fasta-grep <re> (-dna | -prot) [options]
fasta-grep displays the non-overlapping occurrences of a
PERL regular expression in FASTA sequences.
fasta-grep supports the IUPAC
alphabets for amino acids and nucleotides.
A PERL regular expression.
The sequences are DNA or protein, respectively.
Reads FASTA formatted sequences from standard input.
Writes matches to the regular expression to standard output or, optionally, a file. The output is in the form
FASTA sequence ID line followed by number of matches [line 1 of sequence] [match line 1] [line 2 of sequence] [match line 2] ... [last line of sequence] [last match line]For proteins, occurrences are marked on the match lines as:
> start of occurrence < end of occurrenceFor DNA, occurrences are marked on the match line as:
> start of occurrence < end of occurrence * start and end of two occurrences
|-dna||Sequence is DNA.|
|-prot||Sequence is protein.|
|-s||Print whole matching sequences only.|
|-p||Print positions only, not sequence; 1-based. (relative to input strand if DNA; see below)|
|-m||Print IDs of matching sequences only.|
|-x||Print IDs of non-matching sequences only.|
|-o||Print occurrences only in "raw" format.|
|-f||Print occurrences only in FASTA format. 1-based positions (relative to the strand of the match if DNA) are appended to the sequence ID.|
|-a||Print all occurrences (even overlapping ones); ignored unless -o or -f given.|
|-norc||Only print matches to given strand.||print matches for both DNA strands.|
|-prosite||<re> is in PROSITE format.||print matches for both DNA strands.|
|-erase||Replace occurrences with 'N's (-dna) or 'X's (-prot).|
fasta-grep WGATAAN -dna < ~/crp0.s fasta-grep A[AT]G -dna < ~/crp0.fasta