obihead: extracts the first sequence records

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.

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.