fasta2fasta.py - operate on sequences¶

Tags: Sequences

Purpose¶

perform operations (masking, renaming) on a stream of fasta formatted sequences.

Available edit operations are:

translate: translate sequences using the standard genetic code.
translate-to-stop: translate until first stop codon
truncate-at-stop: truncate sequence at first stop codon
back-translate: convert nucleotide sequence to peptide sequence Requires parameter of second fasta file with peptide sequences.
mark-codons: adds a space after each codon
apply-map: rename sequence identifiers from a given map Requires parameter with filename of a map. The map is a tab-separated file mapping old to new names.
build-map: rename sequence identifiers numerically and save output in a tab-separated file. Requires parameter with filename of a map. The map is a tab-separated file mapping new to old names and will be newly created. Any exiting file of the same name will be overwritten.
pseudo-codons: translate, but keep register with codons
interleaved-codons: mix amino acids and codons
filter: remove sequence according to certain criteria. For example, –method=filter –filter-method=min-length=5 –filter-method=max-length=10

map-codons:

remove-gaps: remove all gaps in the sequence
mask-stops: mask all stop codons
mask-seg: mask sequence by running seg
mask-bias: mask sequence by running bias
mask-codons: mask codon sequence given a masked amino acid sequence. Requires parameter with masked amino acids in fasta format.
mask-incomplete-codons: mask codons that are partially masked or gapped
mask-soft: combine hard-masked (NNN) sequences with unmasked sequences to generate soft masked sequence (masked regions in lower case)
remove-stops: remove stop codons
upper: convert sequence to upper case
lower: convert sequence to lower case
reverse-complement: build the reverse complement
shuffle: shuffle each sequence
sample: select a certain proportion of sequences

Parameters are given to the option parameters in a comma-separated list in the order that the edit operations are called upon.

Exclusion/inclusion is tested before applying any id mapping.

Usage¶

Example:

python fasta2fasta.py --method=translate < in.fasta > out.fasta

Type:

python fasta2fasta.py --help

for command line help.

Command line options¶

usage: fasta2fasta [-h] [--version]
                   [-m {translate,translate-to-stop,truncate-at-stop,back-translate,mark-codons,apply-map,build-map,pseudo-codons,filter,interleaved-codons,map-codons,remove-gaps,mask-seg,mask-bias,mask-codons,mask-incomplete-codons,mask-stops,mask-soft,map-identifier,nop,remove-stops,upper,lower,reverse-complement,sample,shuffle}]
                   [-p PARAMETERS] [-x]
                   [--sample-proportion SAMPLE_PROPORTION]
                   [--exclude-pattern EXCLUDE_PATTERN]
                   [--include-pattern INCLUDE_PATTERN]
                   [--filter-method FILTER_METHODS] [-t {aa,na}]
                   [-l TEMPLATE_IDENTIFIER] [--map-tsv-file MAP_TSV_FILE]
                   [--fold-width FOLD_WIDTH] [--timeit TIMEIT_FILE]
                   [--timeit-name TIMEIT_NAME] [--timeit-header]
                   [--random-seed RANDOM_SEED] [-v LOGLEVEL]
                   [--log-config-filename LOG_CONFIG_FILENAME]
                   [--tracing {function}] [-? ?] [-I STDIN] [-L STDLOG]
                   [-E STDERR] [-S STDOUT]
fasta2fasta: error: argument -?: expected one argument