ó
�™xTc           @   sš  d  d l  m Z d  d l m Z d  d l Z d  d l Z d Z d Z d Z d Z	 d Z
 d	 e j f d
 „  ƒ  YZ d e j f d „  ƒ  YZ d e j f d „  ƒ  YZ d e j f d „  ƒ  YZ d Z d Z d Z d Z d Z d e j f d „  ƒ  YZ d e j f d „  ƒ  YZ d e j f d „  ƒ  YZ d e j f d „  ƒ  YZ d Z d Z d  Z d! d" d# d$ d% d& Z d' Z d( Z d) Z d* Z  d+ Z! d, d- d. d/ Z" d0 Z# d1 Z$ d2 Z% d3 Z& d4 Z' d5 e j f d6 „  ƒ  YZ( d7 e j f d8 „  ƒ  YZ) d9 Z* d: Z+ d; e j f d< „  ƒ  YZ, d= e j f d> „  ƒ  YZ- d? „  Z. e j/ ƒ  j0 e ƒ Z1 e j/ ƒ  j0 e ƒ Z2 e j/ ƒ  j0 e ƒ Z3 e j/ ƒ  j0 e ƒ Z4 e j/ ƒ  j0 e ƒ Z5 e j/ ƒ  j0 e ƒ Z6 e j/ ƒ  j0 e ƒ Z7 e j/ ƒ  j0 e ƒ Z8 e j/ ƒ  j0 e( ƒ Z9 e j/ ƒ  j0 e) ƒ Z: e j/ ƒ  j0 e, ƒ Z; e j/ ƒ  j0 e- ƒ Z< e j= e1 e2 e3 e4 e5 e6 e7 e8 e9 e: e; e< g ƒ Z> e? d@ k r–e. ƒ  e j@ dA e jA dB dC ƒ jB e> ƒ n  d S(D   iÿÿÿÿ(   t   division(   t   bioinformaticsNt.   VVKMDGRKHRLILPEAKVQDSGEFECRTEGVSAFFGVTVQDPSGPSt.   LVKFYGRKFVLLFMDQKTFDKYESKLETSGYEKFFIFCMASPISPAs   gi|159164330|pdb|2E6P|At   Q8E5Q5_STRA3s2   Chain %s, Solution Structure Of The Ig-Like Domaint   test_sequencec           B   s   e  Z d  „  Z d „  Z RS(   c      
   C   s@  t  j d t d t ƒ } t  j d t d t ƒ } t  j d t d t d t d ƒ } t  j d t d t d t d ƒ } t  j d t d t d d d t d ƒ } |  j | | ƒ |  j | | ƒ |  j | | ƒ |  j | | ƒ |  j | | ƒ |  j | | ƒ |  j | | ƒ |  j | | ƒ |  j | | ƒ |  j | | ƒ d  S(	   Nt   sequencet   namet   descriptiont   At   Bt   typet   P1t   C(	   R   R   t	   sequence1t   name1t   name2t   fasta_sequencet   description_tmpltt   pir_sequencet   assertEqual(   t   selft   seq1t   seq2t   fasta1t   fasta2t   pir1(    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt   testEquality   s:    							c      
   C   sæ   t  j d t d t ƒ } t  j d t d t ƒ } t  j d t d d t ƒ } t  j d t d t d t d ƒ } t  j d t d t d d d t d ƒ } |  j | | k ƒ |  j | | k ƒ |  j | | k ƒ |  j | | k ƒ d  S(   NR   R   R	   R   R   R   (	   R   R   R   R   t	   sequence2R   R   R   t   assert_(   R   R   R   t   seq3R   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt   testNonEquality=   s,    					
			(   t   __name__t
   __module__R   R   (    (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyR      s   	.t   test_fasta_sequencec           B   s#   e  Z d  „  Z d „  Z d „  Z RS(   c         C   sR   t  j d t d t d t d ƒ |  _ t  j d t d d t d t d ƒ |  _ d  S(   NR   R   R   R	   i   (   R   R   R   R   R   t   shortt   long(   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt   setUpc   s    		
c         C   sL   |  j  |  j j d ƒ d d ƒ |  j  |  j j d ƒ d d d d ƒ d  S(	   NiF   sG   >gi|159164330|pdb|2E6P|A Chain A, Solution Structure Of The Ig-Like Do
R   i   s   >gi|159164330|pdb|2E
s   VVKMDGRKHRLILPEAKVQD
s   SGEFECRTEGVSAFFGVTVQ
t   DPSGPS(   R   R#   t   format(   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt
   testFormatq   s    c         C   sF   |  j  t |  j ƒ d d ƒ |  j  t |  j ƒ d d d d ƒ d  S(   NsG   >gi|159164330|pdb|2E6P|A Chain A, Solution Structure Of The Ig-Like Do
R   sG   VVKMDGRKHRLILPEAKVQDSGEFECRTEGVSAFFGVTVQDPSGPSVVKMDGRKHRLILPEAKVQDSGEF
sG   ECRTEGVSAFFGVTVQDPSGPSVVKMDGRKHRLILPEAKVQDSGEFECRTEGVSAFFGVTVQDPSGPSVV
t,   KMDGRKHRLILPEAKVQDSGEFECRTEGVSAFFGVTVQDPSGPS(   R   t   strR#   R$   (   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt   testStr‚   s    (   R    R!   R%   R(   R+   (    (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyR"   a   s   		t   test_pir_sequencec           B   s#   e  Z d  „  Z d „  Z d „  Z RS(   c      
   C   s^   t  j d t d t d d d t d ƒ |  _ t  j d t d d t d d d t d ƒ |  _ d  S(   NR   R   R   R   R   R	   i   (   R   R   R   R   R   R#   R$   (   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyR%   •   s    		
c         C   sT   |  j  |  j j d ƒ d d d ƒ |  j  |  j j d ƒ d d d d	 d
 ƒ d  S(   NiF   s   >P1;gi|159164330|pdb|2E6P|A
s2   Chain A, Solution Structure Of The Ig-Like Domain
s1     VVKMDGRKHRLILPEAKVQDSGEFECRTEGVSAFFGVTVQDPSGPS*i   s   >P1;gi|159164330|pdb
s   Chain A, Solution St
s     VVKMDGRKHRLILPEAKV
s     QDSGEFECRTEGVSAFFG
s     VTVQDPSGPS*(   R   R#   R'   (   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyR(   ¥   s    c         C   sN   |  j  t |  j ƒ d d d ƒ |  j  t |  j ƒ d d d d d ƒ d  S(   Ns   >P1;gi|159164330|pdb|2E6P|A
s2   Chain A, Solution Structure Of The Ig-Like Domain
s1     VVKMDGRKHRLILPEAKVQDSGEFECRTEGVSAFFGVTVQDPSGPS*sG     VVKMDGRKHRLILPEAKVQDSGEFECRTEGVSAFFGVTVQDPSGPSVVKMDGRKHRLILPEAKVQDSG
sG     EFECRTEGVSAFFGVTVQDPSGPSVVKMDGRKHRLILPEAKVQDSGEFECRTEGVSAFFGVTVQDPSG
s3     PSVVKMDGRKHRLILPEAKVQDSGEFECRTEGVSAFFGVTVQDPSGPS*(   R   R*   R#   R$   (   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyR+   ¸   s    (   R    R!   R%   R(   R+   (    (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyR,   “   s   		t   test_midlinec           B   s#   e  Z d  „  Z d „  Z d „  Z RS(   c         C   s   t  j d d ƒ |  _ d  S(   Nt	   identicalt   #(   R   t   midline(   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyR%   Í   s    c         C   s`   |  j  |  j j d d d d g ƒ |  j j ƒ |  j  |  j j d d d d g ƒ |  j j ƒ d  S(   NR	   R
   (   R   R0   t   conservation_codeR.   t   differ(   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt   testConservationCodeÒ   s    c         C   sB   |  j  |  j j d d g ƒ d ƒ |  j  |  j j g  ƒ d ƒ d  S(   Ns	   ABCD-EFGHs	   ABD--EKGHs	   ##   # ##t    (   R   R0   t   compare(   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt   testMidlineÞ   s    (   R    R!   R%   R3   R6   (    (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyR-   Ë   s   		sK   -KQFTKCELSQLLK--DIDGYGGIALPELICTMFHTSGYDTQAIVENN--ESTEYGLFQISNKLWCKSSQVPQSRsK   -EQLTKCEVFQKLK--DLKDYGGVSLPEWVCTAFHTSGYDTQAIVQNN--DSTEYGLFQINNKIWCKDDQNPHSRsK   GKVYGRCELAAAMKRMGLDNYRGYSLGNWVCAAKFESNFNTGATNRNT-DGSTDYGILQINSRWWCNDGRTPGSKsK   -KVYGRCELAAAMKRLGLDNYRGYSLGNWVCAAKFESNFDTHATNRNT-DGSTDYGILQINSRWWCNDGRTPGSKsK   ---------------------------------------------------------------------------t   test_alignmentc           B   sY   e  Z d  „  Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z	 d „  Z
 RS(	   c         C   s¦   t  j d t t g d d d g ƒ |  _ t  j d t t t t g d d d d d g ƒ |  _ t  j d g  d g  ƒ |  _ t  j d t t t	 g d d d d g ƒ |  _
 d  S(	   Nt
   alignmentst   namest   1hmlt   1hfyt   1hfyat   1ghlat   1lz3t   empty(   R   t	   alignmentt   ali_1hmlt   ali_1hfyt
   alignment1t   ali_1ghlt   ali_1lz3t
   alignment2t
   alignment3t   ali_emptt
   alignment4(   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyR%   ò   s    				c         C   sU   |  j  t t j t t d g d d g ƒ |  j  t t j t t g d d d g ƒ d  S(   NR	   R:   R;   R=   (   t   assertRaisest
   ValueErrorR   R@   RA   (   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt
   test_error  s    	c         C   sh   |  j  |  j j ƒ  d ƒ |  j  |  j j ƒ  d ƒ |  j  |  j j ƒ  d ƒ |  j  |  j j ƒ  d ƒ d  S(   Ni1   i   i    (   R   RC   t   identity_countRF   RG   RI   (   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt   test_identity_count  s    c         C   st   |  j  |  j j ƒ  d d ƒ |  j  |  j j ƒ  d d ƒ |  j  |  j j ƒ  d d ƒ |  j  |  j j ƒ  d d ƒ d  S(   Ngffffffæ?i   g333333Ó?g      ð?(   t   assertAlmostEqualRC   t   identity_fractionRF   RG   RI   (   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt   test_identity_fraction  s    c         C   sh   |  j  |  j j ƒ  d ƒ |  j  |  j j ƒ  d ƒ |  j  |  j j ƒ  d ƒ |  j  |  j j ƒ  d ƒ d  S(   Ni   i   i    i   (   R   RC   t   multiplicityRF   RG   RI   (   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt   test_multiplicity&  s    c         C   sh   |  j  |  j j ƒ  d ƒ |  j  |  j j ƒ  d ƒ |  j  |  j j ƒ  d ƒ |  j  |  j j ƒ  d ƒ d  S(   NiK   i    (   R   RC   t   lengthRF   RG   RI   (   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt   test_length.  s    c         C   sŒ   |  j  j d d d g d d d g d d ƒ } |  j | |  j  k	 ƒ |  j | j d d g ƒ |  j | j d d g ƒ |  j | j d ƒ d  S(	   NR8   t   ABt   BAR9   t   XYt   YXt   gapR/   (   RC   t   copyR   R   R8   R9   RZ   (   R   t   c(    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt	   test_copy6  s    	c         C   s1   |  j  t |  j ƒ d d d d d d ƒ d  S(   Ns   >1hml
sG   -KQFTKCELSQLLK--DIDGYGGIALPELICTMFHTSGYDTQAIVENN--ESTEYGLFQISNKLWCKSSQ
s   VPQSR

s   >1hfy
sG   -EQLTKCEVFQKLK--DLKDYGGVSLPEWVCTAFHTSGYDTQAIVQNN--DSTEYGLFQINNKIWCKDDQ
t   NPHSR(   R   R*   RC   (   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt   test__str__D  s    c         C   sÎ   d d d d g } |  j  j ƒ  } | j d | ƒ |  j | j |  j  j ƒ |  j | j |  j  j ƒ |  j | j d |  j  j d d d	 |  j  j d
 d d |  j  j d d d |  j  j d d g ƒ d  S(   NtM   ABKQFTKCELSQLLKDIDGYGGIALPELICTMFHTSGYDTQAIVENNESTEYGLFQISNKLWCKSSQVPQSRNOPQRtM   CDEEQLTKCEVFQKLKDLKDYGGVSLPEWVCTAFHTSGYDTQAIVQNNDSTEYGLFQINNKIWCKDDQNPHSRSTUVtQ   FGHIGKVYGRCELAAAMKRMGLDNYRGYSLGNWVCAAKFESNFNTGATNRNTDGSTDYGILQINSRWWCNDGRTPGSKXYZtP   JKILMKVYGRCELAAAMKRLGLDNYRGYSLGNWVCAAKFESNFDTHATNRNTDGSTDYGILQINSRWWCNDGRTPGSKABt	   sequencess   AB------------i    s   NOPQR---------s   --CDE---------i   s   -----STUV-----s   -----FGHI-----i   s   ---------XYZ--s   ---------JKILMi   s   ------------AB(   RF   R[   t   extendR   R9   RZ   R8   (   R   Rd   t   ali(    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt   test_extendO  s    	(   R    R!   R%   RL   RN   RQ   RS   RU   R]   R_   Rg   (    (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyR7   ð   s   								t   test_fasta_alignmentc           B   s5   e  Z d  „  Z d „  Z d „  Z d „  Z d „  Z RS(   c      
   C   sI   t  j d t t t t g d d d d d g d d d	 d
 d g ƒ |  _ d  S(   NR8   R9   R:   R<   R=   R>   t   descriptionss   alpha lactalbumin:Homo sapienss   alpha-lactalbumin:Capra hircuss   lysozyme:Phasianus colchicuss   lysozyme:Meleagris gallopavo(   R   t   fasta_alignmentRA   RB   RD   RE   R@   (   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyR%   h  s    	c         C   s5   |  j  t t j t t g d d g d d d g ƒ d  S(   NR:   R;   s   alpha lactalbumin:Homo sapienss   alpha-lactalbumin:Capra hircuss   lysozyme:Phasianus colchicus(   RJ   RK   R   Rj   RA   (   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyRL   u  s    		c         C   sL   |  j  |  j j d ƒ d d d d d d d d	 d
 d d d ƒ d  S(   Ni(   s%   >1hml alpha lactalbumin:Homo sapiens
s)   -KQFTKCELSQLLK--DIDGYGGIALPELICTMFHTSGYD
s%   TQAIVENN--ESTEYGLFQISNKLWCKSSQVPQSR

s&   >1hfya alpha-lactalbumin:Capra hircus
s)   -EQLTKCEVFQKLK--DLKDYGGVSLPEWVCTAFHTSGYD
s%   TQAIVQNN--DSTEYGLFQINNKIWCKDDQNPHSR

s$   >1ghla lysozyme:Phasianus colchicus
s)   GKVYGRCELAAAMKRMGLDNYRGYSLGNWVCAAKFESNFN
s%   TGATNRNT-DGSTDYGILQINSRWWCNDGRTPGSK

s#   >1lz3 lysozyme:Meleagris gallopavo
s)   -KVYGRCELAAAMKRLGLDNYRGYSLGNWVCAAKFESNFD
s#   THATNRNT-DGSTDYGILQINSRWWCNDGRTPGSK(   R   R@   R'   (   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt   test_format„  s    c         C   sI   |  j  t |  j ƒ d d d d d d d d d	 d
 d d ƒ d  S(   Ns%   >1hml alpha lactalbumin:Homo sapiens
sG   -KQFTKCELSQLLK--DIDGYGGIALPELICTMFHTSGYDTQAIVENN--ESTEYGLFQISNKLWCKSSQ
s   VPQSR

s&   >1hfya alpha-lactalbumin:Capra hircus
sG   -EQLTKCEVFQKLK--DLKDYGGVSLPEWVCTAFHTSGYDTQAIVQNN--DSTEYGLFQINNKIWCKDDQ
s   NPHSR

s$   >1ghla lysozyme:Phasianus colchicus
sG   GKVYGRCELAAAMKRMGLDNYRGYSLGNWVCAAKFESNFNTGATNRNT-DGSTDYGILQINSRWWCNDGR
s   TPGSK

s#   >1lz3 lysozyme:Meleagris gallopavo
sG   -KVYGRCELAAAMKRLGLDNYRGYSLGNWVCAAKFESNFDTHATNRNT-DGSTDYGILQINSRWWCNDGR
t   TPGSK(   R   R*   R@   (   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyR_   —  s    c         C   s�   |  j  j d d d d d g ƒ } |  j | j d d d d g ƒ |  j | j |  j  j ƒ |  j | j |  j  j ƒ |  j | j |  j  j ƒ d  S(   NRi   R	   R
   R   t   D(   R@   R[   R   Ri   R8   R9   RZ   (   R   R\   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyR]   ©  s
    !(   R    R!   R%   RL   Rk   R_   R]   (    (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyRh   f  s
   				t   test_pir_alignmentc           B   s5   e  Z d  „  Z d „  Z d „  Z d „  Z d „  Z RS(   c         C   sV   t  j d t t t t g d d d d d g d d g d	 d
 d d d d g ƒ |  _ d  S(   NR8   R9   R:   R<   R=   R>   t   typesR   i   Ri   s   alpha lactalbumin:Homo sapienss   alpha-lactalbumin:Capra hircuss   lysozyme:Phasianus colchicuss   lysozyme:Meleagris gallopavo(   R   t   pir_alignmentRA   RB   RD   RE   R@   (   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyR%   ´  s    	c      	   C   sx   |  j  t t j t t g d d g d d d g d d g ƒ |  j  t t j t t g d d g d d g d d d g ƒ d  S(   NR:   R;   R   s   alpha lactalbumin:Homo sapienss   alpha-lactalbumin:Capra hircuss   lysozyme:Phasianus colchicus(   RJ   RK   R   Rp   RA   (   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyRL   Â  s"    		
			c         C   sL   |  j  |  j j d ƒ d d d d d d d d	 d
 d d d ƒ d  S(   Ni(   s(   >P1;1hml
alpha lactalbumin:Homo sapiens
s)     -KQFTKCELSQLLK--DIDGYGGIALPELICTMFHTSG
s*     YDTQAIVENN--ESTEYGLFQISNKLWCKSSQVPQSR*

s)   >P1;1hfya
alpha-lactalbumin:Capra hircus
s)     -EQLTKCEVFQKLK--DLKDYGGVSLPEWVCTAFHTSG
s*     YDTQAIVQNN--DSTEYGLFQINNKIWCKDDQNPHSR*

s'   >P1;1ghla
lysozyme:Phasianus colchicus
s)     GKVYGRCELAAAMKRMGLDNYRGYSLGNWVCAAKFESN
s*     FNTGATNRNT-DGSTDYGILQINSRWWCNDGRTPGSK*

s&   >P1;1lz3
lysozyme:Meleagris gallopavo
s)     -KVYGRCELAAAMKRLGLDNYRGYSLGNWVCAAKFESN
s(     FDTHATNRNT-DGSTDYGILQINSRWWCNDGRTPGSK*(   R   R@   R'   (   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyRk   Ý  s    c         C   sI   |  j  t |  j ƒ d d d d d d d d d	 d
 d d ƒ d  S(   Ns(   >P1;1hml
alpha lactalbumin:Homo sapiens
sG     -KQFTKCELSQLLK--DIDGYGGIALPELICTMFHTSGYDTQAIVENN--ESTEYGLFQISNKLWCKS
s     SQVPQSR*

s)   >P1;1hfya
alpha-lactalbumin:Capra hircus
sG     -EQLTKCEVFQKLK--DLKDYGGVSLPEWVCTAFHTSGYDTQAIVQNN--DSTEYGLFQINNKIWCKD
s     DQNPHSR*

s'   >P1;1ghla
lysozyme:Phasianus colchicus
sG     GKVYGRCELAAAMKRMGLDNYRGYSLGNWVCAAKFESNFNTGATNRNT-DGSTDYGILQINSRWWCND
s     GRTPGSK*

s&   >P1;1lz3
lysozyme:Meleagris gallopavo
sG     -KVYGRCELAAAMKRLGLDNYRGYSLGNWVCAAKFESNFDTHATNRNT-DGSTDYGILQINSRWWCND
s
     GRTPGSK*(   R   R*   R@   (   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyR_   ð  s    c         C   sÀ   |  j  j d d d d d g d d d d	 d
 g ƒ } |  j | j d d d d g ƒ |  j | j d d d	 d
 g ƒ |  j | j |  j  j ƒ |  j | j |  j  j ƒ |  j | j |  j  j ƒ d  S(   NRi   R	   R
   R   Rm   Ro   R   t   P2t   P3t   P4(   R@   R[   R   Ri   Ro   R8   R9   RZ   (   R   R\   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyR]     s    (   R    R!   R%   RL   Rk   R_   R]   (    (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyRn   ²  s
   				t   test_clustal_alignmentc           B   s,   e  Z d  „  Z d „  Z d „  Z d „  Z RS(   c         C   s=   t  j d t t t t g d d d d d g d d ƒ |  _ d  S(	   NR8   R9   R:   R<   R=   R>   t   programs   CLUSTAL X 1.35(   R   t   clustal_alignmentRA   RB   RD   RE   R@   (   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyR%     s    	c         C   sK   |  j  |  j j d d ƒ d d d d d d d	 d
 d d d ƒ d  S(   Ni(   i
   s,   CLUSTAL X 1.35 multiple sequence alignment

s7   1hml       -KQFTKCELSQLLK--DIDGYGGIALPELICTMFHTSGYD 37
s7   1hfya      -EQLTKCEVFQKLK--DLKDYGGVSLPEWVCTAFHTSGYD 37
s7   1ghla      GKVYGRCELAAAMKRMGLDNYRGYSLGNWVCAAKFESNFN 40
s7   1lz3       -KVYGRCELAAAMKRLGLDNYRGYSLGNWVCAAKFESNFD 39
s5                    **     *      * *  *    *     *   

s2   1hml       TQAIVENN--ESTEYGLFQISNKLWCKSSQVPQSR 70
s2   1hfya      TQAIVQNN--DSTEYGLFQINNKIWCKDDQNPHSR 70
s2   1ghla      TGATNRNT-DGSTDYGILQINSRWWCNDGRTPGSK 74
s2   1lz3       THATNRNT-DGSTDYGILQINSRWWCNDGRTPGSK 73
s.              * *   *    ** **  **    **     * * (   R   R@   R'   (   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyRk     s    c         C   sE   |  j  t |  j ƒ d d d d d d d d d	 d
 d ƒ d  S(   Ns,   CLUSTAL X 1.35 multiple sequence alignment

sP   1hml            -KQFTKCELSQLLK--DIDGYGGIALPELICTMFHTSGYDTQAIVENN--ESTEYGLFQI 55
sP   1hfya           -EQLTKCEVFQKLK--DLKDYGGVSLPEWVCTAFHTSGYDTQAIVQNN--DSTEYGLFQI 55
sP   1ghla           GKVYGRCELAAAMKRMGLDNYRGYSLGNWVCAAKFESNFNTGATNRNT-DGSTDYGILQI 59
sP   1lz3            -KVYGRCELAAAMKRLGLDNYRGYSLGNWVCAAKFESNFDTHATNRNT-DGSTDYGILQI 58
sN                         **     *      * *  *    *     *   * *   *    ** **  **

s#   1hml            SNKLWCKSSQVPQSR 70
s#   1hfya           NNKIWCKDDQNPHSR 70
s#   1ghla           NSRWWCNDGRTPGSK 74
s#   1lz3            NSRWWCNDGRTPGSK 73
s                       **     * * (   R   R*   R@   (   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyR_   *  s    c         C   sw   |  j  j d d ƒ } |  j | j d ƒ |  j | j |  j  j ƒ |  j | j |  j  j ƒ |  j | j |  j  j ƒ d  S(   NRu   t   Foo(   R@   R[   R   Ru   R8   R9   RZ   (   R   R\   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyR]   ;  s
    (   R    R!   R%   Rk   R_   R]   (    (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyRt     s   			s  
Error
>chain_A
 TPDCVTGKVE YTKYNDDDTF TVKVGDKELF TNRWNLQSLL LSAQITGMTV TIKTNACHNG
 GGFSEVIFR
> chain A
 TPDCVTGKVE YTKYNDDDTF TVKVGDKELF TNRWNLQSLL LSAQITGMTV TIKTNACHNG
 GGFSEVIFR

> chain_A
 TPDCVTGKVE YTKYNDDDTF TVKVGDKELF TNRWNLQSLL LSAQITGMTV TIKTNACHNG
 GGFSEVIFR*
>chain_AtE   TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFRsÎ  
Error
>FOSB_MOUSE Protein fosB. 338 bp
     MFQAFPGDYDSGSRCSSSPSAESQYLSSVDSFGSPPTAAASQECAGLGEMPGSFVPTVTA
     ITTSQDLQWLVQPTLISSMAQSQGQPLASQPPAVDPYDMPGTSYSTPGLSAYSTGGASGS
     GGPSTSTTTSGPVSARPARARPRRPREETLTPEEEEKRRVRRERNKLAAAKCRNRRRELT
     DRLQAETDQLEEEKAELESEIAELQKEKERLEFVLVAHKPGCKIPYEEGPGPGPLAEVRD
     LPGSTSAKEDGFGWLLPPPPPPPLPFQSSRDAPPNLTASLFTHSEVQVLGDPFPVVSPSY
     TSSFVLTCPEVSAFAGAQRTSGSEQPSDPLNSPSLLAL

> FOSB_MOUSE Protein fosB. 338 bp
     MFQAFPGDYDSGSRCSSSPSAESQYLSSVDSFGSPPTAAASQECAGLGEMPGSFVPTVTA
     ITTSQDLQWLVQPTLISSMAQSQGQPLASQPPAVDPYDMPGTSYSTPGLSAYSTGGASGS
     GGPSTSTTTSGPVSARPARARPRRPREETLTPEEEEKRRVRRERNKLAAAKCRNRRRELT
     DRLQAETDQLEEEKAELESEIAELQKEKERLEFVLVAHKPGCKIPYEEGPGPGPLAEVRD
     LPGSTSAKEDGFGWLLPPPPPPPLPFQSSRDAPPNLTASLFTHSEVQVLGDPFPVVSPSY
     TSSFVLTCPEVSAFAGAQRTSGSEQPSDPLNSPSLLAL
> 1YJP:A|PDBID|CHAIN|SEQUENCE

     MFQAFPGDYDSGSRCSSSPSAESQYLSSVDSFGSPPTAAASQECAGLGEMPGSFVPTVTA
     ITTSQDLQWLVQPTLISSMAQSQGQPLASQPPAVDPYDMPGTSYSTPGLSAYSTGGASGS
     GGPSTSTTTSGPVSARPARARPRRPREETLTPEEEEKRRVRRERNKLAAAKCRNRRRELT
     DRLQAETDQLEEEKAELESEIAELQKEKERLEFVLVAHKPGCKIPYEEGPGPGPLAEVRD
     LPGSTSAKEDGFGWLLPPPPPPPLPFQSSRDAPPNLTASLFTHSEVQVLGDPFPVVSPSY
     TSSFVLTCPEVSAFAGAQRTSGSEQPSDPLNSPSLLAL


t<   MFQAFPGDYDSGSRCSSSPSAESQYLSSVDSFGSPPTAAASQECAGLGEMPGSFVPTVTAt<   ITTSQDLQWLVQPTLISSMAQSQGQPLASQPPAVDPYDMPGTSYSTPGLSAYSTGGASGSt<   GGPSTSTTTSGPVSARPARARPRRPREETLTPEEEEKRRVRRERNKLAAAKCRNRRRELTt<   DRLQAETDQLEEEKAELESEIAELQKEKERLEFVLVAHKPGCKIPYEEGPGPGPLAEVRDt<   LPGSTSAKEDGFGWLLPPPPPPPLPFQSSRDAPPNLTASLFTHSEVQVLGDPFPVVSPSYt&   TSSFVLTCPEVSAFAGAQRTSGSEQPSDPLNSPSLLALs  
Error
>P1;CRAB_ANAPL
ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
  MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR
  SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH
  GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ
  SDVPERSIPI TREEKPAIAG AQRK*

>P1;CRAB_ANAPL

  MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR
  SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH
  GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ
  SDVPERSIPI TREEKPAIAG AQRK*

>P1;CRAB_ANAPL
ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
  MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR
  SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH
  GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ
  SDVPERSIPI TREEKPAIAG AQRK

> P1;CRAB_ANAPL
ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
  MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR
  SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH
  GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ
  SDVPERSIPI TREEKPAIAG AQRK*

>P11;CRAB_ANAPL
ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
  MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR
  SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH
  GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ
  SDVPERSIPI TREEKPAIAG AQRK*

>P1;CRAB_ ANAPL
ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
  MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR
  SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH
  GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ
  SDVPERSIPI TREEKPAIAG AQRK*

só  
Error
>P1;CRAB_ANAPL
ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
  MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR
  SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH
  GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ
  SDVPERSIPI TREEKPAIAG AQRK*

Error2

>CRAB_ANAPL
ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
  MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR
  SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH
  GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ
  SDVPERSIPI TREEKPAIAG AQRK*

>CRAB_ANAPL

  MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR
  SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH
  GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ
  SDVPERSIPI TREEKPAIAG AQRK
s
  
> anb.pdb
AAKDVKFGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASKANDAAGDGTT
TATVLAQAIITEGLKAVAAGMNPMDLKRGIDKAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKV
GKEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVAKAGKPLL
IIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINK
DTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDYDREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAA
VEEGVVAGGGVALIRVASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAATEEY
GNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLP

AAKDVKFGNDARVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASK
ANDAAGDGTTTATVLAQAIITEGLKAVAAGMNPMDLKRGIDKAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVG
KLIAEAMDKVGKEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLE
AVAKAGKPLLIIAEDVEGEALQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEEAAIQGRVA
QIRQQIEEATSDYDREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGVVAGGGVALIRVASKL
ADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAATEEYGNMIDMGILDPTKVTRSALQ
YAASVAGLMITTECMVTDLP

AAKDVKFGNDARVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVAST
ATVLAQAIITEGLKAVAAGMNPMDLKRGIDKAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKVG
KEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVAKAGKPLLI
IAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINKD
TTTIIDGVGEEAAIQGRVAQIRQQIEEATSDYDREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAV
EEGVVAGGGVALIRVASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGKGGDGNYGYNAATEEYGNMIDMGILDP
TKVTRSALQYAASVAGLMITTECMVTDLP

s  
AAKDVKFGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASKANDAAGDGTT
TATVLAQAIITEGLKAVAAGMNPMDLKRGIDKAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKV
GKEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVAKAGKPLL
IIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINK
DTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDYDREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAA
VEEGVVAGGGVALIRVASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAATEEY
GNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLP

AAKDVKFGNDARVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASK
ANDAAGDGTTTATVLAQAIITEGLKAVAAGMNPMDLKRGIDKAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVG
KLIAEAMDKVGKEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLE
AVAKAGKPLLIIAEDVEGEALQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEEAAIQGRVA
QIRQQIEEATSDYDREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGVVAGGGVALIRVASKL
ADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAATEEYGNMIDMGILDPTKVTRSALQ
YAASVAGLMITTECMVTDLP

s`  
>PDB:1GAG_A
VFPSSVFVPDEWEVSREKITLLRELGQGSFGMVYEGNARDIIKGEAETRVAVKTVNESAS
LRERIEFLNEASVMKGFTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLRSLRPEAEN
NPGRPPPTLQEMIQMAAEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRDI
XETDXXRKGGKGLLPVRWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQ
VLKFVMDGGYLDQPDNCPERVTDLMRMCWQFNPKMRPTFLEIVNLLKDDLHPSFPEVSFF
HSEENK

>PDB:1GAG_B
PATGDFMNMSPVG
t2   MDITIHNPLIRRPLFSWLAPSRIFDQIFGEHLQESELLPASPSLSPFLMRt2   SPIFRMPSWLETGLSEMRLEKDKFSVNLDVKHFSPEELKVKVLGDMVEIHt2   GKHEERQDEHGFIAREFNRKYRIPADVDPLTITSSLSLDGVLTVSAPRKQt   SDVPERSIPITREEKPAIAGAQRKs   CLUSTAL 2.0.10 multiple sequence alignment


Horse           VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKA--- 57
chain_A         VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASED 60
                *** .:   *  .*:** .... :* : * *:* ..* *   * :*.  : .*::**

Horse           ---HGKKVGDALTLAVGHLDDLPGALSDLSNLHAHKLRVDPVNFKLLSHCLLSTLAVHLP 114
chain_A         LKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHP 120
                   ** .*  **   : : ..  . *. *:: ** * ::    ::::*..:: .*  : *

Horse           NDFTPAVHASLDKFLSSVSTVLTSKYR------ 141
chain_A         GDFGADAQGAMNKALELFRKDIAAKYKELGYQG 153
                .** . .:.:::* *. . . :::**:
s|  CLUSTAL X (1.81) multiple sequence alignment

1vkk VVCEVDPELKETLRKFRFR---KETNNAAIIMKVD--KDRQMVVLEDELQ-NISPEELKL
1ahq -GIAVSDDCVQKFNELKLGHQH-----RYVTFKMNASN--TEVVVEHVGGPNATYEDFKS

1vkk ELPERQPRFVVYSYKYVH--DDGRVSYPLCFIFSSPVGCKPEQQMMYAGSKNRLVQTAE-
1ahq QLPERDCRYAIFDYEFQVDG---GQRNKITFILWAPDSAPIKSKMMYTSTKDSIKKKLVG

1vkk L-TKVFEIRTTDD-LTETWLKEKLAFFR
1ahq IQ-VEVQATD-AAEISEDAVSERAKK--
sT  
>P1;Horse

VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKA---
---HGKKVGDALTLAVGHLDDLPGALSDLSNLHAHKLRVDPVNFKLLSHCLLSTLAVHLP
NDFTPAVHASLDKFLSSVSTVLTSKYR------*

>P3;chain_A

VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASED
LKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHP
GDFGADAQGAMNKALELFRKDIAAKYKELGYQG*
sg  
>2QZU:A Putative sulfatase from B. fragilis
QPTPNLVFIXADQYRGDAIGCIGKEPVKTPHLDKLASEGINFTNAISSYP
VSSPARGXLXTGXYPIGSKVT-GNCNSETAPYGVELSQNARCWSDVLKDQ
GYNXGYIGKWHLDAPYKPYVDTYNNRGKVAWNEWCP---PERRHGFDHWI
AYGTYDY-----------------------------H-LKPXYWNTTAPR
DSFYYVNQ-----------WGPEYEASKAIEYINGQKDQKQPFALVVSXN
PPHTGYE--------------LVPDRYKEIYKDLDVEALCKGRPDIP---
-------------------AKG----------------------TEXGDY
FRNNIRNYYACITGVDENVGRIIEALKQNNLFDNTIVVFTSDHGICXG--
---------------AHENAGKD-IFYEESXRIPXILSWPDQIKPRKSDP
--LXIAFA-DLYPTLLSXXGFSKEIPETVQTFDLSNEVLTGKNKKD-LVQ
PYYFVKF--------DNHA------------------TGYRGLRTDRYTY
AVHAT-DGK------------------------IDNVILFDRTNDPHEXN
NIASQ--QLKLTHTFNRQLKTWLEKTNDPF
>3B5Q:B Putative sulfatase from B. thetaiotaomicron
-EKPNFLIIQCDHLTQRVVGAYGQTQGCTLPIDEVASRGVIFSNAYVGCP
LSQPSRAALWSGXXPHQTNVR-SNSS---EPVNTRLPENVPTLGSLFSES
GYEAVHFGKTHDX---------------------------GSLRGFKHKE
P-------------------------------------------------
---VAKPFTDPEFPVNNDSFLDVGTCEDAVAYLSNP--PKEPFICIADFQ
NPHNICGFIGENAGVHTDRPI----------SGPLPEL----PDNFDVED
WSNIPTPVQYICCSHRRXT---QAA-------------------HWNEEN
YRHYIAAFQHYTKXVSKQVDSVLKALYSTPAGRNTIVVIXADHGDGXA--
---------------SHRXVTKHISFYDEXTNVPFIFAG-PGIKQQKKPV
DHLLTQPTLDLLPTLCDLAGIA--VPAEKAGISLAPTLRGEKQKKSHPYV
VSEWHSEYEYVT-------------------------TPGRXVRGPRYKY
THYLE----------------------------GNGEELYDXKKDPGERK
NLAKDPKYSKILAEHRALLDDYITRSKDDY
s  
>2QZU:A
QPTPNLVFIXADQYRGDAIGCIGKEPVKTPHLDKLASEGINFTNAISSYP
VSSPARGXLXTGXYPIGSKVT-GNCNSETAPYGVELSQNARCWSDVLKDQ
GYNXGYIGKWHLDAPYKPYVDTYNNRGKVAWNEWCP---PERRHGFDHWI
AYGTYDY-----------------------------H-LKPXYWNTTAPR
DSFYYVNQ-----------WGPEYEASKAIEYINGQKDQKQPFALVVSXN
PPHTGYE--------------LVPDRYKEIYKDLDVEALCKGRPDIP---
-------------------AKG----------------------TEXGDY
FRNNIRNYYACITGVDENVGRIIEALKQNNLFDNTIVVFTSDHGICXG--
---------------AHENAGKD-IFYEESXRIPXILSWPDQIKPRKSDP
--LXIAFA-DLYPTLLSXXGFSKEIPETVQTFDLSNEVLTGKNKKD-LVQ
PYYFVKF--------DNHA------------------TGYRGLRTDRYTY
AVHAT-DGK------------------------IDNVILFDRTNDPHEXN
NIASQ--QLKLTHTFNRQLKTWLEKTNDPF
>3B5Q:B
-EKPNFLIIQCDHLTQRVVGAYGQTQGCTLPIDEVASRGVIFSNAYVGCP
LSQPSRAALWSGXXPHQTNVR-SNSS---EPVNTRLPENVPTLGSLFSES
GYEAVHFGKTHDX---------------------------GSLRGFKHKE
P-------------------------------------------------
---VAKPFTDPEFPVNNDSFLDVGTCEDAVAYLSNP--PKEPFICIADFQ
NPHNICGFIGENAGVHTDRPI----------SGPLPEL----PDNFDVED
WSNIPTPVQYICCSHRRXT---QAA-------------------HWNEEN
YRHYIAAFQHYTKXVSKQVDSVLKALYSTPAGRNTIVVIXADHGDGXA--
---------------SHRXVTKHISFYDEXTNVPFIFAG-PGIKQQKKPV
DHLLTQPTLDLLPTLCDLAGIA--VPAEKAGISLAPTLRGEKQKKSHPYV
VSEWHSEYEYVT-------------------------TPGRXVRGPRYKY
THYLE----------------------------GNGEELYDXKKDPGERK
NLAKDPKYSKILAEHRALLDDYITRSKDDY
t   test_sequence_parsec           B   sY   e  Z d  „  Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z	 d „  Z
 RS(	   c         C   s—  t  j t ƒ \ } } |  j t | ƒ d ƒ |  j | d d g ƒ |  j | d j d ƒ |  j | d j t ƒ |  j | d j d ƒ |  j | d j t ƒ |  j | d j d ƒ |  j | d j t ƒ t  j t ƒ \ } } |  j t | ƒ d ƒ |  j | d g ƒ |  j | d j d	 ƒ |  j | d j t	 ƒ |  j | d j d	 ƒ |  j | d j t	 ƒ |  j | d j d
 ƒ |  j | d j t	 ƒ d  S(   Ni   s   
Error
s   >chain_Ai    t   chain_Ai   s   chain Ai   s   FOSB_MOUSE Protein fosB. 338 bps   1YJP:A|PDBID|CHAIN|SEQUENCE(
   R   t   seq_sequence_parset   seqR   t   lenR   R   t   seq_sequencet   fastaR   (   R   Rd   t   unknownst   fastas(    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt   testSequenceo  sT    











c         C   s  t  j t ƒ \ } } |  j t | ƒ d ƒ |  j | d g ƒ |  j | d j d ƒ |  j | d j t ƒ |  j | d j d ƒ |  j | d j d ƒ |  j | d j t ƒ |  j | d j d ƒ |  j | d j d ƒ |  j | d j d	 ƒ |  j | d j t ƒ d  S(
   Ni   s   
Error
i    t
   FOSB_MOUSEs   Protein fosB. 338 bpi   i   t   1YJPs   A|PDBID|CHAIN|SEQUENCE(	   R   t   fasta_sequence_parseR‰   R   R‡   R   R   R   R   (   R   R‹   RŠ   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt	   testFasta±  s@    









c         C   s  t  j t ƒ \ } } |  j t | ƒ d ƒ |  j | d t d g ƒ |  j | d j d ƒ |  j | d j d ƒ |  j | d j d ƒ |  j | d j t	 ƒ |  j | d j d ƒ |  j | d j d ƒ |  j | d j d	 ƒ |  j | d j t	 ƒ d  S(
   Ni   s   
Error
iê  i    t
   CRAB_ANAPLR   s/   ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).i   R4   (
   R   t   pir_sequence_parset   pirR   R‡   R   R   R   R   R   (   R   t   pirsRŠ   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt   testPirä  s6    







c         C   sY  t  j t ƒ \ } } |  j t | ƒ d ƒ |  j | d d g ƒ |  j | d j d ƒ |  j | d j d ƒ |  j | d j d ƒ |  j | d j t	 ƒ |  j | d j d	 ƒ |  j | d j d ƒ |  j | d j d ƒ |  j | d j t	 ƒ |  j | d
 j d	 ƒ |  j | d
 j d ƒ |  j | d
 j d ƒ |  j | d
 j t	 ƒ d  S(   Ni   s   
Error
s   Error2

i    s   P1;CRAB_ANAPLR   s/   ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).i   R‘   i   R4   (
   R   t   tolerant_pir_sequence_parset   tolerant_pirR   R‡   R   R   R   R   R   (   R   R”   RŠ   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt   testTolerantPir  sN    











c         C   s  t  j d t ƒ \ } } |  j | g  ƒ |  j t | ƒ d ƒ |  j | d j d ƒ |  j | d j d d d d d	 d
 d ƒ |  j | d j d ƒ |  j | d j d d d d d d d ƒ |  j | d j d ƒ |  j | d j d d d d d d d ƒ d  S(   Nt   texti   i    s   anb.pdbtO   AAKDVKFGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASKANDAAGDGTTtO   TATVLAQAIITEGLKAVAAGMNPMDLKRGIDKAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKVtO   GKEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVAKAGKPLLtO   IIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINKtO   DTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDYDREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAtO   VEEGVVAGGGVALIRVASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAATEEYt(   GNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLPi   tO   AAKDVKFGNDARVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASKtO   ANDAAGDGTTTATVLAQAIITEGLKAVAAGMNPMDLKRGIDKAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVGtO   KLIAEAMDKVGKEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEtO   AVAKAGKPLLIIAEDVEGEALQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEEAAIQGRVAtO   QIRQQIEEATSDYDREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGVVAGGGVALIRVASKLtO   ADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAATEEYGNMIDMGILDPTKVTRSALQt   YAASVAGLMITTECMVTDLPi   tO   AAKDVKFGNDARVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASTtO   ATVLAQAIITEGLKAVAAGMNPMDLKRGIDKAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKVGtO   KEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVAKAGKPLLItO   IAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINKDtO   TTTIIDGVGEEAAIQGRVAQIRQQIEEATSDYDREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVtO   EEGVVAGGGVALIRVASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGKGGDGNYGYNAATEEYGNMIDMGILDPt   TKVTRSALQYAASVAGLMITTECMVTDLP(   R   t   tf_sequence_parset   tfR   R‡   R   R   (   R   t   seqsRŠ   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt   test_tf_parseH  s    


c         C   s×   t  j j d t d d ƒ \ } } |  j | g  ƒ |  j t | ƒ d ƒ |  j | d j d ƒ |  j | d j d d d d	 d
 d d ƒ |  j | d j d ƒ |  j | d j d d d d d d d ƒ d  S(   NR™   R   t   fooi   i    Rš   R›   Rœ   R�   Rž   RŸ   R    i   R¡   R¢   R£   R¤   R¥   R¦   R§   (   R   t   lineseparated_sequence_parset   parset   lineseparatedR   R‡   R   R   (   R   R±   RŠ   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt   test_ls_parsep  s    

c         C   sà   t  j d t ƒ \ } } |  j | g  ƒ |  j t | ƒ d ƒ |  j | d j d ƒ |  j | d j d ƒ |  j | d j d d d d	 d
 d ƒ |  j | d j d ƒ |  j | d j d ƒ |  j | d j d ƒ d  S(   NR™   i   i    t   1GAGR	   t<   VFPSSVFVPDEWEVSREKITLLRELGQGSFGMVYEGNARDIIKGEAETRVAVKTVNESASt<   LRERIEFLNEASVMKGFTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLRSLRPEAENt<   NPGRPPPTLQEMIQMAAEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRDIt<   XETDXXRKGGKGLLPVRWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQt<   VLKFVMDGGYLDQPDNCPERVTDLMRMCWQFNPKMRPTFLEIVNLLKDDLHPSFPEVSFFt   HSEENKi   R
   t   PATGDFMNMSPVG(   R   t   dbfetch_sequence_parset   dbfetchR   R‡   R   t   chainR   (   R   R±   RŠ   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt   test_dbfetch_parse�  s    	
c         C   s9   |  j  t j d ƒ t j ƒ |  j  t j d ƒ d  ƒ d  S(   Ns	   dummy.pirR†   (   R   R   t   sequence_parser_forR’   t   None(   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt   test_filename_selection§  s    
c         C   s2   |  j  t t j ƒ  ƒ d d d d d d g ƒ d  S(   Ns   .dats   .fas   .faas   .fastas   .pirs   .seq(   R   t   sortedR   t   known_sequence_formats(   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt   test_known_formats°  s    (   R    R!   RŒ   R�   R•   R˜   R²   R·   RÃ   RÆ   RÉ   (    (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyRƒ   m  s   	B	3	*	:	(	 			t   test_alignment_parsec           B   s>   e  Z d  „  Z d „  Z d „  Z d „  Z d „  Z d „  Z RS(   c         C   s“  t  j t ƒ \ } } |  j | d ƒ |  j | j d ƒ |  j | j d d g ƒ |  j | j d d d d d	 d
 g ƒ t  j t ƒ \ } } |  j | d ƒ |  j | j d ƒ |  j | j d d g ƒ |  j | j d d d d d d g ƒ t  j d t ƒ \ } } |  j | d t ƒ |  j | d  ƒ t  j d ƒ \ } } |  j | d ƒ |  j | j d ƒ |  j | j g  ƒ |  j | j g  ƒ d  S(   NR4   s   CLUSTAL 2.0.10t   HorseR„   s<   VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKA---s<   ---HGKKVGDALTLAVGHLDDLPGALSDLSNLHAHKLRVDPVNFKLLSHCLLSTLAVHLPs!   NDFTPAVHASLDKFLSSVSTVLTSKYR------t<   VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDt<   LKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPt!   GDFGADAQGAMNKALELFRKDIAAKYKELGYQGs   CLUSTAL X (1.81)t   1vkkt   1ahqs<   VVCEVDPELKETLRKFRFR---KETNNAAIIMKVD--KDRQMVVLEDELQ-NISPEELKLs<   ELPERQPRFVVYSYKYVH--DDGRVSYPLCFIFSSPVGCKPEQQMMYAGSKNRLVQTAE-s   L-TKVFEIRTTDD-LTETWLKEKLAFFRs<   -GIAVSDDCVQKFNELKLGHQH-----RYVTFKMNASN--TEVVVEHVGGPNATYEDFKSs<   QLPERDCRYAIFDYEFQVDG---GQRNKITFILWAPDSAPIKSKMMYTSTKDSIKKKLVGs   IQ-VEVQATD-AAEISEDAVSERAKK--s   
s,   CLUSTAL 2.0.10 multiple sequence alignment

(	   R   t   clustal_alignment_parset   clustal1R   Ru   R9   R8   t   clustal2RÅ   (   R   Rf   RŠ   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt   testClustal¹  s2    c         C   sK  t  j t ƒ \ } } |  j | d ƒ |  j | j d d g ƒ |  j | j d d g ƒ |  j | j d d g ƒ |  j | j d d d d	 d
 d g ƒ t  j d t ƒ \ } } |  j | d t ƒ |  j | d  ƒ t  j d ƒ \ } } |  j | d ƒ |  j | j g  ƒ |  j | j g  ƒ |  j | j g  ƒ |  j | j g  ƒ d  S(   NR4   RË   R„   R   Rr   s<   VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKA---s<   ---HGKKVGDALTLAVGHLDDLPGALSDLSNLHAHKLRVDPVNFKLLSHCLLSTLAVHLPs!   NDFTPAVHASLDKFLSSVSTVLTSKYR------RÌ   RÍ   RÎ   s   
(
   R   t   pir_alignment_parset   pir_ali1R   R9   Ro   Ri   R8   RÓ   RÅ   (   R   Rf   RŠ   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyR•   ð  s$    c         C   sÔ   t  j t ƒ \ } } |  j | d ƒ |  j | j d d g ƒ |  j | j d d g ƒ |  j | j d d d d	 d
 d d d d d d d d d d d d d d d d d d d d d g ƒ d  S(    NR4   s   2QZU:As   3B5Q:Bs#   Putative sulfatase from B. fragiliss+   Putative sulfatase from B. thetaiotaomicront2   QPTPNLVFIXADQYRGDAIGCIGKEPVKTPHLDKLASEGINFTNAISSYPs2   VSSPARGXLXTGXYPIGSKVT-GNCNSETAPYGVELSQNARCWSDVLKDQs2   GYNXGYIGKWHLDAPYKPYVDTYNNRGKVAWNEWCP---PERRHGFDHWIs2   AYGTYDY-----------------------------H-LKPXYWNTTAPRs2   DSFYYVNQ-----------WGPEYEASKAIEYINGQKDQKQPFALVVSXNs2   PPHTGYE--------------LVPDRYKEIYKDLDVEALCKGRPDIP---s2   -------------------AKG----------------------TEXGDYs2   FRNNIRNYYACITGVDENVGRIIEALKQNNLFDNTIVVFTSDHGICXG--s2   ---------------AHENAGKD-IFYEESXRIPXILSWPDQIKPRKSDPs2   --LXIAFA-DLYPTLLSXXGFSKEIPETVQTFDLSNEVLTGKNKKD-LVQs2   PYYFVKF--------DNHA------------------TGYRGLRTDRYTYs2   AVHAT-DGK------------------------IDNVILFDRTNDPHEXNs   NIASQ--QLKLTHTFNRQLKTWLEKTNDPFs2   -EKPNFLIIQCDHLTQRVVGAYGQTQGCTLPIDEVASRGVIFSNAYVGCPs2   LSQPSRAALWSGXXPHQTNVR-SNSS---EPVNTRLPENVPTLGSLFSESs2   GYEAVHFGKTHDX---------------------------GSLRGFKHKEs2   P-------------------------------------------------s2   ---VAKPFTDPEFPVNNDSFLDVGTCEDAVAYLSNP--PKEPFICIADFQs2   NPHNICGFIGENAGVHTDRPI----------SGPLPEL----PDNFDVEDs2   WSNIPTPVQYICCSHRRXT---QAA-------------------HWNEENs2   YRHYIAAFQHYTKXVSKQVDSVLKALYSTPAGRNTIVVIXADHGDGXA--s2   ---------------SHRXVTKHISFYDEXTNVPFIFAG-PGIKQQKKPVs2   DHLLTQPTLDLLPTLCDLAGIA--VPAEKAGISLAPTLRGEKQKKSHPYVs2   VSEWHSEYEYVT-------------------------TPGRXVRGPRYKYs2   THYLE----------------------------GNGEELYDXKKDPGERKt   NLAKDPKYSKILAEHRALLDDYITRSKDDY(   R   t   fasta_alignment_parset
   fasta_ali1R   R9   Ri   R8   (   R   Rf   RŠ   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyR�     s    
3c         C   s»   t  j t ƒ \ } } |  j | d ƒ |  j | j d d g ƒ |  j | j d d d d d d	 d
 d d d d d d d d d d d d d d d d d d d g ƒ d  S(   NR4   s   2QZU:As   3B5Q:BR×   s2   VSSPARGXLXTGXYPIGSKVT-GNCNSETAPYGVELSQNARCWSDVLKDQs2   GYNXGYIGKWHLDAPYKPYVDTYNNRGKVAWNEWCP---PERRHGFDHWIs2   AYGTYDY-----------------------------H-LKPXYWNTTAPRs2   DSFYYVNQ-----------WGPEYEASKAIEYINGQKDQKQPFALVVSXNs2   PPHTGYE--------------LVPDRYKEIYKDLDVEALCKGRPDIP---s2   -------------------AKG----------------------TEXGDYs2   FRNNIRNYYACITGVDENVGRIIEALKQNNLFDNTIVVFTSDHGICXG--s2   ---------------AHENAGKD-IFYEESXRIPXILSWPDQIKPRKSDPs2   --LXIAFA-DLYPTLLSXXGFSKEIPETVQTFDLSNEVLTGKNKKD-LVQs2   PYYFVKF--------DNHA------------------TGYRGLRTDRYTYs2   AVHAT-DGK------------------------IDNVILFDRTNDPHEXNs   NIASQ--QLKLTHTFNRQLKTWLEKTNDPFs2   -EKPNFLIIQCDHLTQRVVGAYGQTQGCTLPIDEVASRGVIFSNAYVGCPs2   LSQPSRAALWSGXXPHQTNVR-SNSS---EPVNTRLPENVPTLGSLFSESs2   GYEAVHFGKTHDX---------------------------GSLRGFKHKEs2   P-------------------------------------------------s2   ---VAKPFTDPEFPVNNDSFLDVGTCEDAVAYLSNP--PKEPFICIADFQs2   NPHNICGFIGENAGVHTDRPI----------SGPLPEL----PDNFDVEDs2   WSNIPTPVQYICCSHRRXT---QAA-------------------HWNEENs2   YRHYIAAFQHYTKXVSKQVDSVLKALYSTPAGRNTIVVIXADHGDGXA--s2   ---------------SHRXVTKHISFYDEXTNVPFIFAG-PGIKQQKKPVs2   DHLLTQPTLDLLPTLCDLAGIA--VPAEKAGISLAPTLRGEKQKKSHPYVs2   VSEWHSEYEYVT-------------------------TPGRXVRGPRYKYs2   THYLE----------------------------GNGEELYDXKKDPGERKRØ   (   R   t   ali_alignment_parset   ali_ali1R   R9   R8   (   R   Rf   RŠ   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt   testAliE  s    3c         C   s9   |  j  t j d ƒ t j ƒ |  j  t j d ƒ d  ƒ d  S(   Ns	   dummy.pirt   clustal(   R   R   t   alignment_parser_forRÕ   RÅ   (   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyRÆ   l  s    
c      	   C   s5   |  j  t t j ƒ  ƒ d d d d d d d g ƒ d  S(   Ns   .alis   .alns   .clustals   .fas   .fastas   .hhrs   .pir(   R   RÇ   R   t   known_alignment_formats(   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyRÉ   u  s    (   R    R!   RÔ   R•   R�   RÝ   RÆ   RÉ   (    (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyRÊ   ·  s   	7	&	/	'		s1  
Query         Thu_Sep_09_20:47:04_+0200_2010
Match_columns 205
No_of_seqs    280 out of 1436
Neff          7.1
Searched_HMMs 22773
Date          Thu Sep  9 20:51:32 2010
Command       /cluster/toolkit/production/bioprogs/hhpred/hhsearch -cpu 4 -v 1 -i /cluster/toolkit/production/tmp/production/426773/3338418.hhm -d /cluster/toolkit/production/databases/hhpred/new_dbs/pdb70_9Sep10/db/pdb.hhm -o /cluster/toolkit/production/tmp/production/426773/3338418.hhr -p 20 -P 20 -Z 100 -B 100 -seq 1 -aliw 80 -local -ssm 2 -norealign -sc 1 -dbstrlen 10000 -cs /cluster/toolkit/production/bioprogs/csblast/data/clusters.prf

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 3cng_A Nudix hydrolase; struct 100.0 4.5E-28   2E-32  196.5  15.7  139   59-204    27-172 (189)
  2 3i7u_A AP4A hydrolase; nudix p  99.9 1.4E-27 6.2E-32  182.2  13.1  127   69-196     4-130 (134)

No 1
>3cng_A Nudix hydrolase; structural genomics, APC7497, PSI-2, protein structure initiative, midwest center for structural genomics; 2.00A {Nitrosomonas europaea atcc 19718}
Probab=99.96  E-value=4.5e-28  Score=196.52  Aligned_cols=139  Identities=21%  Similarity=0.317  Sum_probs=0.0

Q ss_pred             hccCCC---CCceEEEEEEEEEECCEEEEEEcCC----CEEECCceeeCCCCCHHHHHHHHHHHHhCCccccceEEEEEe
Q Thu_Sep_09_20:   59 FCNETG---YQTPKLDTRAAIFQEDKILLVQEND----GLWSLPGGWCDVDQSVKDNVVKEVKEEAGLDVEAQRVVAILD  131 (205)
Q Consensus        59 ~~~~~g---y~Tpkv~v~a~v~~d~kiLLv~~~~----g~W~lPGG~ve~gEs~~eaa~REv~EETGl~v~~~~ll~v~~  131 (205)
                       |+.||   |+.|++.|.++|.++++|||++|+.    |.|+||||++|.|||+++||+||++||||+++....+++++.
T Consensus        27 ~C~~C~~~~y~~P~v~v~~ii~~~~~vLLv~r~~~~~~g~W~lPGG~ve~GEs~e~aa~REv~EEtGl~v~~~~l~~~~~  106 (189)
T 3cng_A           27 ICPKCHTIHYQNPKVIVGCIPEWENKVLLCKRAIAPYRGKWTLPAGFMENNETLVQGAARETLEEANARVEIRELYAVYS  106 (189)
T ss_dssp             EETTTTEEECCCCEEEEEEEEEETTEEEEEEESSSSSTTCEECSEEECCTTCCHHHHHHHHHHHHHCCCEEEEEEEEEEE
T ss_pred             eCCCCCCcccCCCceEEEEEeecCceEEEEeccCCCCCCCEeCCcccCcCCCCHHHHHHHHHHhhhceeeeeeEEEEEee


Q ss_pred             eccccCCCCceEEEEEEEEEEecCCccCCCCCeEeEEEEcHHHCccccccCCCHHHHHHHHHHHhCCCCCCCc
Q Thu_Sep_09_20:  132 KHKNNPAKSAHRVTKVFILCRLLGGEFQPNSETVASGFFSLDDLPPLYLGKNTAEQLALCLEASRSEHWETRF  204 (205)
Q Consensus       132 ~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~E~~e~~Wf~~deLp~Ls~~r~~~~~i~~~f~~~r~~~~~t~f  204 (205)
                      ....       +...++|.|...++.+.++.|+.+++||++++||...+.-....+.-+.|...+..+....+
T Consensus       107 ~~~~-------~~~~~~f~~~~~~~~~~~~~E~~e~~wf~~~elp~~~la~~~~~~~l~~~~~~~~~g~~~~~  172 (189)
T 3cng_A          107 LPHI-------SQVYMLFRAKLLDLDFFPGIESLEVRLFGEQEIPWNDIAFRVIHDPLKRYMEERHHGQPAFH  172 (189)
T ss_dssp             EGGG-------TEEEEEEEEEECCSCCCCCTTEEEEEEECTTTCCGGGBSCHHHHHHHHHHHHHHHHSSCCCE
T ss_pred             cccc-------ceeEEEEEEEeccCcccCcccceeEEEEcHHHCCchhcCcHHHHHHHHHHHHHhhcCCCccc


No 2
>3i7u_A AP4A hydrolase; nudix protein, diadenosine polyphosphate, structural genomics, NPPSFA; HET: PGE; 1.80A {Aquifex aeolicus} PDB: 2pq1_A* 3i7u_A* 3i7v_A*
Probab=99.95  E-value=1.4e-27  Score=182.17  Aligned_cols=127  Identities=20%  Similarity=0.336  Sum_probs=0.0

Q ss_pred             EEEEEEEEEECCEEEEEEcCCCEEECCceeeCCCCCHHHHHHHHHHHHhCCccccceEEEEEeeccccCCCCceEEEEEE
Q Thu_Sep_09_20:   69 KLDTRAAIFQEDKILLVQENDGLWSLPGGWCDVDQSVKDNVVKEVKEEAGLDVEAQRVVAILDKHKNNPAKSAHRVTKVF  148 (205)
Q Consensus        69 kv~v~a~v~~d~kiLLv~~~~g~W~lPGG~ve~gEs~~eaa~REv~EETGl~v~~~~ll~v~~~~~~~~~~~~~~~~~~~  148 (205)
                      ++.++|+|+++|+|||+++.+|.|++|||++|.|||+.+||+||++||||+++....+++..+.. +.......+...++
T Consensus         4 ~~aAg~vv~~~~~vLlv~r~~~~w~~PgG~ve~gEt~~~aa~RE~~EEtGl~~~~~~~~~~~~~~-~~~~~~~~~~~~~~   82 (134)
T 3i7u_A            4 EFSAGGVLFKDGEVLLIKTPSNVWSFPKGNIEPGEKPEETAVREVWEETGVKGEILDYIGEIHYW-YTLKGERIFKTVKY   82 (134)
T ss_dssp             EEEEEEEEEETTEEEEEECTTSCEECCEEECCTTCCHHHHHHHHHHHHHSEEEEEEEEEEEEEEE-EEETTEEEEEEEEE
T ss_pred             EEEEEEEEEECCEEEEEEeCCCcEECceeEeCCCCCHHHHHHhhhhheeceeEEEeeeeeeeeee-ccCCCceEEEEEEE


Q ss_pred             EEEEecCCccCCCCCeEeEEEEcHHHCccccccCCCHHHHHHHHHHHh
Q Thu_Sep_09_20:  149 ILCRLLGGEFQPNSETVASGFFSLDDLPPLYLGKNTAEQLALCLEASR  196 (205)
Q Consensus       149 f~~~~~~~~~~~~~E~~e~~Wf~~deLp~Ls~~r~~~~~i~~~f~~~r  196 (205)
                      |.+...++++.++.|+.+++|+++++++++....+....|..+++..+
T Consensus        83 f~~~~~~~~~~~~~E~~~~~W~~~~e~~~~l~~~~~r~il~~~~~l~~  130 (134)
T 3i7u_A           83 YLMKYKEGEPRPSWEVKDAKFFPIKEAKKLLKYKGDKEIFEKALKLKE  130 (134)
T ss_dssp             EEEEEEEECCCCCTTSSEEEEEEHHHHHHHCCSHHHHHHHHHHHHHHH
T ss_pred             EEEeccCCcccCChhheEEEEEeHHHHHhhcCChHHHHHHHHHHHHHh


Done!
s¤  
Query         1XVQ.pdb
Match_columns 155
No_of_seqs    111 out of 3723
Neff          9.0
Searched_HMMs 0
Date          Tue Jul 13 19:50:02 2010
Command       /work/dimaio/sequence/hhsearch/hhalign -i 1XVQ.hhm -t 1FOH.hhm -glob -o 1FOH_1XVQ.hhr

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 1FOH_aln.pdb                     1.0       1       1   56.1  11.5  141    1-155   460-631 (649)

No 1
>1FOH_aln.pdb
Probab=1.00    E-value=1  Score=56.09  Aligned_columns=141  Identities=11%

Q ss_pred             CCCCCCCCCCCCCCEEEEC-CCCCEEEHHH-HC--CCEEEEEEECCCCCCCHHHHHHHHHHHHHHC--------------
Q ss_conf             9988554688178517897-9997764889-69--9848999832437711126669999998420--------------
Q 1XVQ.pdb          1 TVGELPAVGSPAPAFTLTG-GDLGVISSDQ-FR--GKSVLLNIFPSVDTPVCATSVRTFDERAAAS--------------   62 (155)
Q Consensus         1 ~~~~~p~vG~~aPdF~l~~-~~G~~v~ls~-~~--Gk~vvl~f~~~~~~p~c~~~~~~l~~~~~~~--------------   62 (155)
                      -...-+.+|..+|+.-+.. .+|....+.+ +.  |++.++.|......+.-...+..+.+...................
T Consensus       460 ~~~~~~~~G~r~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  539 (649)
T 1FOH_aln.pdb    460 ELAKNCVVGTRFKSQPVVRHSEGLWMHFGDRLVTDGRFRIIVFAGKATDATQMSRIKKFSAYLDSENSVISLYTPKVSDR  539 (649)
T ss_pred             CCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCEEEECCCCCCCC
T ss_conf             33688888864688503532788831125541278837999943888761135678888875204563011022466766


Q ss_pred             --CEEECCCCCCCHH-----HHHHHHHHHCCCC------EEECCCCCHHHHHHCCCCCCCCCCCCCEEEEEEEECCCCEE
Q ss_conf             --1000023467889-----9999999828975------11014433488997077344565557101279998699839
Q 1XVQ.pdb         63 --GATVLCVSKDLPF-----AQKRFCGAEGTEN------VMPASAFRDSFGEDYGVTIADGPMAGLLARAIVVIGADGNV  129 (155)
Q Consensus        63 --g~~v~~i~~~~~~-----~~~~~~~~~~~~~------~~~~~d~~~~~~~~~g~~~~~~~~~~~~~p~~fiID~~G~I  129 (155)
                        .+.++.|......     .............      .....|........||+..+        ..+.+||=|||-|
T Consensus       540 ~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~g~~~~--------~~~~vlVRPD~~V  611 (649)
T 1FOH_aln.pdb    540 NSRIDVITIHSCHRDDIEMHDFPAPALHPKWQYDFIYADCDSWHHPHPKSYQAWGVDET--------KGAVVVVRPDGYT  611 (649)
T ss_pred             CCCEEEEEEECCCCCCCCHHHCHHHHCCCCCCCEEEEECCCCCCCCCHHHHHHHCCCHH--------CCEEEEECCCCEE
T ss_conf             56168999854776544233320200246742016650444444667789998098711--------4379998699558


Q ss_pred             EEEEECCCCCCCCCHHHHHHHHHHHC
Q ss_conf             99998178888889999999998519
Q 1XVQ.pdb        130 AYTELVPEIAQEPNYEAALAALGATS  155 (155)
Q Consensus       130 ~~~~~~~~~~~~~~~~~il~~lkal~  155 (155)
                      .++.  +    .-+.+++.+.+...=
T Consensus       612 a~~~--~----~~~~~~l~~~~~~~l  631 (649)
T 1FOH_aln.pdb    612 SLVT--D----LEGTAEIDRYFSGIL  631 (649)
T ss_pred             EEEE--C----HHHHHHHHHHHHHHC
T ss_conf             9997--3----013589999999742


Done!
t   test_hhsearch_parserc           B   s,   e  Z d  „  Z d „  Z d „  Z d „  Z RS(   c         C   s   t  j d t ƒ |  _ d  S(   Nt   output(   R   t   hhsearch_parsert   hhsearchoutt   hss(   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyR%   õ  s    c         C   sž   |  j  |  j j d ƒ |  j  |  j j d ƒ |  j  |  j j d	 ƒ |  j  |  j j d ƒ |  j  |  j j d ƒ |  j  |  j j d ƒ |  j  |  j j d ƒ d  S(
   Ns   Thu_Sep_09_20:47:04_+0200_2010iÍ   i  iœ  s   7.1iõX  s   Thu Sep  9 20:51:32 2010s®  /cluster/toolkit/production/bioprogs/hhpred/hhsearch -cpu 4 -v 1 -i /cluster/toolkit/production/tmp/production/426773/3338418.hhm -d /cluster/toolkit/production/databases/hhpred/new_dbs/pdb70_9Sep10/db/pdb.hhm -o /cluster/toolkit/production/tmp/production/426773/3338418.hhr -p 20 -P 20 -Z 100 -B 100 -seq 1 -aliw 80 -local -ssm 2 -norealign -sc 1 -dbstrlen 10000 -cs /cluster/toolkit/production/bioprogs/csblast/data/clusters.prf(   i  iœ  (	   R   Rå   t   queryt   match_columnst   no_of_sequencest   nefft   searched_hmmst   datet   command(   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt   test_process_headerú  s    	c         C   s  |  j  |  j j d d g ƒ |  j  |  j j d d g ƒ |  j  |  j j d d g ƒ |  j  |  j j d d g ƒ |  j |  j j d d	 g d ƒ |  j |  j j d
 d g d ƒ |  j |  j j	 d d g d ƒ |  j  |  j j
 d d g ƒ |  j |  j j d d g d ƒ |  j |  j j d d g d ƒ |  j |  j j d d g d ƒ |  j  |  j j d d g ƒ |  j  |  j j d d g ƒ |  j  |  j j d d g ƒ |  j  |  j j d d d d g ƒ |  j  |  j j d  d! d" d# g ƒ |  j  |  j j d$ d% d& d' g ƒ |  j  |  j j d( d) d* d+ g ƒ |  j  |  j j d, d- g ƒ |  j  |  j j d. d/ g ƒ |  j  |  j j d0 d1 g ƒ |  j  |  j j d2 d3 d4 d5 g ƒ |  j  |  j j d6 d7 d8 d9 g ƒ |  j  |  j j d: d; d< d= g ƒ |  j  |  j j d> d? d@ dA g ƒ d  S(B   Ni   i   t   3CNGt   3I7UR	   s¤   Nudix hydrolase; structural genomics, APC7497, PSI-2, protein structure initiative, midwest center for structural genomics; 2.00A {Nitrosomonas europaea atcc 19718}s–   AP4A hydrolase; nudix protein, diadenosine polyphosphate, structural genomics, NPPSFA; HET: PGE; 1.80A {Aquifex aeolicus} PDB: 2pq1_A* 3i7u_A* 3i7v_A*g=
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×£pÅf@i‹   i   i   i   g}?5^ºIÔ?g/Ý$�Õ?i   i    i;   iE   iÌ   iÄ   iÍ   sP   FCNETG---YQTPKLDTRAAIFQEDKILLVQEND----GLWSLPGGWCDVDQSVKDNVVKEVKEEAGLDVEAQRVVAILDtI   KHKNNPAKSAHRVTKVFILCRLLGGEFQPNSETVASGFFSLDDLPPLYLGKNTAEQLALCLEASRSEHWETRFtP   KLDTRAAIFQEDKILLVQENDGLWSLPGGWCDVDQSVKDNVVKEVKEEAGLDVEAQRVVAILDKHKNNPAKSAHRVTKVFt0   ILCRLLGGEFQPNSETVASGFFSLDDLPPLYLGKNTAEQLALCLEASRsP   ~~~~~g---y~Tpkv~v~a~v~~d~kiLLv~~~~----g~W~lPGG~ve~gEs~~eaa~REv~EETGl~v~~~~ll~v~~sI   ~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~E~~e~~Wf~~deLp~Ls~~r~~~~~i~~~f~~~r~~~~~t~fsP   kv~v~a~v~~d~kiLLv~~~~g~W~lPGG~ve~gEs~~eaa~REv~EETGl~v~~~~ll~v~~~~~~~~~~~~~~~~~~~s0   f~~~~~~~~~~~~~E~~e~~Wf~~deLp~Ls~~r~~~~~i~~~f~~~rsP   hccCCC---CCceEEEEEEEEEECCEEEEEEcCC----CEEECCceeeCCCCCHHHHHHHHHHHHhCCccccceEEEEEetI   eccccCCCCceEEEEEEEEEEecCCccCCCCCeEeEEEEcHHHCccccccCCCHHHHHHHHHHHhCCCCCCCctP   EEEEEEEEEECCEEEEEEcCCCEEECCceeeCCCCCHHHHHHHHHHHHhCCccccceEEEEEeeccccCCCCceEEEEEEt0   EEEEecCCccCCCCCeEeEEEEcHHHCccccccCCCHHHHHHHHHHHhsP    |+.||   |+.|++.|.++|.++++|||++|+.    |.|+||||++|.|||+++||+||++||||+++....+++++.sI   ....       +...++|.|...++.+.++.|+.+++||++++||...+.-....+.-+.|...+..+....+sP   ++.++|+|+++|+|||+++.+|.|++|||++|.|||+.+||+||++||||+++....+++..+.. +.......+...++s0   |.+...++++.++.|+.+++|+++++++++....+....|..+++..+i   i   i¬   i‚   i½   i†   tP   eCCCCCCcccCCCceEEEEEeecCceEEEEeccCCCCCCCEeCCcccCcCCCCHHHHHHHHHHhhhceeeeeeEEEEEeesI   cccc-------ceeEEEEEEEeccCcccCcccceeEEEEcHHHCCchhcCcHHHHHHHHHHHHHhhcCCCcccsP   EEEEEEEEEECCEEEEEEeCCCcEECceeEeCCCCCHHHHHHhhhhheeceeEEEeeeeeeeeee-ccCCCceEEEEEEEt0   EEEeccCCcccCChhheEEEEEeHHHHHhhcCChHHHHHHHHHHHHHhtP   EETTTTEEECCCCEEEEEEEEEETTEEEEEEESSSSSTTCEECSEEECCTTCCHHHHHHHHHHHHHCCCEEEEEEEEEEEsI   EGGG-------TEEEEEEEEEECCSCCCCCTTEEEEEEECTTTCCGGGBSCHHHHHHHHHHHHHHHHSSCCCEsP   EEEEEEEEEETTEEEEEECTTSCEECCEEECCTTCCHHHHHHHHHHHHHSEEEEEEEEEEEEEEE-EEETTEEEEEEEEEt0   EEEEEEEECCCCCTTSSEEEEEEHHHHHHHCCSHHHHHHHHHHHHHHHsP   ~C~~C~~~~y~~P~v~v~~ii~~~~~vLLv~r~~~~~~g~W~lPGG~ve~GEs~e~aa~REv~EEtGl~v~~~~l~~~~~sI   ~~~~-------~~~~~~f~~~~~~~~~~~~~E~~e~~wf~~~elp~~~la~~~~~~~l~~~~~~~~~g~~~~~sP   ~~aAg~vv~~~~~vLlv~r~~~~w~~PgG~ve~gEt~~~aa~RE~~EEtGl~~~~~~~~~~~~~~-~~~~~~~~~~~~~~s0   f~~~~~~~~~~~~~E~~~~~W~~~~e~~~~l~~~~~r~il~~~~~l~~tP   ICPKCHTIHYQNPKVIVGCIPEWENKVLLCKRAIAPYRGKWTLPAGFMENNETLVQGAARETLEEANARVEIRELYAVYSsI   LPHI-------SQVYMLFRAKLLDLDFFPGIESLEVRLFGEQEIPWNDIAFRVIHDPLKRYMEERHHGQPAFHsP   EFSAGGVLFKDGEVLLIKTPSNVWSFPKGNIEPGEKPEETAVREVWEETGVKGEILDYIGEIHYW-YTLKGERIFKTVKYt0   YLMKYKEGEPRPSWEVKDAKFFPIKEAKKLLKYKGDKEIFEKALKLKE(   R   Rå   t   indicest   pdbst   chainst   annotationst   assertIterablesAlmostEqualt   probabst   e_valuest   scorest   aligned_colst
   identitiest   similaritiest	   sum_probst   query_startst
   query_endst   query_otherst   query_alignmentst   query_consensit   query_ss_predst   midlinest
   hit_startst   hit_endst
   hit_otherst   hit_ss_predst   hit_ss_dsspst   hit_consensit   hit_alignments(   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt   test_process_hits  sˆ    	
								c         C   sS   |  j  t | ƒ t | ƒ ƒ x0 t | | ƒ D] \ } } |  j | | | ƒ q, Wd  S(   N(   R   R‡   t   zipRO   (   R   t   i1t   i2t   digitst   ot   e(    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyR   m  s    (   R    R!   R%   Rí   R  R   (    (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyRá   ó  s   			et   test_hhalign_parserc           B   s,   e  Z d  „  Z d „  Z d „  Z d „  Z RS(   c         C   s   t  j d t ƒ |  _ d  S(   NRâ   (   R   t   hhalign_parsert
   hhalignoutRå   (   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyR%   w  s    c         C   sž   |  j  |  j j d ƒ |  j  |  j j d ƒ |  j  |  j j d	 ƒ |  j  |  j j d ƒ |  j  |  j j d ƒ |  j  |  j j d ƒ |  j  |  j j d ƒ d  S(
   Ns   1XVQ.pdbi›   io   i‹  s   9.0i    s   Tue Jul 13 19:50:02 2010sU   /work/dimaio/sequence/hhsearch/hhalign -i 1XVQ.hhm -t 1FOH.hhm -glob -o 1FOH_1XVQ.hhr(   io   i‹  (	   R   Rå   Ræ   Rç   Rè   Ré   Rê   Rë   Rì   (   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyRí   |  s    	c         C   s~  |  j  |  j j d g ƒ |  j  |  j j d g ƒ |  j |  j j d g d ƒ |  j |  j j d g d ƒ |  j |  j j d g d ƒ |  j  |  j j d g ƒ |  j |  j j	 d g d ƒ |  j  |  j j
 d g ƒ |  j  |  j j d g ƒ |  j  |  j j d g ƒ |  j  |  j j d	 d
 d g ƒ |  j  |  j j d d d g ƒ |  j  |  j j d d d g ƒ |  j  |  j j d d d g ƒ |  j  |  j j d d d g ƒ |  j  |  j j d g ƒ |  j  |  j j d g ƒ |  j  |  j j d g ƒ |  j  |  j j d d d g ƒ |  j  |  j j d d d  g ƒ |  j  |  j j d! d" d# g ƒ |  j  |  j j d$ d% d& g ƒ d  S('   Ni   s   1FOH_aln.pdbg      ð?i   gìQ¸…L@i�   i   i›   sP   TVGELPAVGSPAPAFTLTG-GDLGVISSDQ-FR--GKSVLLNIFPSVDTPVCATSVRTFDERAAAS--------------sP   --GATVLCVSKDLPF-----AQKRFCGAEGTEN------VMPASAFRDSFGEDYGVTIADGPMAGLLARAIVVIGADGNVt   AYTELVPEIAQEPNYEAALAALGATSsP   ~~~~~p~vG~~aPdF~l~~-~~G~~v~ls~-~~--Gk~vvl~f~~~~~~p~c~~~~~~l~~~~~~~--------------sP   --g~~v~~i~~~~~~-----~~~~~~~~~~~~~------~~~~~d~~~~~~~~~g~~~~~~~~~~~~~p~~fiID~~G~Is   ~~~~~~~~~~~~~~~~~il~~lkal~sP   CCCCCCCCCCCCCCEEEEC-CCCCEEEHHH-HC--CCEEEEEEECCCCCCCHHHHHHHHHHHHHHC--------------sP   --CEEECCCCCCCHH-----HHHHHHHHHCCCC------EEECCCCCHHHHHHCCCCCCCCCCCCCEEEEEEEECCCCEEt   EEEEECCCCCCCCCHHHHHHHHHHHCsP   9988554688178517897-9997764889-69--9848999832437711126669999998420--------------sP   --1000023467889-----9999999828975------11014433488997077344565557101279998699839t   99998178888889999999998519sP   -...-+.+|..+|+.-+.. .+|....+.+ +.  |++.++.|......+.-...+..+.+...................sP     .+.++.|......     .............      .....|........||+..+        ..+.+||=|||-|s   .++.  +    .-+.+++.+.+...=iÌ  iw  i‰  tP   CCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCEEEECCCCCCCCsP   CCCEEEEEEECCCCCCCCHHHCHHHHCCCCCCCEEEEECCCCCCCCCHHHHHHHCCCHH--------CCEEEEECCCCEEs   EEEE--C----HHHHHHHHHHHHHHCtP   33688888864688503532788831125541278837999943888761135678888875204563011022466766sP   56168999854776544233320200246742016650444444667789998098711--------4379998699558s   9997--3----013589999999742sP   ~~~~~~~~G~r~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~sP   ~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~g~~~~--------~~~~vlVRPD~~Vs   a~~~--~----~~~~~~l~~~~~~~ltP   ELAKNCVVGTRFKSQPVVRHSEGLWMHFGDRLVTDGRFRIIVFAGKATDATQMSRIKKFSAYLDSENSVISLYTPKVSDRsP   NSRIDVITIHSCHRDDIEMHDFPAPALHPKWQYDFIYADCDSWHHPHPKSYQAWGVDET--------KGAVVVVRPDGYTs   SLVT--D----LEGTAEIDRYFSGIL(   R   Rå   Rü   Rÿ   R   R  R  R  R  R  R  R	  R
  R  R  R  t   query_ss_confsR  R  R  R  R  t   hit_ss_confsR  R  (   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyR  Š  sP    									c         C   sS   |  j  t | ƒ t | ƒ ƒ x0 t | | ƒ D] \ } } |  j | | | ƒ q, Wd  S(   N(   R   R‡   R  RO   (   R   R  R  R  R  R  (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyR   æ  s    (   R    R!   R%   Rí   R  R   (    (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyR  u  s   			\c          C   s�   t  d d ƒ j d ƒ d }  t j d d g d |  d d g ƒ t j |  ƒ \ } } t | ƒ d	 k rw t | ƒ d
 k s} t ‚ d  S(   Ns   tmp_iotbx_bioinfo.fat   ws   > 9zzz
ARGLYS
> 8xxx
PHETYRs   tmp_iotbx_bioinfo_merged.fat
   file_namest   output_fileRd   t   SERTHRi   i    (   t   opent   writeR   t   merge_sequence_filest   any_sequence_formatR‡   t   AssertionError(   R*  t   seq_int   nc(    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt   exercise_merge_sequencesí  s    		
t   __main__t   streamt	   verbosityi   (C   t
   __future__R    t   iotbxR   t   unittestt   sysR   R   R   R   R   t   TestCaseR   R"   R,   R-   RA   RB   RD   RE   RH   R7   Rh   Rn   Rt   R†   Rˆ   R‰   R   R“   R—   R°   R¶   RÁ   R   RÒ   RÓ   RÖ   RÚ   RÜ   Rƒ   RÊ   Rä   R  Rá   R  R3  t
   TestLoadert   loadTestsFromTestCaset   suite_sequencet   suite_fasta_sequencet   suite_pir_sequencet   suite_midlinet   suite_alignmentt   suite_fasta_alignmentt   suite_pir_alignmentt   suite_clustal_alignmentt   suite_sequence_parset   suite_alignment_parset   suite_hhsearch_parsert   suite_hhalign_parsert	   TestSuitet   alltestsR    t   TextTestRunnert   stdoutt   run(    (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/regression/tst_bioinformatics.pyt   <module>   sª   T28vL\B/ÿ Kÿ 4‚x													