#fagrep This is a modified version of GNU grep that allows it to print out fasta/fastq records. The modifications a basic and currently most of the options are broken or I've not tried to see if they are broken.

I'd love contributions by anyone who knows a bit of C and has some time up their hands.

for printing fasta records from fasta formatted files:

grep --fasta ...

for printing fastq record from fastq formatted files:

grep --fastq ...

without the fasta/q options this version of grep should (I hope) perform identically to regular GNU grep.

GNU grep is fast for a number of reasons but one of them is that it reads a file into a large buffer then searches the entire buffer. If it finds a match grep then finds the beginning and end of a line and prints it out. Consider the opposite scenario where the file is parsed first to identify the bounds of each fasta or fastq record, after which a search can then take place. The grep way is faster because there will probably be large portions of an input file that will not contain a match and therefore the parse-then-search method will send alot of time reading in records that will never need to be printed out.

When switching from line orientated output to record output using --fasta or --fastq, the following logic is used:

When in fasta mode, fagrep will look for the '>' character and set this as the bounds of the record. This character is assumed to be unique so if it exists in the sequence name or description it will cause formatting errors.

When in fastq mode, fagrep will look for the '@' at the beginning of a line that is not preceeded by the '+' character. This means that the fastq file must not contain any extra information in the 'comment' line, the one that begins with '+'.

@seq1
AAAAA
+
hahah
@seq2
TTTTT
+
@haah  <- An @ char as the first qual will not match
@seq3
GGGGG
+seq3
@haha <- This will be called the start of a record by accident

--color
-c
-l
-n
-h/-H
-v

-v with -c, but either on their own is fine
-A
-B
-C

Grep can prefix lines with a variety of things such as the line number, file offset, file name. These options work but they are printed before the record separator and not on any of the following lines of the record, which makes the output have invalid formatting.