ó
¿×Ic           @   sñ  d  Z  d d l m Z d d l m Z m Z d e f d „  ƒ  YZ d e f d „  ƒ  YZ e d k ríd	 GHd
 Z	 d Z
 d Z d Z d d l m Z e e e e
 ƒ ƒ ƒ Z e e ƒ d k sÁ t ‚ e e d j ƒ  ƒ d k sã t ‚ g  e d j ƒ  D] Z e j ^ qô d d g k st ‚ e e e e	 ƒ ƒ ƒ Z e e ƒ d k sKt ‚ e e d j ƒ  ƒ d k smt ‚ g  e d j ƒ  D] Z e j ^ q~d d d d g k s«t ‚ e e e e
 e	 ƒ ƒ ƒ Z e e ƒ d k sßt ‚ e e d j ƒ  ƒ d k st ‚ e e d j ƒ  ƒ d k s#t ‚ g  e d j ƒ  D] Z e j ^ q4d d g k s[t ‚ g  e d j ƒ  D] Z e j ^ qld d d d g k s™t ‚ e e e e ƒ ƒ ƒ Z e e ƒ d k sÉt ‚ e e d j ƒ  ƒ d k sët ‚ g  e d j ƒ  D] Z e j ^ qüd d g k s#t ‚ g  e d j ƒ  D] Z e j ^ q4d d g k s[t ‚ e e e e ƒ ƒ ƒ Z e e ƒ d k s‹t ‚ e e d j ƒ  ƒ d k s­t ‚ g  e d j ƒ  D] Z e j ^ q¾d d g k såt ‚ d GHn  d S(   sa  
Bio.AlignIO support for the "emboss" alignment output from EMBOSS tools.

You are expected to use this module via the Bio.AlignIO functions (or the
Bio.SeqIO functions if you want to work directly with the gapped sequences).

This module contains a parser for the EMBOSS pairs/simple file format, for
example from the alignret, water and needle tools.
iÿÿÿÿ(   t	   Alignment(   t   AlignmentIteratort   SequentialAlignmentWritert   EmbossWriterc           B   s)   e  Z d  Z d „  Z d „  Z d „  Z RS(   sß   Emboss alignment writer (WORK IN PROGRESS).

    Writes a simplfied version of the EMBOSS pairs/simple file format.
    A lot of the information their tools record in their headers is not
    available and is ommitted.
    c         C   s`   |  j  } | j d ƒ | j d ƒ y | j d | j ƒ Wn t k
 rN n X| j d ƒ d  S(   Ns)   ########################################
s   # Program: Biopython
s   # Report_file: %s
(   t   handlet   writet   namet   AttributeError(   t   selfR   (    (    s‡   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/EmbossIO.pyt   write_header   s    	c         C   s'   |  j  } | j d ƒ | j d ƒ d  S(   Ns)   #---------------------------------------
(   R   R   (   R   R   (    (    s‡   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/EmbossIO.pyt   write_footer%   s    	c         C   sÜ   |  j  } | j ƒ  } | j d ƒ | j d ƒ | j d t | ƒ ƒ x8 t | ƒ D]* \ } } | j d | d | j f ƒ qS W| j d ƒ | j d | j ƒ  ƒ | j d ƒ | j d ƒ | j d ƒ t sØ t ‚ d S(	   s=   Use this to write (another) single alignment to an open file.s)   #=======================================
s   #
s   # Aligned_sequences: %i
s	   # %i: %s
i   s   # Length: %i
s   
N(	   R   t   get_all_seqsR   t   lent	   enumeratet   idt   get_alignment_lengtht   Falset   AssertionError(   R   t	   alignmentR   t   recordst   it   record(    (    s‡   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/EmbossIO.pyt   write_alignment*   s    	"(   t   __name__t
   __module__t   __doc__R	   R
   R   (    (    (    s‡   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/EmbossIO.pyR      s   	
	t   EmbossIteratorc           B   s   e  Z d  Z d „  Z RS(   s”   Emboss alignment iterator.

    For reading the (pairwise) alignments from EMBOSS tools in what they
    call the "pairs" and "simple" formats.
    c         C   sõ  |  j  } y |  j } |  ` Wn t k
 r; | j ƒ  } n X| sF d  Sx, | j ƒ  d k rt | j ƒ  } | sI d  SqI Wd  } d  } g  } g  } xB| d d k rÑ| d j d d ƒ } | d j ƒ  j ƒ  } | d k rt	 | d j ƒ  ƒ } t
 | ƒ d k st ‚ xy t | ƒ D]k }	 | j ƒ  } | d j ƒ  j d d ƒ } |	 d t	 | d j ƒ  ƒ k sgt ‚ | j | d j ƒ  ƒ qWt
 | ƒ | k st ‚ n  | d k rÂt	 | d j ƒ  ƒ } n  | j ƒ  } q W| d  k rít d ƒ ‚ n  | d  k rt d	 ƒ ‚ n  |  j d  k	 rB|  j | k rBt d
 | |  j f ƒ ‚ n  g  | D] }
 d ^ qI} g  } d } xÏ| r8t
 | ƒ d k rÒ| d  j ƒ  j d  d ƒ } | d j ƒ  j d  d ƒ } t
 | ƒ d k røt
 | ƒ d k rø| \ }
 } | \ } } | | k rAt
 | j d d ƒ ƒ d k s&t ‚ t	 | ƒ } t	 | ƒ } n t	 | ƒ d } t	 | ƒ } d | k ru| | k  s‹t d | | f ƒ ‚ |
 | | k s»|
 | | t
 |
 ƒ  k s»t ‚ t
 | ƒ | k rÝ| j | ƒ n  | | | t
 | | j d d ƒ ƒ k sCt d t
 | | j d d ƒ ƒ | |
 | | | | f ƒ ‚ | | c | 7<| | | t
 | | j d d ƒ ƒ k s­t d t
 | | ƒ |
 | t | | ƒ f ƒ ‚ | d 7} | | k rÏd } qÏqøn& | j ƒ  d k rçn | GHt søt ‚ | j ƒ  } | j ƒ  d k s(| j ƒ  d k rj| |  _ PqjqjW| d k sKt ‚ |  j d  k	 r‘|  j t
 | ƒ k r‘t d
 t
 | ƒ |  j f ƒ ‚ n  t |  j ƒ } xN t | | ƒ D]= \ }
 } t
 | ƒ | k rÝt d ƒ ‚ n  | j |
 | ƒ q°W| S(   Ns(   #=======================================i    t   #i   t   :t   aligned_sequencest   lengths   Number of sequences missing!s   Length of sequences missing!s5   Found %i records in this alignment, told to expect %it    i   i   t   -s!   Expected index %i in range [0,%i)sF   Found %i chars so far for sequence %i (%s, %s), line says start %i:
%ss2   Found %i chars so far for %s, file says end %i:
%ss(   #---------------------------------------se   Error parsing alignment - sequences of different length? You could be using an old version of EMBOSS.(   R   t   _headerR   t   readlinet   Nonet   rstript   splitt   lowert   stript   intR   R   t   ranget   appendt
   ValueErrort   records_per_alignmentt   replacet   reprR   R    t   alphabett   zipt   add_sequence(   R   R   t   linet   length_of_seqst   number_of_seqst   idst   seqst   partst   keyR   R   t
   seq_startst   indext   id_startt   seq_endt   startt   seqt   endR   (    (    s‡   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/EmbossIO.pyt   nextD   sº    		
&	$$0-&-*
	(   R   R   R   R@   (    (    (    s‡   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/EmbossIO.pyR   =   s   t   __main__s   Running a quick self-tests‡  ########################################
# Program:  alignret
# Rundate:  Wed Jan 16 17:16:13 2002
# Report_file: stdout
########################################
#=======================================
#
# Aligned_sequences: 4
# 1: IXI_234
# 2: IXI_235
# 3: IXI_236
# 4: IXI_237
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 131
# Identity:      95/131 (72.5%)
# Similarity:   127/131 (96.9%)
# Gaps:          25/131 (19.1%)
# Score: 100.0
#
#
#=======================================

IXI_234            1 TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQAT     50
IXI_235            1 TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCCSAAPRRPQAT     41
IXI_236            1 TSPASIRPPAGPSSRPAMVSSR--RPSPPPPRRPPGRPCCSAAPPRPQAT     48
IXI_237            1 TSPASLRPPAGPSSRPAMVSSRR-RPSPPGPRRPT----CSAAPRRPQAT     45
                     |||||:|||||||||:::::::  |||||:||||:::::|||||:|||||

IXI_234           51 GGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAG    100
IXI_235           42 GGWKTCSGTCTTSTSTRHRGRSGW----------RASRKSMRAACSRSAG     81
IXI_236           49 GGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSR--G     96
IXI_237           46 GGYKTCSGTCTTSTSTRHRGRSGYSARTTTAACLRASRKSMRAACSR--G     93
                     ||:||||||||||||||||||||:::::::::::|||||||||||||  |

IXI_234          101 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE    131
IXI_235           82 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE    112
IXI_236           97 SRPPRFAPPLMSSCITSTTGPPPPAGDRSHE    127
IXI_237           94 SRPNRFAPTLMSSCLTSTTGPPAYAGDRSHE    124
                     |||:||||:|||||:|||||||::|||||||


#---------------------------------------
#---------------------------------------

s¾  ########################################
# Program:  water
# Rundate:  Wed Jan 16 17:23:19 2002
# Report_file: stdout
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: IXI_234
# 2: IXI_235
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 131
# Identity:     112/131 (85.5%)
# Similarity:   112/131 (85.5%)
# Gaps:          19/131 (14.5%)
# Score: 591.5
#
#
#=======================================

IXI_234            1 TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQAT     50
                     |||||||||||||||         ||||||||||||||||||||||||||
IXI_235            1 TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCCSAAPRRPQAT     41

IXI_234           51 GGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAG    100
                     ||||||||||||||||||||||||          ||||||||||||||||
IXI_235           42 GGWKTCSGTCTTSTSTRHRGRSGW----------RASRKSMRAACSRSAG     81

IXI_234          101 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE    131
                     |||||||||||||||||||||||||||||||
IXI_235           82 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE    112


#---------------------------------------
#---------------------------------------       


s  ########################################
# Program: needle
# Rundate: Sun 27 Apr 2007 17:20:35
# Commandline: needle
#    [-asequence] Spo0F.faa
#    [-bsequence] paired_r.faa
#    -sformat2 pearson
# Align_format: srspair
# Report_file: ref_rec .needle
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: ref_rec
# 2: gi|94968718|receiver
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 124
# Identity:      32/124 (25.8%)
# Similarity:    64/124 (51.6%)
# Gaps:          17/124 (13.7%)
# Score: 112.0
# 
#
#=======================================

ref_rec            1 KILIVDD----QYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDL     46
                      :|:.||    :.|.|::|.:  :.|.....:|.:|.||:.:..:..|.:
gi|94968718|r      1 -VLLADDHALVRRGFRLMLED--DPEIEIVAEAGDGAQAVKLAGELHPRV     47

ref_rec           47 VLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALT     96
                     |::|..:|||.|::..|:::....:|.|:::|.:.|...::.:.|.||..
gi|94968718|r     48 VVMDCAMPGMSGMDATKQIRTQWPDIAVLMLTMHSEDTWVRLALEAGANG     97

ref_rec           97 HFAK-PFDIDEIRDAV--------    111
                     :..| ..|:|.|: ||        
gi|94968718|r     98 YILKSAIDLDLIQ-AVRRVANGET    120


#=======================================
#
# Aligned_sequences: 2
# 1: ref_rec
# 2: gi|94968761|receiver
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 119
# Identity:      34/119 (28.6%)
# Similarity:    58/119 (48.7%)
# Gaps:           9/119 ( 7.6%)
# Score: 154.0
# 
#
#=======================================

ref_rec            1 KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLD     50
                      ||||||:......|:..|...|::.....|.::||:|...:..||:|.|
gi|94968761|r      1 -ILIVDDEANTLASLSRAFRLAGHEATVCDNAVRALEIAKSKPFDLILSD     49

ref_rec           51 MKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAK    100
                     :.:||.||:.:|:.:|.......|::|:....::|..::..||||....|
gi|94968761|r     50 VVMPGRDGLTLLEDLKTAGVQAPVVMMSGQAHIEMAVKATRLGALDFLEK     99

ref_rec          101 PFDIDEIRDAV--------    111
                     |...|::...|        
gi|94968761|r    100 PLSTDKLLLTVENALKLKR    118


#=======================================
#
# Aligned_sequences: 2
# 1: ref_rec
# 2: gi|94967506|receiver
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 120
# Identity:      29/120 (24.2%)
# Similarity:    53/120 (44.2%)
# Gaps:           9/120 ( 7.5%)
# Score: 121.0
# 
#
#=======================================

ref_rec            1 -KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLL     49
                      .|::|||..|..:.:..||.:.|:..........|.:.:.....||.::
gi|94967506|r      1 LHIVVVDDDPGTCVYIESVFAELGHTCKSFVRPEAAEEYILTHPVDLAIV     50

ref_rec           50 DMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFA     99
                     |:.:....|:|:|:|.:|....:..:|:|....|:|...|...||:.:..
gi|94967506|r     51 DVYLGSTTGVEVLRRCRVHRPKLYAVIITGQISLEMAARSIAEGAVDYIQ    100

ref_rec          100 KPFDIDEIRDAV--------    111
                     ||.|||.:.:..        
gi|94967506|r    101 KPIDIDALLNIAERALEHKE    120


#=======================================
#
# Aligned_sequences: 2
# 1: ref_rec
# 2: gi|94970045|receiver
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 118
# Identity:      30/118 (25.4%)
# Similarity:    64/118 (54.2%)
# Gaps:           9/118 ( 7.6%)
# Score: 126.0
# 
#
#=======================================

ref_rec            1 KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTK--ERPDLVL     48
                      :|:|:|:..:|....:.....||:...|.:|.:||.:.:|  ||.|:::
gi|94970045|r      1 -VLLVEDEEALRAAAGDFLETRGYKIMTARDGTEALSMASKFAERIDVLI     49

ref_rec           49 LDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHF     98
                     .|:.:||:.|..:.:.:..|....:|:.|:.|.: :.:..:.|:.:.:.|
gi|94970045|r     50 TDLVMPGISGRVLAQELVKIHPETKVMYMSGYDD-ETVMVNGEIDSSSAF     98

ref_rec           99 -AKPFDID----EIRDAV    111
                      .|||.:|    :||:.:
gi|94970045|r     99 LRKPFRMDALSAKIREVL    116


#=======================================
#
# Aligned_sequences: 2
# 1: ref_rec
# 2: gi|94970041|receiver
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 125
# Identity:      35/125 (28.0%)
# Similarity:    70/125 (56.0%)
# Gaps:          18/125 (14.4%)
# Score: 156.5
# 
#
#=======================================

ref_rec            1 KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIV--TKERPDLVL     48
                     .:|:|:|:.|:|.|:..:.:::||...:|.:|.:||:||  :.::.|::|
gi|94970041|r      1 TVLLVEDEEGVRKLVRGILSRQGYHVLEATSGEEALEIVRESTQKIDMLL     50

ref_rec           49 LDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHF     98
                     .|:.:.||.|.|:.:|:::...:::||.|:.|.:..:::.    |.||..
gi|94970041|r     51 SDVVLVGMSGRELSERLRIQMPSLKVIYMSGYTDDAIVRH----GVLTES     96

ref_rec           99 A----KPFDIDEIRDAV--------    111
                     |    |||..|.:...|        
gi|94970041|r     97 AEFLQKPFTSDSLLRKVRAVLQKRQ    121


#---------------------------------------
#---------------------------------------

sz  ########################################
# Program: needle
# Rundate: Mon 14 Jul 2008 11:45:42
# Commandline: needle
#    [-asequence] asis:TGTGGTTAGGTTTGGTTTTATTGGGGGCTTGGTTTGGGCCCACCCCAAATAGGGAGTGGGGGTATGACCTCAGATAGACGAGCTTATTTTAGGGCGGCGACTATAATTATTTCGTTTCCTACAAGGATTAAAGTTTTTTCTTTTACTGTGGGAGGGGGTTTGGTATTAAGAAACGCTAGTCCGGATGTGGCTCTCCATGATACTTATTGTGTAGTAGCTCATTTTCATTATGTTCTTCGAATGGGAGCAGTCATTGGTATTTTTTTGGTTTTTTTTTGAAATTTTTAGGTTATTTAGACCATTTTTTTTTGTTTCGCTAATTAGAATTTTATTAGCCTTTGGTTTTTTTTTATTTTTTGGGGTTAAGACAAGGTGTCGTTGAATTAGTTTAGCAAAATACTGCTTAAGGTAGGCTATAGGATCTACCTTTTATCTTTCTAATCTTTTGTTTTAGTATAATTGGTCTTCGATTCAACAATTTTTAGTCTTCAGTCTTTTTTTTTATTTTGAAAAGGTTTTAACACTCTTGGTTTTGGAGGCTTTGGCTTTCTTCTTACTCTTAGGAGGATGGGCGCTAGAAAGAGTTTTAAGAGGGTGTGAAAGGGGGTTAATAGC
#    [-bsequence] asis:TTATTAATCTTATGGTTTTGCCGTAAAATTTCTTTCTTTATTTTTTATTGTTAGGATTTTGTTGATTTTATTTTTCTCAAGAATTTTTAGGTCAATTAGACCGGCTTATTTTTTTGTCAGTGTTTAAAGTTTTATTAATTTTTGGGGGGGGGGGGAGACGGGGTGTTATCTGAATTAGTTTTTGGGAGTCTCTAGACATCTCATGGGTTGGCCGGGGGCCTGCCGTCTATAGTTCTTATTCCTTTTAAGGGAGTAAGAATTTCGATTCAGCAACTTTAGTTCACAGTCTTTTTTTTTATTAAGAAAGGTTT
#    -filter
# Align_format: srspair
# Report_file: stdout
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: asis
# 2: asis
# Matrix: EDNAFULL
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 667
# Identity:     210/667 (31.5%)
# Similarity:   210/667 (31.5%)
# Gaps:         408/667 (61.2%)
# Score: 561.0
# 
#
#=======================================

asis               1 TGTGGTTAGGTTTGGTTTTATTGGGGGCTTGGTTTGGGCCCACCCCAAAT     50
                                                                       
asis               0 --------------------------------------------------      0

asis              51 AGGGAGTGGGGGTATGACCTCAGATAGACGAGCTTATTTTAGGGCGGCGA    100
                                                                       
asis               0 --------------------------------------------------      0

asis             101 CTATAATTATTTCGTTTCCTACAAGGATTAAAGTTTTTTCTTTTACTGTG    150
                                                                       
asis               0 --------------------------------------------------      0

asis             151 GGAGGGGGTTTGGTATTAAGAAACGCTAGTCCGGATGTGGCTCTCCATGA    200
                                 .||||||                               
asis               1 ------------TTATTAA-------------------------------      7

asis             201 TACTTATTGT------GTAGTAGCTCATTTTCATTATGTTCTTCGAATGG    244
                      .|||||.||      |||..|..||  ||||.||||.||.|    ||.|
asis               8 -TCTTATGGTTTTGCCGTAAAATTTC--TTTCTTTATTTTTT----ATTG     50

asis             245 GAGCAGTCATTGGTATTTTTTTGGTTTTTTTTT------GAAATTTTTAG    288
                              ||.|.|||||.|||.||||.||||      | |||||||||
asis              51 ---------TTAGGATTTTGTTGATTTTATTTTTCTCAAG-AATTTTTAG     90

asis             289 GTTATTTAGACC-----ATTTTTTTTT--GTTTCGCTAATTAGAATTTTA    331
                     ||.|.|||||||     ||||||||.|  ||.|      |||.|.|||||
asis              91 GTCAATTAGACCGGCTTATTTTTTTGTCAGTGT------TTAAAGTTTTA    134

asis             332 TTAGCCTTTGGTTTTTTTTTATTTTT----TGGGGTTAAGACAAGGTGTC    377
                     |||                 ||||||    .||||...||||..|||||.
asis             135 TTA-----------------ATTTTTGGGGGGGGGGGGAGACGGGGTGTT    167

asis             378 GT-TGAATTAGTTTAGCAAAATACTGCTTAAGGTAGGCTATA--------    418
                     .| |||||||||||             ||  ||.||.||.||        
asis             168 ATCTGAATTAGTTT-------------TT--GGGAGTCTCTAGACATCTC    202

asis             419 -------------GGATCTACCTTTTATCTTTCTAAT--CTTTT----GT    449
                                  ||..||.||.|.|||..||||.||  |||||    | 
asis             203 ATGGGTTGGCCGGGGGCCTGCCGTCTATAGTTCTTATTCCTTTTAAGGG-    251

asis             450 TTTAGT-ATAATTGGTCTTCGATTCAACAATTTTTAGTCTTCAGTCTTTT    498
                        ||| |.|||     |||||||||.||| .||||||...|||||||||
asis             252 ---AGTAAGAAT-----TTCGATTCAGCAA-CTTTAGTTCACAGTCTTTT    292

asis             499 TTTTTATTTTGAAAAGGTTTTAACACTCTTGGTTTTGGAGGCTTTGGCTT    548
                     ||||||||..| ||||||||                              
asis             293 TTTTTATTAAG-AAAGGTTT------------------------------    311

asis             549 TCTTCTTACTCTTAGGAGGATGGGCGCTAGAAAGAGTTTTAAGAGGGTGT    598
                                                                       
asis             311 --------------------------------------------------    311

asis             599 GAAAGGGGGTTAATAGC    615
                                      
asis             311 -----------------    311


#---------------------------------------
#---------------------------------------(   t   StringIOi   i    i   t   IXI_234t   IXI_235i   t   IXI_236t   IXI_237i   t   ref_recs   gi|94968718|receivers   gi|94970041|receivert   asist   DoneN(   R   t   Bio.Align.GenericR    t
   InterfacesR   R   R   R   R   t   simple_examplet   pair_examplet   pair_example2t   pair_example3RB   t   listt
   alignmentsR   R   R   t   rR   (    (    (    s‡   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/EmbossIO.pyt   <module>   sT   *—3,¬Y"#"#""##"##"#