Converting FASTA format

The FASTA file format is very simple and is quite similar to the MEGA file format. This is an example of a sample input file:

>G019uabh 400 bp

ATACATCATAACACTACTTCCTACCCATAAGCTCCTTTTAACTTGTTAAAGTCTTGCTTG

AATTAAAGACTTGTTTAAACACAAAAATTTAGAGTTTTACTCAACAAAAGTGATTGATTG

ATTGATTGATTGATTGATGGTTTACAGTAGGACTTCATTCTAGTCATTATAGCTGCTGGC

AGTATAACTGGCCAGCCTTTAATACATTGCTGCTTAGAGTCAAAGCATGTACTTAGAGTT

GGTATGATTTATCTTTTTGGTCTTCTATAGCCTCCTTCCCCATCCCCATCAGTCTTAATC

AGTCTTGTTACGTTATGACTAATCTTTGGGGATTGTGCAGAATGTTATTTTAGATAAGCA

AAACGAGCAAAATGGGGAGTTACTTATATTTCTTTAAAGC

>G028uaah 268 bp

CATAAGCTCCTTTTAACTTGTTAAAGTCTTGCTTGAATTAAAGACTTGTTTAAACACAAA

ATTTAGACTTTTACTCAACAAAAGTGATTGATTGATTGATTGATTGATTGATGGTTTACA

GTAGGACTTCATTCTAGTCATTATAGCTGCTGGCAGTATAACTGGCCAGCCTTTAATACA

TTGCTGCTTAGAGTCAAAGCATGTACTTAGAGTTGGTATGATTTATCTTTTTGGTCTTCT

ATAGCCTCCTTCCCCATCCCATCAGTCT

The MEGA file converter looks for a line that begin with a greater-than sign (‘>’), replaces it with a pound sign (‘#’), takes the word following the pound sign as the sequence name, deletes the rest of the line, and takes the following lines (up to the next line beginning with a ‘>’) as the sequence data. The MEGA file above would convert as follows:

#mega

Title: infile.fasta

#G019uabh