Source Code for Module Bio.Sequencing.Applications._Novoalign

  1  # Copyright 2009 by Osvaldo Zagordi.  All rights reserved. 
  2  # Revisions copyright 2010 by Peter Cock. 
  3  # This code is part of the Biopython distribution and governed by its 
  4  # license.  Please see the LICENSE file that should have been included 
  5  # as part of this package. 
  6  """Command line wrapper for the short read aligner Novoalign by Novocraft.""" 
  7  import types 
  8  from Bio.Application import _Option, AbstractCommandline 
  9   
 10   
 11 -class NovoalignCommandline(AbstractCommandline): 
 12      """Command line wrapper for novoalign by Novocraft. 
 13   
 14      See www.novocraft.com - novoalign is a short read alignment program. 
 15   
 16      Example: 
 17   
 18      >>> from Bio.Sequencing.Applications import NovoalignCommandline 
 19      >>> novoalign_cline = NovoalignCommandline(database='some_db', 
 20      ...                                        readfile='some_seq.txt') 
 21      >>> print novoalign_cline 
 22      novoalign -d some_db -f some_seq.txt 
 23   
 24      As with all the Biopython application wrappers, you can also add or 
 25      change options after creating the object: 
 26   
 27      >>> novoalign_cline.format = 'PRBnSEQ' 
 28      >>> novoalign_cline.r_method='0.99' # limited valid values 
 29      >>> novoalign_cline.fragment = '250 20' # must be given as a string 
 30      >>> novoalign_cline.miRNA = 100 
 31      >>> print novoalign_cline 
 32      novoalign -d some_db -f some_seq.txt -F PRBnSEQ -r 0.99 -i 250 20 -m 100 
 33   
 34      You would typically run the command line with novoalign_cline() or via 
 35      the Python subprocess module, as described in the Biopython tutorial. 
 36   
 37      Last checked against version: 2.05.04 
 38      """ 
 39 -    def __init__(self, cmd="novoalign", **kwargs): 
 40   
 41          READ_FORMAT = ['FA', 'SLXFQ', 'STDFQ', 'ILMFQ', 'PRB', 'PRBnSEQ'] 
 42          REPORT_FORMAT = ['Native', 'Pairwise', 'SAM'] 
 43          REPEAT_METHOD = ['None', 'Random', 'All', 'Exhaustive', '0.99'] 
 44   
 45          self.parameters = \ 
 46             [ 
 47              _Option(["-d", "database"], 
 48                      "database filename", 
 49                      filename=True, 
 50                      equate=False), 
 51              _Option(["-f", "readfile"], 
 52                      "read file", 
 53                      filename=True, 
 54                      equate=False), 
 55              _Option(["-F", "format"], 
 56                      "Format of read files.\n\nAllowed values: %s" 
 57                      % ", ".join(READ_FORMAT), 
 58                      checker_function=lambda x: x in READ_FORMAT, 
 59                      equate=False), 
 60   
 61              # Alignment scoring options 
 62              _Option(["-t", "threshold"], 
 63                      "Threshold for alignment score", 
 64                      checker_function=lambda x: isinstance(x, types.IntType), 
 65                      equate=False), 
 66              _Option(["-g", "gap_open"], 
 67                      "Gap opening penalty [default: 40]", 
 68                      checker_function=lambda x: isinstance(x, types.IntType), 
 69                      equate=False), 
 70              _Option(["-x", "gap_extend"], 
 71                      "Gap extend penalty [default: 15]", 
 72                      checker_function=lambda x: isinstance(x, types.IntType), 
 73                      equate=False), 
 74              _Option(["-u", "unconverted"], 
 75                      "Experimental: unconverted cytosines penalty in bisulfite mode\n\n" 
 76                      "Default: no penalty", 
 77                      checker_function=lambda x: isinstance(x, types.IntType), 
 78                      equate=False), 
 79   
 80              # Quality control and read filtering 
 81              _Option(["-l", "good_bases"], 
 82                      "Minimum number of good quality bases [default: log(N_g, 4) + 5]", 
 83                      checker_function=lambda x: isinstance(x, types.IntType), 
 84                      equate=False), 
 85              _Option(["-h", "homopolymer"], 
 86                      "Homopolymer read filter [default: 20; disable: negative value]", 
 87                      checker_function=lambda x: isinstance(x, types.IntType), 
 88                      equate=False), 
 89   
 90              # Read preprocessing options 
 91              _Option(["-a", "adapter3"], 
 92                      "Strips a 3' adapter sequence prior to alignment.\n\n" 
 93                      "With paired ends two adapters can be specified", 
 94                      checker_function=lambda x: isinstance(x, types.StringType), 
 95                      equate=False), 
 96              _Option(["-n", "truncate"], 
 97                      "Truncate to specific length before alignment", 
 98                      checker_function=lambda x: isinstance(x, types.IntType), 
 99                      equate=False), 
100              _Option(["-s", "trimming"], 
101                      "If fail to align, trim by s bases until they map or become shorter than l.\n\n" 
102                      "Ddefault: 2", 
103                      checker_function=lambda x: isinstance(x, types.IntType), 
104                      equate=False), 
105              _Option(["-5", "adapter5"], 
106                      "Strips a 5' adapter sequence.\n\n" 
107                      "Similar to -a (adaptor3), but on the 5' end.", 
108                      checker_function=lambda x: isinstance(x, types.StringType), 
109                      equate=False), 
110              # Reporting options 
111              _Option(["-o", "report"], 
112                      "Specifies the report format.\n\nAllowed values: %s\nDefault: Native" 
113                      % ", ".join(REPORT_FORMAT), 
114                      checker_function=lambda x: x in REPORT_FORMAT, 
115                      equate=False), 
116              _Option(["-Q", "quality"], 
117                      "Lower threshold for an alignment to be reported [default: 0]", 
118                      checker_function=lambda x: isinstance(x, types.IntType), 
119                      equate=False), 
120              _Option(["-R", "repeats"], 
121                      "If score difference is higher, report repeats.\n\n" 
122                      "Otherwise -r read method applies [default: 5]", 
123                      checker_function=lambda x: isinstance(x, types.IntType), 
124                      equate=False), 
125              _Option(["-r", "r_method"], 
126                      "Methods to report reads with multiple matches.\n\n" 
127                      "Allowed values: %s\n" 
128                      "'All' and 'Exhaustive' accept limits." 
129                      % ", ".join(REPEAT_METHOD), 
130                      checker_function=lambda x: x.split()[0] in REPEAT_METHOD, 
131                      equate=False), 
132              _Option(["-e", "recorded"], 
133                      "Alignments recorded with score equal to the best.\n\n" 
134                      "Default: 1000 in default read method, otherwise no limit.", 
135                      checker_function=lambda x: isinstance(x, types.IntType), 
136                      equate=False), 
137              _Option(["-q", "qual_digits"], 
138                      "Decimal digits for quality scores [default: 0]", 
139                      checker_function=lambda x: isinstance(x, types.IntType), 
140                      equate=False), 
141   
142              # Paired end options 
143              _Option(["-i", "fragment"], 
144                      "Fragment length (2 reads + insert) and standard deviation [default: 250 30]", 
145                      checker_function=lambda x: len(x.split()) == 2, 
146                      equate=False), 
147              _Option(["-v", "variation"], 
148                      "Structural variation penalty [default: 70]", 
149                      checker_function=lambda x: isinstance(x, types.IntType), 
150                      equate=False), 
151   
152              # miRNA mode 
153              _Option(["-m", "miRNA"], 
154                      "Sets miRNA mode and optionally sets a value for the region scanned [default: off]", 
155                      checker_function=lambda x: isinstance(x, types.IntType), 
156                      equate=False), 
157   
158              # Multithreading 
159              _Option(["-c", "cores"], 
160                      "Number of threads, disabled on free versions [default: number of cores]", 
161                      checker_function=lambda x: isinstance(x, types.IntType), 
162                      equate=False), 
163   
164              # Quality calibrations 
165              _Option(["-k", "read_cal"], 
166                      "Read quality calibration from file (mismatch counts)", 
167                      checker_function=lambda x: isinstance(x, types.StringType), 
168                      equate=False), 
169              _Option(["-K", "write_cal"], 
170                      "Accumulate mismatch counts and write to file", 
171                      checker_function=lambda x: isinstance(x, types.StringType), 
172                      equate=False), 
173              ] 
174          AbstractCommandline.__init__(self, cmd, **kwargs) 
175   
176   
177 -def _test(): 
178      """Run the module's doctests (PRIVATE).""" 
179      print "Running Novoalign doctests..." 
180      import doctest 
181      doctest.testmod() 
182      print "Done" 
183   
184  if __name__ == "__main__": 
185      _test() 
186