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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

The N first sequence records of the file are discarded from the analysis and not reported to the output file

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

Input file is in genbank format.

Input file is in embl format.

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

Input file is in Sanger fastq format (standard fastq used by HiSeq/MiSeq sequencers).

Input file is in fastq format produced by Solexa (Ga IIx) sequencers.

Input file is in ecoPCR format.

Input is an ecoPCR database.

Specifying the sequence type

Input file contains nucleic sequences.

Input file contains protein sequences.

COMMON OPTIONS

Shows this help message and exits.

Sets logging in debug mode.

AUTHOR

The OBITools Development Team - LECA

COPYRIGHT

2019 - 2015, OBITool Development Team

January 28, 2019 1.02 12