FASTA format
In bioinformatics, long character strings are often encoded in a format called FASTA. A FASTA file can contain several strings, each identified by a name marked by a “>” character at the beginning of the line.
Write a program that reads a FASTA file such as:
>Rosetta_Example_1 THERECANBENOSPACE >Rosetta_Example_2 THERECANBESEVERAL LINESBUTTHEYALLMUST BECONCATENATED
And prints the following output:
Rosetta_Example_1: THERECANBENOSPACE Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
Note that a high-quality implementation will not hold the entire file in memory at once; real FASTA files can be multiple gigabytes in size.
Perl 6
Certainly not the most elegant way to do it, but that's a start: <lang Perl 6>say "{.[0]}: {.[1]>>.comb(/\N+/).join}" for ">Rosetta_Example_1 THERECANBENOSPACE >Rosetta_Example_2 THERECANBESEVERAL LINESBUTTHEYALLMUST BECONCATENATED".comb: / '>' (\N+)\n (<!before '>'>\N+\n?)+ /, :match</lang>
Tcl
<lang tcl>proc fastaReader {filename} {
set f [open $filename] set sep "" while {[gets $f line] >= 0} {
if {[string match >* $line]} { puts -nonewline "$sep[string range $line 1 end]: " set sep "\n" } else { puts -nonewline $line }
} puts "" close $f
}
fastaReader ./rosettacode.fasta</lang>
- Output:
Rosetta_Example_1: THERECANBENOSPACE Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED