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OBIUNIQ(1) OBITools OBIUNIQ(1)

NAME

obiuniq - description of obiuniq

The obiuniq command is in some way analog to the standard Unix uniq -c command.

Instead of working text line by text line as the standard Unix tool, the processing is done on sequence records.

A sequence record is a complex object composed of an identifier, a set of attributes (key=value), a definition, and the sequence itself.

The obiuniq command groups together sequence records. Then, for each group, a sequence record is printed.

A group is defined by the sequence and optionally by the values of a set of attributes specified with the -c option.

As the identifier, the set of attributes (key=value) and the definition of the sequence records that are grouped together may be different, two options (-m and -i) allow refining how these parts of the records are reported.

  • By default, only attributes with identical values within a group of sequence records are kept.
  • A count attribute is set to the total number of sequence records for each group.
  • For each attribute specified by the -m option, a new attribute whose key is prefixed by merged_ is created. These new attributes contain the number of times each value occurs within the group of sequence records.



OBIUNIQ AND TAXONOMIC INFORMATION

When a taxonomy is loaded (-d or -t options), the merged_taxid attribute is created and records the number of times each taxid has been found in the group (it may be empty if no sequence record has a taxid attribute in the group). In addition, a set of taxonomy-related attributes are generated for each group having at least one sequence record with a taxid attribute. The taxid attribute of the sequence group is set to the last common ancestor of the taxids of the group. All other taxonomy-related attributes created (species, genus, family, species_name, genus_name, family_name, rank, scientific_name) give information on the last common ancestor.

OBIUNIQ SPECIFIC OPTIONS

Attribute to merge.

Example:

> obiuniq -m sample seq1.fasta > seq2.fasta


Dereplicates sequences and keeps the value distribution of the sample attribute in the new attribute merged_sample.




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

Adds one attribute to the list of attributes used to define sequence groups (this option can be used several times).

Example:

> obiuniq -c sample seq1.fasta > seq2.fasta


Dereplicates sequences within each sample.




Dereplication is done based on prefix matching:
1.
The shortest sequence of each group is a prefix of any sequence of its group
2.
The shortest sequence of a group is the prefix of only the sequences belonging to its group




TAXONOMY RELATED OPTIONS

ecoPCR taxonomy Database name

NCBI Taxonomy dump repository name

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.

COMMON OPTIONS

Shows this help message and exits.

Sets logging in debug mode.

OBIUNIQ ADDED SEQUENCE ATTRIBUTES

  • count
  • merged_*
  • merged
  • scientific_name
  • rank

  • family
  • family_name
  • genus
  • genus_name

  • order
  • order_name
  • species
  • species_name




OBIUNIQ USED SEQUENCE ATTRIBUTE

•
taxid



AUTHOR

The OBITools Development Team - LECA

COPYRIGHT

2019 - 2015, OBITool Development Team

July 27, 2019 1.02 13