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python-biopython  1.60
Classes | Functions | Variables
nextorf Namespace Reference

Classes

class  ProteinX
class  MissingTable
class  NextOrf

Functions

def makeTableX
def help

Variables

tuple proteinX = ProteinX()
dictionary options
list args = sys.argv[1:]
tuple show_help = len(sys.argv)
string shorts = 'hv'
tuple longs = map(lambda x: x +'=', options.keys())
list file = args[0]
tuple nextorf = NextOrf(file, options)

Function Documentation

def nextorf.help ( )

Definition at line 200 of file nextorf.py.

00200 
00201 def help():
00202     global options
00203     print 'Usage:', sys.argv[0], '(<options>) <FASTA file>'
00204     
00205     print 'Options:                                                       default'
00206     print '--start       Start position in sequence                             0'
00207     print '--stop        Stop position in sequence            (end of seqence)'
00208     print '--minlength   Minimum length of orf in bp                          100'
00209     print '--maxlength   Maximum length of orf in bp, default           100000000'
00210     print '--strand      Strand to analyse [both, plus, minus]               both'
00211     print '--frame       Frame to analyse [1 2 3]                             all'
00212     print '--noframe     Ignore start codons [0 1]                              0'  
00213     print '--output      Output to generate [aa nt pos]                        aa'
00214     print '--gc          Creates GC statistics of ORF [0 1]                     0'
00215     print '--table       Genetic code to use (see below)                        1'
00216     
00217 #    for a,b in options.items(): print '\t', a,b
00218 #    print ''
00219     print "\nNCBI's Codon Tables:"
00220     for key, table in CodonTable.ambiguous_dna_by_id.items():
00221         print '\t',key, table._codon_table.names[0]
00222     print '\ne.g.\n./nextorf.py --minlength 5 --strand plus --output nt --gc 1 testjan.fas'
00223     sys.exit(0)
00224     

def nextorf.makeTableX (   table)

Definition at line 38 of file nextorf.py.

00038 
00039 def makeTableX(table):
00040   assert table.protein_alphabet == IUPAC.extended_protein
00041   return CodonTable.CodonTable(table.nucleotide_alphabet, proteinX,
00042                                MissingTable(table.forward_table),
00043                                table.back_table, table.start_codons,
00044                                table.stop_codons)
00045 
00046 


Variable Documentation

list nextorf.args = sys.argv[1:]

Definition at line 239 of file nextorf.py.

list nextorf.file = args[0]

Definition at line 259 of file nextorf.py.

tuple nextorf.longs = map(lambda x: x +'=', options.keys())

Definition at line 243 of file nextorf.py.

Definition at line 260 of file nextorf.py.

dictionary nextorf.options
Initial value:
00001 {
00002     'start': 0,
00003     'stop': 0,
00004     'minlength': 100,
00005     'maxlength': 100000000,
00006     'strand': 'both',
00007     'output': 'aa',
00008     'frames': [1,2,3],
00009     'gc': 0,
00010     'nostart': 0,
00011     'table': 1,
00012     }

Definition at line 225 of file nextorf.py.

Definition at line 26 of file nextorf.py.

string nextorf.shorts = 'hv'

Definition at line 242 of file nextorf.py.

tuple nextorf.show_help = len(sys.argv)

Definition at line 240 of file nextorf.py.