FastA index (.fai) handler compatible with samtools faidx. .fai is extended with 4 columns storing counts for A, C, G & T for each sequence.
- Python >= 3
-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
# 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
sudo pip install -U FastaIndex