Provided by: obitools_1.2.12+dfsg-2_amd64 
NAME
obigrep - description of obigrep
The obigrep command is in some way analog to the standard Unix grep command. It selects a
subset of sequence records from a sequence file.
A sequence record is a complex object composed of an identifier, a set of attributes
(key=value), a definition, and the sequence itself.
Instead of working text line by text line as the standard Unix tool, selection is done
sequence record by sequence record. A large set of options allows refining selection on
any of the sequence record elements.
Moreover obigrep allows specifying simultaneously several conditions (that take the value
TRUE or FALSE) and only the sequence records that fulfill all the conditions (all
conditions are TRUE) are selected.
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.
AUTHOR
The OBITools Development Team - LECA
COPYRIGHT
2019 - 2015, OBITool Development Team
1.02 12 Jan 28, 2019 OBIGREP(1)