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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 2.7


-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

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