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