mgkit.workflow.fasta_utils module¶
New in version 0.3.0.
Scripts that includes some functionality to help use FASTA files with the framework
split command¶
Used to split a fasta file into smaller fragments
translate command¶
Used to translate nucleotide sequences into amino acids.
uid command¶
Used to change a FASTA file headers to a unique ID. A table (tab separated) with the changes made can be kept, using the –table option.
filter¶
Used to filter a FASTA file by length and also for sequence/header if a pattern is contained. A list of headers to keep can be passed using the -f option.
info¶
Gets information about a FASTA file, prints seq_id (trimmed at first space), length and hash (default sha1) and optionally the sequence, GC content and in GFF format if wanted.
rename¶
Renames the headers of a FASTA file, appending a random suffix and an optional prefix
Changes¶
New in version 0.3.0.
Changed in version 0.3.1: added translate and uid command
Changed in version 0.3.4: ported to click
Changed in version 0.5.5: added option -1 to output only the forward/frame0 and -w to avoid wrap at 60 chars to the translate command
Changed in version 0.5.7: added filter and info commands for simple fasta file filtering and info