Provided by: obitools_1.2.12+dfsg-2_amd64 
NAME
obiannotate - description of obiannotate
obiannotate is the command that allows adding/modifying/removing annotation attributes
attached to sequence records.
Once such attributes are added, they can be used by the other OBITools commands for
filtering purposes or for statistics computing.
Example 1:
> obiannotate -S short:'len(sequence)<100' seq1.fasta > seq2.fasta
The above command adds an attribute named short which has a boolean value indicating
whether the sequence length is less than 100bp.
Example 2:
> obiannotate --seq-rank seq1.fasta | \
obiannotate -C --set-identifier '"'FungA'_%05d" % seq_rank' \
> seq2.fasta
The above command adds a new attribute whose value is the sequence record entry number
in the file. Then it clears all the sequence record attributes and sets the identifier
to a string beginning with FungA_ followed by a suffix with 5 digits containing the
sequence entry number.
Example 3:
> obiannotate -d my_ecopcr_database \
--with-taxon-at-rank=genus seq1.fasta > seq2.fasta
The above command adds taxonomic information at the genus rank to the sequence records.
Example 4:
> obiannotate -S 'new_seq:str(sequence).replace("a","t")' \
seq1.fasta | obiannotate --set-sequence new_seq > seq2.fasta
The overall aim of the above command is to edit the sequence object itself, by
replacing all nucleotides a by nucleotides t. First, a new attribute named new_seq is
created, which contains the modified sequence, and then the former sequence is replaced
by the modified one.
SEQUENCE RECORD EDITING OPTIONS
--seq-rank
Adds a new attribute named seq_rank to the sequence record indicating its entry
number in the sequence file.
-R <OLD_NAME>:<NEW_NAME>, --rename-tag=<OLD_NAME>:<NEW_NAME>
Changes attribute name <OLD_NAME> to <NEW_NAME>. When attribute named <OLD_NAME> is
missing, the sequence record is skipped and the next one is examined.
--delete-tag=<KEY>
Deletes attribute named <ATTRIBUTE_NAME>.When this attribute is missing, the
sequence record is skipped and the next one is examined.
-S <KEY>:<PYTHON_EXPRESSION>, --set-tag=<KEY>:<PYTHON_EXPRESSION>
Creates a new attribute named with a key <KEY> and a value computed from
<PYTHON_EXPRESSION>.
--tag-list=<FILENAME>
<FILENAME> points to a file containing attribute names and values to modify for
specified sequence records.
--set-identifier=<PYTHON_EXPRESSION>
Sets sequence record identifier with a value computed from <PYTHON_EXPRESSION>.
--run=<PYTHON_EXPRESSION>
Runs a python expression on each selected sequence.
--set-sequence=<PYTHON_EXPRESSION>
Changes the sequence itself with a value computed from <PYTHON_EXPRESSION>.
-T, --set-definition=<PYTHON_EXPRESSION>
Sets sequence definition with a value computed from <PYTHON_EXPRESSION>.
-O, --only-valid-python
Allows only valid python expressions.
-C, --clear
Clears all attributes associated to the sequence records.
-k <KEY>, --keep=<KEY>
Keeps only attribute with key <KEY>. Several -k options can be combined.
--length
Adds attribute with seq_length as a key and sequence length as a value.
--with-taxon-at-rank=<RANK_NAME>
Adds taxonomic annotation at taxonomic rank <RANK_NAME>.
-m <MCLFILE>, --mcl=<MCLFILE>
Creates a new attribute containing the number of the cluster the sequence record
was assigned to, as indicated in file <MCLFILE>.
--uniq-id
Forces sequence record ids to be unique.
SEQUENCE RECORD SELECTION OPTIONS
-s <REGULAR_PATTERN>, --sequence=<REGULAR_PATTERN>
Regular expression pattern to be tested against the sequence itself. The pattern
is case insensitive.
Examples:
> obigrep -s 'GAATTC' seq1.fasta > seq2.fasta
Selects only the sequence records that contain an EcoRI restriction site.
> obigrep -s 'A{10,}' seq1.fasta > seq2.fasta
Selects only the sequence records that contain a stretch of at least 10 A.
> obigrep -s '^[ACGT]+$' seq1.fasta > seq2.fasta
Selects only the sequence records that do not contain ambiguous nucleotides.
-D <REGULAR_PATTERN>, --definition=<REGULAR_PATTERN>
Regular expression pattern to be tested against the definition of the sequence
record. The pattern is case sensitive.
Example:
> obigrep -D '[Cc]hloroplast' seq1.fasta > seq2.fasta
Selects only the sequence records whose definition contains chloroplast or
Chloroplast.
-I <REGULAR_PATTERN>, --identifier=<REGULAR_PATTERN>
Regular expression pattern to be tested against the identifier of the sequence
record. The pattern is case sensitive.
Example:
> obigrep -I '^GH' seq1.fasta > seq2.fasta
Selects only the sequence records whose identifier begins with GH.
--id-list=<FILENAME>
<FILENAME> points to a text file containing the list of sequence record
identifiers to be selected. The file format consists in a single identifier per
line.
Example:
> obigrep --id-list=my_id_list.txt seq1.fasta > seq2.fasta
Selects only the sequence records whose identifier is present in the
my_id_list.txt file.
-a <KEY>:<REGULAR_PATTERN>,
--attribute=<KEY>:<REGULAR_PATTERN>
Regular expression pattern matched against the attributes of the sequence
record. the value of this attribute is of the form : key:regular_pattern. The
pattern is case sensitive. Several -a options can be used on the same command
line and in this last case, the selected sequence records will match all
constraints.
Example:
> obigrep -a 'family_name:Asteraceae' seq1.fasta > seq2.fasta
Selects the sequence records containing an attribute whose key is family_name
and value is Asteraceae.
-A <ATTRIBUTE_NAME>, --has-attribute=<KEY>
Selects sequence records having an attribute whose key = <KEY>.
Example:
> obigrep -A taxid seq1.fasta > seq2.fasta
Selects only the sequence records having a taxid attribute defined.
-p <PYTHON_EXPRESSION>, --predicat=<PYTHON_EXPRESSION>
Python boolean expression to be evaluated for each sequence record. The
attribute keys defined for each sequence record can be used in the expression as
variable names. An extra variable named ‘sequence’ refers to the sequence
record itself. Several -p options can be used on the same command line and in
this last case, the selected sequence records will match all constraints.
Example:
> obigrep -p '(forward_error<2) and (reverse_error<2)' \
seq1.fasta > seq2.fasta
Selects only the sequence records whose forward_error and reverse_error
attributes have a value smaller than two.
-L <##>, --lmax=<##>
Keeps sequence records whose sequence length is equal or shorter than lmax.
Example:
> obigrep -L 100 seq1.fasta > seq2.fasta
Selects only the sequence records that have a sequence length equal or shorter
than 100bp.
-l <##>, --lmin=<##>
Selects sequence records whose sequence length is equal or longer than lmin.
Examples:
> obigrep -l 100 seq1.fasta > seq2.fasta
Selects only the sequence records that have a sequence length equal or longer
than 100bp.
-v, --inverse-match
Inverts the sequence record selection.
Examples:
> obigrep -v -l 100 seq1.fasta > seq2.fasta
Selects only the sequence records that have a sequence length shorter than
100bp.
TAXONOMY RELATED OPTIONS
-d <FILENAME>, --database=<FILENAME>
ecoPCR taxonomy Database name
-t <FILENAME>, --taxonomy-dump=<FILENAME>
NCBI Taxonomy dump repository name
--require-rank=<RANK_NAME>
select sequence with taxid tag containing a parent of rank <RANK_NAME>
-r <TAXID>, --required=<TAXID>
required taxid
-i <TAXID>, --ignore=<TAXID>
ignored taxid
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.
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.
OBIANNOTATE ADDED SEQUENCE ATTRIBUTES
· seq_length
· seq_rank
· cluster
· scientific_name
· taxid
· rank
· family
· family_name
· genus
· genus_name
· order
· order_name
· species
· species_name
AUTHOR
The OBITools Development Team - LECA
COPYRIGHT
2019 - 2015, OBITool Development Team
1.02 12 Jan 28, 2019 OBIANNOTATE(1)