pfasta

pfasta is a command-line tool for working with FASTA files to filter and sanitize them based on various criterion. This includes:

• Filtering out sequences that contain invalid amino acids
• Take sequences that contain invalid characters and replace/fix them
• Filter a set of sequences by a maximum and/or minimum sequence length
• Sub-sample a set of sequences for building a reduced set of randomly selected sequences

At it’s basline, pfasta takes a single sequence file as input and writes a new output sequence. There are a series of flags that can be applied, as outlined in the Usage section below.

Usage

pfasta <flags> filename.fasta

-o <output filename> (default: output.fasta)
   Define the name of the output FASAT file

--non-unique-header
  Flag that, if provided allows multiple FASTA records to have identical headers

--duplicate-record (default: fail)
  Flag that provides a keyword that defines how duplicate FASTA records are dealt with.
  Options are:
      fail   : throws an exception and exits the parsing
      ignore : duplicate records are retained
      remove : duplicate records are removed

--duplicate-sequence (default: fail)
  Flag that provides a keyword that defines how duplicate sequences are dealt with.
  Options are:
      fail   : throws an exception and exits the parsing
      ignore : duplicate sequences are retained
      remove : duplicate sequences are removed

--invalid-sequence (default: fail)
  Flag that provides a keyword that defines how invalid sequences are dealt with.
  Options are:
      fail                : throws an exception and exits the parsing
      ignore              : invalid sequences are retained
      remove              : invalid sequences are removed
      convert-all         : invalid residues are converted according to the standard conversion table
                            (shown below) but if OTHER invalid residues are found an exception is raised
                            B->N,    U->C,    X->G,    Z->Q,    '*'->'',    '-'->''
      convert-res         : invalid residues are converted according to the standard conversion table
                            with the exception of sequence-alignment gaps ('-')
      convert-all-ignore  : invalid residues are converted according to the standard conversion table,
                            and if OTHER invalid residues are found they are ignored
      convert-res-ignore  : invalid residues are converted according to the standard conversion table,
                            with the exception of the sequence-aligment gap ('-') character, but
                            if OTHER invalid residues are found they are ignored

--number-lines (default: 60)
  Flag that defines the number of lines in the output FASTA file

--shortest-seq-lines (default: None)
  Flag that defines a filter that sets the shortest sequence returned

--longest-seq-lines (default: None)
  Flag that defines a filter that sets the longest sequence returned

--random-subsample (default: None)
  Flag that defines the number of randomly sub-sampled sequences. Allows a test FASTA file to be
  generated as a sub-set for testing analysis pipelines

--print-statistics
  Flag that, if provided, means statistics about the FINAL set of sequences written

--no-outputfile
  Flag that, if provided, means NO outputfile is generated.

--silent
  Flag that, if provided, means pfasta generates ZERO output to STDOUT