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 …