Imported modules
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from Bio import Fasta, Alphabet
from Bio.Alphabet import IUPAC
from Bio.Data import IUPACData, CodonTable
from Bio.Seq import Seq
from Bio.Tools import Translate
from PropertyManager import default_manager
import getopt
import os
import re
import sys
import time
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Functions
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GC
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GC ( seq )
calculates G+C content
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GC123
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GC123 ( seq )
calculates totla G+C content plus first, second and third position
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GC_Frame
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GC_Frame ( seq, genetic_code=1 )
just an alias for six_frame_translations
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GC_skew
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GC_skew ( seq, window=100 )
calculates GC skew (G-C)/(G+C)
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antiparallel
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antiparallel ( seq )
returns reversed complementary sequence ( = other strand )
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apply_on_multi_fasta
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apply_on_multi_fasta (
file,
function,
*args,
)
apply function on each sequence in a multiple FASTA file
Exceptions
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NotImplementedError, "%s not implemented" % function
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complement
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complement ( seq )
returns the complementary sequence (NOT antiparallel)
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fasta_uniqids
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fasta_uniqids ( file )
checks and changes the name/ID's to be unique identifiers by adding numbers
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makeTableX
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makeTableX ( table )
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molecular_weight
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molecular_weight ( seq )
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nt_search
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nt_search ( seq, subseq )
search for a DNA subseq in sequence
use ambiguous values (like N = A or T or C or G, R = A or G etc.)
searches only on forward strand
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quick_FASTA_reader
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quick_FASTA_reader ( file )
simple and FASTA reader, preferable to be used on large files
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quicker_apply_on_multi_fasta
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quicker_apply_on_multi_fasta (
file,
function,
*args,
)
apply function on each sequence in a multiple FASTA file
Exceptions
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NotImplementedError, "%s not implemented" % function
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reverse
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reverse ( seq )
reverse the sequence
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six_frame_translations
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six_frame_translations ( seq, genetic_code=1 )
nice looking 6 frame translation with GC content - code from xbbtools
similar to DNA Striders six-frame translation
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translate
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translate (
seq,
frame=1,
genetic_code=1,
translator=None,
)
translation of DNA in one of the six different reading frames
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xGC_skew
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xGC_skew (
seq,
window=1000,
zoom=100,
r=300,
px=100,
py=100,
)
calculates and plots normal and accumulated GC skew (GRAPHICS !!!)
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Classes
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