column name will be name but Source if no name is specified.

-d

Maximum depth when using nor to list the content of a folder. Defaults to infinite

-m

Show modification date when using nor to list the content of a folder.

Examples

In the following example, we are using NOR to open the Variant Effect Predictor (VEP) impact map table. We are setting the -h flag on the NOR query in order to read the first line as a header and the -i option to ignore all empty lines.

nor -h -i ref/VEP_impact.map

We often want to open up the contents of a GOR Dictionary table, such as the WES varcalls dictionary, rather than opening the files it references. To do this we use the -asdict option:

nor -asdict source/var/wes_varcalls.gord

Using custom NOR Dictionary table, with filter and custom source column name:

nor  custom.nord -f PN-001,PN-005,PN-010 -s PN

Reserved Metacharacters

Note that some characters are reserved in the nor file and will be automatically replaced if used in the data rows:

Reserved Metacharacters

./*+-‘$;,