test.fa
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.

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

test.fq
1@seq1
2ATGC
3+
4IIII
5@seq2
6ATGCC
7+
8IIIII
example
1filterx fq test.fq -e "print('{name}: {qual(seq)}')"
output
1# output
2seq1: 4.245115
3seq2: 3.9658952