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OBICOMPLEMENT(1) OBITools OBICOMPLEMENT(1)

NAME

obicomplement - description of obicomplement

obicomplement reverse-complements the sequence records.

TIP:

The identifiers of the sequence records are modified by appending to them the _CMP suffix.


TIP:

a attribute with key complemented and value sets to True is added on each reversed complemented sequence record.




By using the selection option set, it is possible to reverse complement only a subset of the sequence records included in the input file. The selected sequence are reversed complemented, others are stored without modification

Example 1: 

> obicomplement seq.fasta > seqRC.fasta


Reverses complements all sequence records from the seq.fasta file and stores the result to the seqRC.fasta file.

Example 2:

> obicomplement -s 'A{10,}$' seq.fasta > seqRC.fasta


Reverses complements sequence records from the seq.fasta file only if they finish by at least 10 A. Others sequences are stored without modification.



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
Input file is in fasta format (including OBITools fasta extensions).

--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
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.

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