Scroll to navigation

OBISELECT(1) OBITools OBISELECT(1)

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

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.




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.




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.




Adds a merged attribute containing the list of sequence record ids merged within this group.

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.

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.

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.

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.

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

The N first sequence records of the file are discarded from the analysis and not reported to the output file

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

Input file is in genbank format.

Input file is in embl format.

Input file is in fasta format (including OBITools fasta extensions).

Input file is in Sanger fastq format (standard fastq used by HiSeq/MiSeq sequencers).

Input file is in fastq format produced by Solexa (Ga IIx) sequencers.

Input file is in ecoPCR format.

Input is an ecoPCR database.

Specifying the sequence type

Input file contains nucleic sequences.

Input file contains protein sequences.

TAXONOMY RELATED OPTIONS

ecoPCR taxonomy Database name

NCBI Taxonomy dump repository name

OPTIONS TO SPECIFY OUTPUT FORMAT

Standard output format

--fasta-output
Output sequences in OBITools fasta format

Output sequences in Sanger fastq format

Generating an ecoPCR database

--ecopcrdb-output=<PREFIX_FILENAME>
Creates an ecoPCR database from sequence records results

Miscellaneous option

Print sequences in upper case (default is lower case)

COMMON OPTIONS

Shows this help message and exits.

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

January 28, 2019 1.02 12