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OBICUT(1) OBITools OBICUT(1)

NAME

obicut - description of obicut

obicut is a command that trims sequence objects based on two integer values: the -b option gives the first position of the sequence to be kept, and the -e option gives the last position to be kept. Both values can be computed using a python expression.

Example: 

> obicut -b 50 -e seq_length seq1.fasta > seq2.fasta


Keeps only the sequence part from the fiftieth position to the end.



Example:

> obicut -b 50 -e seq_length-50 seq1.fasta > seq2.fasta


Trims the first and last 50 nucleotides of the sequence object.





OBICUT SPECIFIC OPTIONS

-b <INTEGER>, --begin=<INTEGER>
Integer value (possibly calculated using a python expression) indicating the first position of the sequence to be kept.

-e <INTEGER>, --end=<INTEGER>
Integer value (possibly calculated using a python expression) indicating the last position of the sequence to be kept.

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

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
January 28, 2019 1.02 12