FastaIndex

FastA index (.fai) handler compatible with samtools faidx. .fai is extended with 4 columns storing counts for A, C, G & T for each sequence.

Usage

Dependencies

• Python 2.7

Parameters

-h, --help	show this help message and exit
--version	show program's version number and exit
-v, --verbose	verbose
-i FASTA, --fasta FASTA
	FASTA file(s)
-o OUT, --out OUT
	output stream [stdout]
-r REGIONS, --regions REGIONS
	contig(s) or contig region(s) to output (returns reverse complement if end larger than start)
-N N	calculate NXX and exit ie N50
-L L	calculate LXX and exit ie L50
-S, --stats	return FastA stats aka fasta_stats

Examples

# retrieve sequence of scaffold00001 starting at 100 and ending at 200 base (0-based)
FastaIndex -i contigs.fa -r 'scaffold00001:100-200'

# retrieve reverse complement of the same region
FastaIndex -i contigs.fa -r 'scaffold00001:200-100'

# calculate N50 of FastA file
FastaIndex -i contigs.fa -N50

# more statistics of FastA file
FastaIndex -i contigs.fa -S
# or
fasta_stats -i contigs.fa

Installation

sudo pip install -U FastaIndex