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¶
|
Instructs the query to read the first line as a header. |
|
Tells the query to return the metadata content of the dictionary table. |
|
Ignore empty lines in the input stream. |
|
List of tags to filter files and file contents on. Used with .nord and .gord files. |
|
Read tags from a tag file and filter files and file contents on. Also accepts a nested query. Used with .nord and .gord files. |
|
Silent filter, filter tags don’t need to be in the dictionary table. Only applicable with the -f or -ff options. |
|
Write source name into output (alias if present in dictionary table, else filename).
Column name will be |
|
Maximum depth when using nor to list the content of a folder. Defaults to infinite |
|
Show modification date when using nor to list the content of a folder. |
|
Don’t follow links 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