filter¶
filter filters one or more placefiles by placement name.
usage: filter [options] placefile[s]
Options¶
-o | Specify the filename to write to. |
--out-dir | Specify the directory to write files to. |
--prefix | Specify a string to be prepended to filenames. |
-Vr | Exclude every placement name by default (by default everything included). |
-Ir | Include placements whose name matches the given regexp. May be passed multiple times. |
-Er | Exclude placements whose name matches the given regexp. May be passed multiple times. |
-c | Reference package path. |
--cutoff | Use this cutoff for determining how likely a match is for a tax_id. Default: 0.9 |
--pp | Use posterior probability for our criteria. |
-Vx | Exclude every tax_id by default (by default everything included). |
-Ix | Include placements which are likely matches for the given tax_id. May be passed multiple times. |
-Ex | Exclude placements which are likely matches for the given tax_id. May be passed multiple times. |
--mass-gt | Include pqueries with a mass greater than the specified value. |
--mass-le | Include pqueries with a mass less than or equal to the specified value. |
Details¶
This subcommand will filter pqueries in one or more placefiles. Placements can be filtered either by name or by tax_id.
By default, all pqueries present in any input file will be present in the
output file. In this case, adding -Er
or -Ex
flags will
cause pqueries to be excluded from the output if they match any of the provided
regexps or tax_ids. Adding -Ir
or -Ix
flags will re-add any
pqueries which would have otherwise been excluded.
If the options -Vr
or -Vx
are provided, the default will
instead be to exclude all pqueries, unless (respectively) -Ir
or
-Ix
are provided to include (respectively) specific placement names
or tax_ids. In this case, adding -Er
or -Ex
flags will
exclude pqueries which would have otherwise been included.
Whether or not -Vr
or -Vx
have been provided, a placement
will be included or excluded if any (as opposed to all) of the provided
inclusions or exclusions match.
When using the -Ix
or -Ex
options, it is required to also
pass the -c
option to provide a reference package for looking up
taxonomic data. The –cutoff` flag also controls whether -Ix
or
-Ex
will match for a particular placement: neither flag will match
unless the likelihood that the placement matches that tax_id is greater than
the value provided for the –cutoff flag.
Since pqueries can have multiple names, the -Ir
and -Er
flags will filter the names a placement has. If a placement has had all of its
names filtered out, it won’t be present in the output.