This perl script will convert WGS assembly file (.fasta format) to Standard AGP file format. The rules for format conversion are followed by the NCBI guidelines given here.
NAME:
FastaToAGPFileFormatConverter.pl
DESCRIPTION:
This code will convert standard fasta file
into AGP v.2.0 file format.
This code is work for only scaffold level and
contig level assemblies.
AUTHOR:
Nitin N.
Email: nitinnarwade1504@gmail.com
OPTIONS:
-i
Specify input file in standard fasta format.
This option require input file name as an argument.
(eg. -i inputFileName.fasta)
Mandatory argument.
-o
Specify output file.
This option require output file name as an argument.
(eg. -o ouptutIFleame.agp)
Optional argument. By deffault output file name is 'ASSEMBLYLEVEL.agp'.
-h
print detailed help on consol.
This option does not require any argument.
(eg. perl FastaToAGPFileFormatConverter.pl -h).
-a
Specify the assembly level. This option require an argument.
(eg. -a scaffold OR -a contig).
[Optional argument. Default Value = scaffold].
-l
Specify the scaffold length cutoff.
[Optional argument. Default Value = 0].
-p
Specify the prefix for id.
[Optional argument. Defualt Value = HG].
--org
Specify organism name
[Optional argument. Default Value = "-"].
--taxanomicID
Specify taxanomic Identifier for organism.
[Optional argument. Default Value = "-"].
--date
Specify the date of assembly.
[Optional argument. Default Value = "-"].
--center
Specify the assembly center.
[Optional argument. Default Value = "-"].
-t
Specifiy assembly Type.
[Optional argument. Default Value = "-"]
EXAMPLE:
perl FastaToAGPFileFormatConverter.pl -i datafile.fa