eFASTA: extracting nucleotide segments from FASTA file
Use gcj compiler to compile the program from the code source. To create the binary eFASTA from the terminal, go to the directory containing the source code EFASTA.java and type:
make
Launch eFASTA without arguments to read the documentation.
USAGE: eFASTA <options>
where options are:
-fasta, -f <infile>
(mandatory) FASTA-formatted nucleotide sequence file name
-coord, -c <pattern:start-end>
(mandatory) DNA segment to extract from [infile] defined by the first FASTA header containing [pattern] and the region comprised between nucleotide indexes [start] and [end] (both inclusive); if [start] > [end], the extracted nucleotide segment is reverse-complemented
-outname, -o <basename>
extracted nucleotide segment is written into the FASTA-formatted output file [basename].fna (default: "seq")
-cds
to indicate that the extracted DNA segment is a CDS, leading to the writing of its amino acid translation (standard genetic code) into a second FASTA-formatted output file [basename].faa
-fcds
same as option -cds but to search for the full CDS that includes the specified region, i.e. first occuring codon START before index [start] and first occuring codon STOP after index [end]