pip install git+https://github.com/nanoporetech/pychopper.git

git clone https://github.com/nanoporetech/pychopper.git

python setup.py install

python setup.py develop

make test

make docs

usage: cdna_classifier.py [-h] -b primers [-i input_format] [-g aln_params]
                          [-t target_length] [-s score_percentile]
                          [-n sample_size] [-r report_pdf] [-u unclass_output]
                          [-S stats_output] [-A scores_output] [-x]
                          [-l heu_stringency] [-T nr_cores]
                          input_fastx output_fastx

Tool to identify full length cDNA reads. Primers have to be specified as they
are on the forward strand.

positional arguments:
  input_fastx          Input file.
  output_fastx         Output file.

optional arguments:
  -h, --help           show this help message and exit
  -b primers           Primers fasta.
  -i input_format      Input/output format (fastq).
  -g aln_params        Alignment parameters (match,
                       mismatch,gap_open,gap_extend).
  -t target_length     Number of bases to scan at each end (200).
  -s score_percentile  Score cutoff percentile (98).
  -n sample_size       Number of samples when calculating score cutoff
                       (100000).
  -r report_pdf        Report PDF.
  -u unclass_output    Write unclassified reads to this file.
  -S stats_output      Write statistics to this file.
  -A scores_output     Write alignment scores to this file.
  -x                   Use more sensitive (and error prone) heuristic mode
                       (False).
  -l heu_stringency    Stringency in heuristic mode (0.25).