Ubuntu Manpage: BaitFilter-v1.0.5 - manual page for BaitFilter-v1.0.5

Provided by: baitfisher_1.0+dfsg-2_amd64

NAME

       BaitFilter-v1.0.5 - manual page for BaitFilter-v1.0.5

DESCRIPTION

USAGE:

./BaitFilter-v1.0.5
-i <string> [-o <string>] [-c <string>] [-m <string>] [--blast-second-hit-evalue
<floating point number>] [--blast-first-hit-evalue <floating point number>]
[--blast-min-hit-coverage-of-baits-in-tiling-stack <floating point number>]
[--ref-blast-db <string>] [--blast-extra-commandline <string>]
[--blast-evalue-cutoff <floating point number>] [-B <string>] [-t <positive
integer>] [--ID-prefix <string>] [--verbosity <unsigned integer>] [-S] [--]
[--version] [-h]

Where:

-i <string>, --input-bait-file-name <string>

(required)
Name of the input bait locus file. This is the bait file

obtained from the Bait-Fisher program.

-o <string>, --output-bait-file-name <string>

Name of the output bait file. This is the file the contains the filtered bait loci
and the baits.

-c <string>, --convert <string>

Allows the user to produce the final output file for the bait producing company. In
this mode, BaitFilter reads the input bait file and instead of doing a filtering
step, it produces a costumn bait file that can be uploaded to the baits producing
company. In order to avoid confuction a filtering step cannot be done in the same
run as the conversion. If you want to filter a bait file and convert the output,
you will need to call this program twice, first to do the filtering and second to
do the conversion. Allowed conversion parameters currently are: "Agilent-Germany".

New output formats can be added upon request. Please contact the author: Christoph
Mayer, Email: Mayer Christoph <c.mayer.zfmk@uni-bonn.de>

-m <string>, --mode <string>

Appart form the input file this is the most essential option. This option specifies
which filter mode Bait-Filter uses. (See the user manual for more details):

"ab": Retain only the best bait locus for each alignemntfile

(e.g. gene) when using the optimality criterion
to

minimize the total number of required baits.

"as": Retain only the best bait locus for each alignemntfile

(e.g. gene) when using the optimality criterion
to

maximize the number of sequences the result is based on.

"fb": Retain only the best bait locus for each feature (e.g. CDS)

when using the optimality criterion
to minimize the total

number of required baits. Only applicable if alignment cutting has been used in
Bait-Fisher.

"fs": Retain only the best bait locus for each feature (e.g. CDS)

when using the optimality criterion
to maximize the number

of sequences the result is based on. Only applicable if alignment cutting has been
used in Bait-Fisher.

"blast-a": Remove all bait loci of ALIGNMENTs for which one or more baits have
multiple good hits to a reference genome.

"blast-f": Remove all bait loci of FEATUREs for which one or more baits have
multiple good hits to a reference genome.

"blast-l": Remove bait LOCI that contain a bait that hos multiple good hits to a
reference genome.

"thin-b":
Thin out a bait file to every Nth bait region, by finding

the start position that minimizes the number of baits.

"thin-s":
Thin out a bait file to every Nth bait region, by finding

the start position that maximizes the number of sequences.

--blast-second-hit-evalue <floating point number>

Maximum evalue for the second hit. A bait is characterized to bind ambiguously, if
we have two good hits. This option is the evalue threshold for the second hit.

--blast-first-hit-evalue <floating point number>

Maximum evalue for the first hit. A bait is characterized to bind ambiguously, if
we have two good hits. This option is the evalue threshold for the first hit.

--blast-min-hit-coverage-of-baits-in-tiling-stack <floating point

number>

Specifies a minimum hit coverage for the primary hit which at least one bait has to
have in each tiling stack. Otherwise the bait region is discarded. If not
specified, no hit coverage is checked. This parameter can only be used in
conjunction with other filters. Since the order in which the coverage filter and
the other filters are applied matters, the order is defined as follows: For the
mode options: ab, as, fb, fs the coverage is checked before determining the optimal
bait region. For the mode options: blast-a, blast-f, blast-l the hit coverage is
checked after filtering for baits with multiple good hits to the reference genome.

--ref-blast-db <string>

Base name to a blast data base file. This name is passed to the blast command. This
is the name of the fasta file of your reference genome. IMPORTANT: The makeblastdb
program has to be called before starting the Bait-Filter program. makeblastdb takes
the fasta file and creates data base files out of it.

--blast-extra-commandline <string>

When invoking the blast command, extra commandline parameters can be passed to the
blast command. As an example with this option it is possible to specifiy the number
of threads the blast command should use.

--blast-evalue-cutoff <floating point number>

When invoking the blast command, a default value of twice the
--<blast-first-hit-evalue is used. This should guarantee that all hits necessary
for the blast filter are found. However, for the coverage filtering a smaller
threshold might be necessary. This can be specified here.

-B <string>, --blast-executable <string>

Name of or path+name to the blast executable. Default: nblast. Minimum version
number: Blast+ 2.2.x

-t <positive integer>, --thinning-step-width <positive integer>

Thin out the bait file by retaining only every Nth bait region. This option
specified the step width N. If one of the moded thin-b, thin-s is active, this
option is required, otherwise it is not allowed to set this parameter.

--ID-prefix <string>

In the conversion mode Agilent-Germany each converted file should get a unique
ProdeID prefix, since even among multiple files, ProbeIDs are not allowed to be
identical. This this option the user is able to specifiy a prefix string to all
probe IDs in this file.

--verbosity <unsigned integer>

The verbosity option controls the amount of information Bait-Filter writes to the
console while running. 0: report only error messages that lead to exiting the
program. 1: report also wanrings, 2: report also progress, 3: report more detailed
progress, >10: debug output. 10000: all possible dignostic output.

-S, --stats

Compute stats for the input file and report these. This mode is automatically used
for all modes specified with -m or the conversion mode specified with -c.The
purpose of the -S option is to compute stats without having to filter or convert
the input file. In particular, the -S mode does not require specifying an output
file.

This option has no effect if combined with the -m or -c modes.

--, --ignore_rest

Ignores the rest of the labeled arguments following this flag.

--version

Displays version information and exits.

-h, --help

Displays usage information and exits.

This program can be used to produce the final output file for creating baits, or it
can be used to filter bait loci obtained from the Bait-Fisher program according to
different criteria. The bait file produced by BaitFisher computes a tiling desing
for each possible starting position. The purpuse of BaitFilter is to determine for
each target alignment/gene/feature the optimal bait region. As input it requires
the bait file generated by the BaitFisher program or a BaitFile generated by a
previous filtering run of BaitFilter. This bait file is specified with the -i
command line parameter (see below). Furthermore, the user has to specifiy an output
file name with the -o parameter and a filter mode with the -m parameter.

To convert a file to a customn output format, see the -c option below.

To compute stats of an input file, see the -S option below.

The different filter modes provided by BaitFilter are the following:

1a) Retain only the best bait locus per alignment file. Criterion: Minimize number
of required baits.

1b) Retain only the best bait locus per alignment file. Criterion: Maximize number
of sequenences.

2a) Retain only best bait locus per feature (requires that features were selected
in Bait-Fisher). Criterion: Minimize number of required baits.

2b) Retain only best bait locus per feature (requires that features were selected
in Bait-Fisher). Criterion: Maximize number of sequenences.

3) Use a blast search of the bait sequences against a reference genome to detect
putative non-unique target loci. Non unique target sites will have multiple good
hits against the reference genome. Furthermore, a minimum coverage of the best
blast hit of bait sequence against the genome can be specified. Note that all blast
modes require additional command line parameters! These modes remove bait regions
for which multiple blast hits where found. Different versions of this mode are
available:

3a) If a single bait is not unique, remove all bait regions from the current gene.

3b) If a single bait is not unique, remove all bait regions from the current
feature (if applicable).

3c) If a single bait is not unique, remove only the bait region that contains this
bait.

4) Thin out the given bait file: Retain only every Nth bait region, where N has to
be specified by the user. Two submodes are available:

4a) Thin out bait regions by retaining only every Nth bait region in a bait file.
The starting offset will by chosen such that the number of required baits is
minimized.

4b) Thin out bait regions by retaining only every Nth bait region in a bait file.
The starting offset will by chosen such that the number of sequences the result is
baised on is maximized.

./BaitFilter-v1.0.5 version: 1.0.5

NAME

DESCRIPTION

SEE ALSO