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python-biopython  1.60
Classes | Functions | Variables
Bio.AlignIO.PhylipIO Namespace Reference

Classes

class  PhylipWriter
class  PhylipIterator
class  RelaxedPhylipWriter
class  RelaxedPhylipIterator
class  SequentialPhylipWriter
class  SequentialPhylipIterator

Functions

def any

Variables

int _PHYLIP_ID_WIDTH = 10
string phylip_text
tuple handle = StringIO(phylip_text)
int count = 0
string expected
string phylip_text2
string phylip_text3
tuple list2 = list(PhylipIterator(handle))
tuple list3 = list(PhylipIterator(handle))
string phylip_text4
string phylip_text5
string phylip_text5a
tuple list4 = list(PhylipIterator(handle))
tuple list5 = list(PhylipIterator(handle))
tuple list6 = list(PhylipIterator(handle))

Function Documentation

def Bio.AlignIO.PhylipIO.any (   iterable)

Definition at line 46 of file PhylipIO.py.

00046 
00047     def any(iterable):
00048         for element in iterable:
00049             if element:
00050                return True
00051         return False

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Variable Documentation

Definition at line 52 of file PhylipIO.py.

Definition at line 502 of file PhylipIO.py.

Initial value:
00001 """mkklvlslsl vlafssataa faaipqniri gtdptyapfe sknsqgelvg
00002     fdidlakelc krintqctfv enpldalips lkakkidaim sslsitekrq qeiaftdkly
00003     aadsrlvvak nsdiqptves lkgkrvgvlq gttqetfgne hwapkgieiv syqgqdniys
00004     dltagridaafqdevaaseg flkqpvgkdy kfggpsvkde klfgvgtgmg lrkednelre
00005     alnkafaemradgtyeklak kyfdfdvygg"""

Definition at line 510 of file PhylipIO.py.

Definition at line 501 of file PhylipIO.py.

Definition at line 540 of file PhylipIO.py.

Definition at line 546 of file PhylipIO.py.

Definition at line 593 of file PhylipIO.py.

Definition at line 600 of file PhylipIO.py.

Definition at line 627 of file PhylipIO.py.

Definition at line 444 of file PhylipIO.py.

Initial value:
00001 """5 60
00002 Tax1        CCATCTCACGGTCGGTACGATACACCTGCTTTTGGCAG
00003 Tax2        CCATCTCACGGTCAGTAAGATACACCTGCTTTTGGCGG
00004 Tax3        CCATCTCCCGCTCAGTAAGATACCCCTGCTGTTGGCGG
00005 Tax4        TCATCTCATGGTCAATAAGATACTCCTGCTTTTGGCGG
00006 Tax5        CCATCTCACGGTCGGTAAGATACACCTGCTTTTGGCGG
00007 
00008 GAAATGGTCAATATTACAAGGT
00009 GAAATGGTCAACATTAAAAGAT
00010 GAAATCGTCAATATTAAAAGGT
00011 GAAATGGTCAATCTTAAAAGGT
00012 GAAATGGTCAATATTAAAAGGT"""

Definition at line 519 of file PhylipIO.py.

Initial value:
00001 """5 60
00002 Tax1        CCATCTCACGGTCGGTACGATACACCTGCTTTTGGCAGGAAATGGTCAATATTACAAGGT
00003 Tax2        CCATCTCACGGTCAGTAAGATACACCTGCTTTTGGCGGGAAATGGTCAACATTAAAAGAT
00004 Tax3        CCATCTCCCGCTCAGTAAGATACCCCTGCTGTTGGCGGGAAATCGTCAATATTAAAAGGT
00005 Tax4        TCATCTCATGGTCAATAAGATACTCCTGCTTTTGGCGGGAAATGGTCAATCTTAAAAGGT
00006 Tax5        CCATCTCACGGTCGGTAAGATACACCTGCTTTTGGCGGGAAATGGTCAATATTAAAAGGT"""

Definition at line 532 of file PhylipIO.py.

Initial value:
00001 """  5    42
00002 Turkey    AAGCTNGGGC ATTTCAGGGT
00003 Salmo gairAAGCCTTGGC AGTGCAGGGT
00004 H. SapiensACCGGTTGGC CGTTCAGGGT
00005 Chimp     AAACCCTTGC CGTTACGCTT
00006 Gorilla   AAACCCTTGC CGGTACGCTT
00007 
00008 GAGCCCGGGC AATACAGGGT AT
00009 GAGCCGTGGC CGGGCACGGT AT
00010 ACAGGTTGGC CGTTCAGGGT AA
00011 AAACCGAGGC CGGGACACTC AT
00012 AAACCATTGC CGGTACGCTT AA"""

Definition at line 558 of file PhylipIO.py.

Initial value:
00001 """  5    42
00002 Turkey    AAGCTNGGGC ATTTCAGGGT
00003 GAGCCCGGGC AATACAGGGT AT
00004 Salmo gairAAGCCTTGGC AGTGCAGGGT
00005 GAGCCGTGGC CGGGCACGGT AT
00006 H. SapiensACCGGTTGGC CGTTCAGGGT
00007 ACAGGTTGGC CGTTCAGGGT AA
00008 Chimp     AAACCCTTGC CGTTACGCTT
00009 AAACCGAGGC CGGGACACTC AT
00010 Gorilla   AAACCCTTGC CGGTACGCTT
00011 AAACCATTGC CGGTACGCTT AA"""

Definition at line 573 of file PhylipIO.py.

Initial value:
00001 """  5    42
00002 Turkey    AAGCTNGGGC ATTTCAGGGT GAGCCCGGGC AATACAGGGT AT
00003 Salmo gairAAGCCTTGGC AGTGCAGGGT GAGCCGTGGC CGGGCACGGT AT
00004 H. SapiensACCGGTTGGC CGTTCAGGGT ACAGGTTGGC CGTTCAGGGT AA
00005 Chimp     AAACCCTTGC CGTTACGCTT AAACCGAGGC CGGGACACTC AT
00006 Gorilla   AAACCCTTGC CGGTACGCTT AAACCATTGC CGGTACGCTT AA"""

Definition at line 585 of file PhylipIO.py.