seqfu rotate
Rotate a sequence setting a new starting position, using a new position or an oligonucleotide.
Introduced with SeqFu 1.8.6.
sage:
fu-rotate [options] -i POS [<fastq-file>...]
fu-rotate [options] -m STR [<fastq-file>...]
Rotate the sequences of one or more sequence files using
coordinates or motifs.
Position based:
-i, --start-pos POS Restart from base POS, where 1 is the first base [default: 1]
Motif based:
-m, --motif STR Rotate sequences using motif STR as the new start,
where STR is a string of bases
-s, --skip-unmached If a motif is provided, skip sequences that do not
match the motif
-r, --revcomp Also scan for reverse complemented motif
Other options:
-v, --verbose Verbose output
-h, --help Show this help
Examples
Given an input file with a single sequence:
>polyA
ACACGTACTACTGAAAAAAAAAACTGCTACTA
Rotate by new position
seqfu rotate -i 14 data/homopolymer.fa
Output:
>polyA
AAAAAAAAAACTGCTACTAACACGTACTACTG
Rotate by oligonucleotide
rotation by oligo will only produce an output if the match is unique
seqfu rotate -m AAAAAAAAAA data/homopolymer.fa
Output:
>polyA
AAAAAAAAAACTGCTACTAACACGTACTACTG
Rotate by oligonucleotide (also in reverse)
seqfu rotate -r -m GTTTTTTTTTT data/homopolymer.fa
Output:
>polyA
GTTTTTTTTTTCAGTAGTACGTGTTAGTAGCA
Screenshot
