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.
- --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.
- --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.
- --nuc
- Input file contains nucleic sequences.
- --prot
- Input file contains protein sequences.
- --DEBUG
- Sets logging in debug mode.
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