Provided by: obitools_1.2.12+dfsg-2_amd64 
NAME
obiselect - description of obiselect
obiselect command allows to select a subset of sequences records from a sequence file by
describing sequence record groups and defining how many and which sequence records from
each group must be retrieved.
In each group as definied by a set of -c options, sequence records are ordered according
to a score function. The N first sequences (N`is selected using the `-n option) are kept
in the result subset of sequence records.
By default the score function is a random function and one sequence record is retrieved
per group. This leads to select randomly one sequence per group.
OBISELECT SPECIFIC OPTIONS
-c <KEY>, --category-attribute=<KEY>
Attribute used to categorize the sequence records. Several -c options can be
combined.
TIP:
The <KEY> can be simply the key of an attribute, or a Python expression
similarly to the -p option of obigrep.
Example:
> obiselect -c sample -c seq_length seq.fasta
This command select randomly one sequence record per sample and sequence length
from the sequence records included in the seq.fasta file. The selected sequence
records are printed on the screen.
-n <INTEGER>, --number=<INTEGER>
Indicates how many sequence records per group have to be retrieved. If the size
of the group is lesser than this NUMBER, the whole group is retrieved.
Example:
> obiselect -n 2 -c sample -c seq_length seq.fasta
This command has the same effect than the previous example except that two
sequences are retrieved by class of sample/length.
--merge=<KEY>
Attribute to merge.
Example:
> obiselect -c seq_length -n 2 -m sample seq1.fasta > seq2.fasta
This command keeps two sequences per sequence length, and records how many times
they were observed for each sample in the new attribute merged_sample.
--merge-ids
Adds a merged attribute containing the list of sequence record ids merged within
this group.
-m, --min
Sets the function used for scoring sequence records into a group to the minimum
function. The minimum function is applied to the values used to define categories
(see option -c). Sequences will be ordered according to the distance of their
values to the minimum value.
-M, --max
Sets the function used for scoring sequence records into a group to the maximum
function. The maximum function is applied to the values used to define categories
(see option -c). Sequences will be ordered according to the distance of their
values to the maximum value.
-a, --mean
Sets the function used for scoring sequence records into a group to the mean
function. The mean function is applied to the values used to define categories
(see option -c). Sequences will be ordered according to the distance of their
values to the mean value.
--median
Sets the function used for scoring sequence records into a group to the median
function. The median function is applied to the values used to define categories
(see option -c). Sequences will be ordered according to the distance of their
values to the median value.
-f FUNCTION, --function=FUNCTION
Sets the function used for scoring sequence records into a group to a user define
function. The user define function is declared using Python syntax. Attribute keys
can be used as variables. An extra sequence variable representing the full
sequence record is available. If option for loading a taxonomy database is
provided, a taxonomy variable is also available. The function is estimated for
each sequence record and the minimum value of this function in each group.
Sequences will be ordered in each group according to the distance of their function
estimation to the minimum value of their group.
OPTIONS TO SPECIFY INPUT FORMAT
Restrict the analysis to a sub-part of the input file
--skip <N>
The N first sequence records of the file are discarded from the analysis and not
reported to the output file
--only <N>
Only the N next sequence records of the file are analyzed. The following sequences
in the file are neither analyzed, neither reported to the output file. This option
can be used conjointly with the –skip option.
Sequence annotated format
--genbank
Input file is in genbank format.
--embl Input file is in embl format.
fasta related format
--fasta
Input file is in fasta format (including OBITools fasta extensions).
fastq related format
--sanger
Input file is in Sanger fastq format (standard fastq used by HiSeq/MiSeq
sequencers).
--solexa
Input file is in fastq format produced by Solexa (Ga IIx) sequencers.
ecoPCR related format
--ecopcr
Input file is in ecoPCR format.
--ecopcrdb
Input is an ecoPCR database.
Specifying the sequence type
--nuc Input file contains nucleic sequences.
--prot Input file contains protein sequences.
TAXONOMY RELATED OPTIONS
-d <FILENAME>, --database=<FILENAME>
ecoPCR taxonomy Database name
-t <FILENAME>, --taxonomy-dump=<FILENAME>
NCBI Taxonomy dump repository name
OPTIONS TO SPECIFY OUTPUT FORMAT
Standard output format
--fasta-output
Output sequences in OBITools fasta format
--fastq-output
Output sequences in Sanger fastq format
Generating an ecoPCR database
--ecopcrdb-output=<PREFIX_FILENAME>
Creates an ecoPCR database from sequence records results
Miscellaneous option
--uppercase
Print sequences in upper case (default is lower case)
COMMON OPTIONS
-h, --help
Shows this help message and exits.
--DEBUG
Sets logging in debug mode.
OBISELECT ADDED SEQUENCE ATTRIBUTES
· class
· distance
· merged
· class
· merged_*
· select
OBISELECT USED SEQUENCE ATTRIBUTE
· taxid
AUTHOR
The OBITools Development Team - LECA
COPYRIGHT
2019 - 2015, OBITool Development Team
1.02 12 Jan 28, 2019 OBISELECT(1)