usage: find_candidates.py [-h] [--n_core N_CORE] [--len_th LEN_TH] fasta_file

find candidates of subreads adaptor unremoved

positional arguments:
  fasta_file       a file that contains the subread information

optional arguments:
  -h, --help       show this help message and exit
  --n_core N_CORE  number of processes
  --len_th LEN_TH  length threshold of k-mer matching region

usage: validate_unremoved_adaptor.py [-h] [--lalign LALIGN] [--n_core N_CORE]
                                     [--len_th LEN_TH]
                                     candidate_file fasta_file

validate the candidates and get alignments between the plus strand and the
minus strand

positional arguments:
  candidate_file   a file that lists candidates of adaptor unremoved subreads
  fasta_file       a file that contains the subread information

optional arguments:
  -h, --help       show this help message and exit
  --lalign LALIGN  the directory of lalign
  --n_core N_CORE  number of processes
  --len_th LEN_TH  length threshold of k-mer matching region

usage: resolve_length_info.py [-h] [--n_core N_CORE] fasta_file

determine the number of splitting adaptor unremoved subreads

positional arguments:
  fasta_file       a file that contains the subread information

optional arguments:
  -h, --help       show this help message and exit
  --n_core N_CORE  number of processes

usage: resolve_length_info_with_validate.py [-h] [--n_core N_CORE]
                                            fasta_file validate_file

determine the number of splitting adaptor unremoved subreads with even/odd
information

positional arguments:
  fasta_file       a file that contains the subread information
  validate_file    output file of validate_unremoved_adaptor.py

optional arguments:
  -h, --help       show this help message and exit
  --n_core N_CORE  number of processes

$ source VIRTUAL_ENV_DIR/bin/activate
$ python find_candidates.py --n_core 12 --len_th 35 subreads.fasta > candidates
$ python validate_unremoved_adaptor.py --n_core 12 --lalign LALIGN_DIR candidates subreads.fasta > overlap
$ ./extractValidatedSubreads.pl overlap > overlap.extracted
$ python resolve_length_info_with_validate.py --n_core 12 subreads.fasta overlap.extracted > result