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OBIHEAD(1) OBITools OBIHEAD(1)

NAME

obihead - description of obihead

obihead command is in some way analog to the standard Unix head command. It selects the head of a sequence file. But instead of working text line by text line as the standard Unix tool, selection is done at the sequence record level. You can specify the number of sequence records to select.

Example: 

> obihead -n 150 seq1.fasta > seq2.fasta


Selects the 150 first sequence records from the seq1.fasta file and stores them into the seq2.fasta file.





OBIHEAD SPECIFIC OPTIONS

-n <INTEGER>, --sequence-count=<INTEGER>
Number of sequence records to be selected (default value : 10).

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