IgPostProcessor usage examples

##All options

usage: IgPostProcessor.py [-h] -i [INPUT] [-s SUPPORT] [-p PATTERN PATTERN]
                          [-c COLUMN COLUMN COLUMN] [-x CLUSTER]
                          [-o OUTPUT [OUTPUT ...]] [-l LENGTH] [-r] [-t]

Read IgSCUEAL output files.

optional arguments:
  -h, --help            show this help message and exit
  -i [INPUT], --input [INPUT]
                        The tab-separated file produced by IgSCUEAL. Must have
                        at least 10 columns
  -s SUPPORT, --support SUPPORT
                        Minimum assignment support required to process a read
                        (default is 0.9)
  -p PATTERN PATTERN, --pattern PATTERN PATTERN
                        A regular expression pattern for pulling out reads
                        that match a particular pattern in a particular
                        column, e.g. "Subtype V3-21,J3"
  -c COLUMN COLUMN COLUMN, --column COLUMN COLUMN COLUMN
                        A column [l,g,e] length argument to select lines based
                        on the length of the string in a given column, e.g.
                        JUNCTION_AA g 10 (all lines with JUNCTIONS_AA with
                        more than 10 chars)
  -x CLUSTER, --cluster CLUSTER
                        Only keep sequences which represent unique clonotypes
  -o OUTPUT [OUTPUT ...], --output OUTPUT [OUTPUT ...]
                        Output mode (default fasta): either summarize filtered
                        reads by column value (supply the column name), print
                        FASTA for the reads matching selection criteria
                        (fasta), or output JSON (json) for matching reads.
                        Finally specify "json output bin [bin2...]" to output
                        a json of "ID": "output" for each unique value of
                        "bin+bin2" (group by)
  -l LENGTH, --length LENGTH
                        Summarize the lengths of sequences in a given column
  -r, --rearrangement   Summarize all reads by
                        [H-family,H-allele,D-allele,J-allele]
  -t, --light_chain     If set, assume that the reads come from a light Ig
                        chain (no d-region)