1>seq1
2ACGGGGT
3>seq2
4ACGTAAAAAA

gc#

computes the GC content of a sequence.

1filterx fasta test.fa -e 'gc(seq) >= 0.5'

1### Output
2>seq1
3ACGGGGT

rev & rev_#

rev_ reverses a sequence in place, while rev will return a new reversed sequence.

reverses a sequence.

1filterx fasta test.fa -e 'rev_(seq)'
2
3### Output
4>seq1
5TGGGGCA
6>seq2
7AAAAAAAGCA

revcomp & revcomp_#

reverses and complements a sequence.

1filterx fasta test.fa -e 'revcomp_(seq)'
2
3### Output
4>seq1
5ACCCCGT
6>seq2
7TTTTTTACGT

to_fasta & to_fa#

converts a sequence to a FASTA format. Only available for fasta and fastq files.

1>seq1
2ACGGGGT
3>seq2
4ACGTAAAAAA
5aa

1filterx fasta test.fa -e 'to_fasta()'
2
3### Output
4>seq1
5ACGGGGT
6>seq2
7ACGTAAAAAAaa

1@name
2ACGGGGT
3+
4~~~~~~~
5@name2
6ACGTAAAAAA
7+
8~~~~~~~~~~

1filterx fastq test.fq -e 'to_fa()'
2
3### Output
4>name
5ACGGGGT
6>name2
7ACGTAAAAAA

Not only to_fasta/to_fa can convert to FASTA, while using filterx fq --no-qual test.fq will remove the quality information, and auto-convert to FASTA.

1filterx fq --no-qual test.fq
2
3### Output
4>name
5ACGGGGT
6>name2
7ACGTAAAAAA

to_fastq & to_fq#

same as to_fasta but for fastq files. Only available for fasta and fastq files.

phred#

get the phred type of a fastq file.

qual#

Compute the mean quality of a sequence.

1@seq1
2ATGC
3+
4IIII
5@seq2
6ATGCC
7+
8IIIII

1filterx fq test.fq -e "print('{name}: {qual(seq)}')"

1# output
2seq1: 4.245115
3seq2: 3.9658952