--- name: "obiannotate" section: "1" platform: "linux" package: "obitools" version: "1.2.12+dfsg-2" release: "Debian 10 (Buster)" platforms: ["linux"] url: "https://new.carta.tech/obiannotate" --- # obiannotate(1) 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: Example 2: Example 3: Example 4: ## 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 \:\, --rename-tag=\:\** Changes attribute name \ to \. When attribute named \ is missing, the sequence record is skipped and the next one is examined. - **--delete-tag=\** Deletes attribute named \.When this attribute is missing, the sequence record is skipped and the next one is examined. - **-S \:\, --set-tag=\:\** Creates a new attribute named with a key \ and a value computed from \. - **--tag-list=\** \ points to a file containing attribute names and values to modify for specified sequence records. - **--set-identifier=\** Sets sequence record identifier with a value computed from \. - **--run=\** Runs a python expression on each selected sequence. - **--set-sequence=\** Changes the sequence itself with a value computed from \. - **-T, --set-definition=\** Sets sequence definition with a value computed from \. - **-O, --only-valid-python** Allows only valid python expressions. - **-C, --clear** Clears all attributes associated to the sequence records. - **-k \, --keep=\** Keeps only attribute with 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=\** Adds taxonomic annotation at taxonomic rank \. - **-m \, --mcl=\** Creates a new attribute containing the number of the cluster the sequence record was assigned to, as indicated in file \. - **--uniq-id** Forces sequence record ids to be unique. ## SEQUENCE RECORD SELECTION OPTIONS - **-s \, --sequence=\** 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 \, --definition=\** 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 \, --identifier=\** 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=\** **\** 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 \:\,** - **--attribute=\:\** 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 \, --has-attribute=\** Selects sequence records having an attribute whose key = \. *Example:* ``` > obigrep -A taxid seq1.fasta > seq2.fasta ``` Selects only the sequence records having a *taxid* attribute defined. - **-p \, --predicat=\** 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 \, --database=\** ecoPCR taxonomy Database name - **-t \, --taxonomy-dump=\** NCBI Taxonomy dump repository name - **--require-rank=\** select sequence with taxid tag containing a parent of rank \ - **-r \, --required=\** required taxid - **-i \, --ignore=\** ignored taxid ## OPTIONS TO SPECIFY INPUT FORMAT ### Restrict the analysis to a sub-part of the input file - **--skip \** The N first sequence records of the file are discarded from the analysis and not reported to the output file - **--only \** 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=\** 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