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python-biopython  1.60
Functions | Variables
test_SeqUtils Namespace Reference

Functions

def u_crc32
def simple_LCC
def windowed_LCC

Variables

string dna_fasta_filename = "Fasta/f002"
 quick_FASTA_reader #
tuple tuple_records = quick_FASTA_reader(dna_fasta_filename)
tuple seq_records = list(SeqIO.parse(open(dna_fasta_filename),"fasta"))
tuple CAI = CodonAdaptationIndex()
 CodonUsage #.
string dna_genbank_filename = "GenBank/NC_005816.gb"
tuple record = SeqIO.read(open(dna_genbank_filename), "genbank")
list records = []
 start = feature.location.start.position
 end = feature.location.end.position
tuple table = int(feature.qualifiers["transl_table"][0])
list seq = record.seq[start:end]
string a = "M"
list b = feature.qualifiers["translation"]
list description = feature.qualifiers["product"]
tuple handle = open(dna_fasta_filename, "w")
string str_light_chain_one = "QSALTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGK"
 crc64 collision #
string str_light_chain_two = "QSALTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGK"
list examples
 main checksum/LCC tests #
tuple value = checksum(seq_str)

Function Documentation

Definition at line 126 of file test_SeqUtils.py.

00126 
00127     def simple_LCC(s):
00128         return "%0.2f" % lcc_simp(s)

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def test_SeqUtils.u_crc32 (   seq)

Definition at line 116 of file test_SeqUtils.py.

00116 
00117 def u_crc32(seq):
00118     #NOTE - On Python 2 crc32 could return a signed int, but on Python 3 it is
00119     #always unsigned
00120     #Docs suggest should use crc32(x) & 0xffffffff for consistency.
00121     return crc32(seq) & 0xffffffff 

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Definition at line 129 of file test_SeqUtils.py.

00129 
00130     def windowed_LCC(s):
00131         return ", ".join(["%0.2f" % v for v in lcc_mult(s,20)])

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Variable Documentation

string test_SeqUtils.a = "M"

Definition at line 60 of file test_SeqUtils.py.

list test_SeqUtils.b = feature.qualifiers["translation"]

Definition at line 61 of file test_SeqUtils.py.

CodonUsage #.

Definition at line 38 of file test_SeqUtils.py.

list test_SeqUtils.description = feature.qualifiers["product"]

Definition at line 64 of file test_SeqUtils.py.

string test_SeqUtils.dna_fasta_filename = "Fasta/f002"

quick_FASTA_reader #

Definition at line 22 of file test_SeqUtils.py.

string test_SeqUtils.dna_genbank_filename = "GenBank/NC_005816.gb"

Definition at line 45 of file test_SeqUtils.py.

test_SeqUtils.end = feature.location.end.position

Definition at line 52 of file test_SeqUtils.py.

Initial value:
00001 [str_light_chain_one, str_light_chain_two,
00002             "ATGCGTATCGATCGCGATACGATTAGGCGGAT"]

main checksum/LCC tests #

Definition at line 113 of file test_SeqUtils.py.

Definition at line 68 of file test_SeqUtils.py.

tuple test_SeqUtils.record = SeqIO.read(open(dna_genbank_filename), "genbank")

Definition at line 46 of file test_SeqUtils.py.

Definition at line 47 of file test_SeqUtils.py.

list test_SeqUtils.seq = record.seq[start:end]

Definition at line 55 of file test_SeqUtils.py.

tuple test_SeqUtils.seq_records = list(SeqIO.parse(open(dna_fasta_filename),"fasta"))

Definition at line 26 of file test_SeqUtils.py.

test_SeqUtils.start = feature.location.start.position

Definition at line 51 of file test_SeqUtils.py.

string test_SeqUtils.str_light_chain_one = "QSALTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGK"

crc64 collision #

Definition at line 94 of file test_SeqUtils.py.

string test_SeqUtils.str_light_chain_two = "QSALTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGK"

Definition at line 97 of file test_SeqUtils.py.

tuple test_SeqUtils.table = int(feature.qualifiers["transl_table"][0])

Definition at line 53 of file test_SeqUtils.py.

tuple test_SeqUtils.tuple_records = quick_FASTA_reader(dna_fasta_filename)

Definition at line 24 of file test_SeqUtils.py.

tuple test_SeqUtils.value = checksum(seq_str)

Definition at line 134 of file test_SeqUtils.py.