p3-file-filter

Filter a File Against Contents of a Second File

p3-file-filter.pl [options] filterFile filterCol1 filterCol2 ...

Filter the standard input using the contents of a file. The output will contain only those rows in the input file whose key value matches a value from the specified column of the specified filter file. To have the output contain only those rows in the input file that do NOT match, use the --reverse option. This is similar to p3-merge, except that script operates on whole lines instead of a set of key fields.

Parameters

The positional parameters are the name of the filter file and the indices (1-based) or names of the key columns in the filter file. If the latter parameter is absent, the value of the --col parameter will be used (same name or index as the input file).

The standard input can be overridden using the options in Input Options.

Additional command-line options are the following.

• reverse

Instead of only keeping input records that match a filter record, only keep records that do NOT match.

• col

The name or index of the key column in the input file. If more than one value is specified, the columns are matched one-for-one with the corresponding filter file columns.

Example

This command is shown in the tutorial p3-common-tasks.html;

p3-file-filter –reverse –col=feature.role aRoles.tbl feature.role <cRoles.tbl

feature.role count 2,3-dihydroxybenzoate-AMP ligase (EC 2.7.7.58) of siderophore biosynthesis 33 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase (EC 1.14.13.-) 1 2-pyrone-4,6-dicarboxylic acid hydrolase (EC 3.1.1.57) 14 23S ribosomal RNA rRNA prediction is too short 1 …