Lc@sdZddlZddlZddlmZddlmZddlmZddl m Z dZ dZ d fd YZ d fd YZed dZedkrdGHddlmZddlmZdZdZe j idd6dd6dd6dd6e jejZejeeeZxeD]ZejjGHq2Wdej GHe eZ!e!j"ddZ#e#GHe!j$ddZ#e#GHHe!j%ddgde#GHHe!j&deddgGHHd GHej'ej(ej)dd!Z*ee*Z+e+j,d"d#e+j,d$d%e+j,d&d'e+GHde+j GHe e+Z-e-j"dd(Z.e.GHe-j$dd(Z.e.GHHe-j%ddd!gde.GHe-j&ddd!gGHd)GHndS(*sExtract information from alignment objects. In order to try and avoid huge alignment objects with tons of functions, functions which return summary type information about alignments should be put into classes in this module. classes: o SummaryInfo o PSSM iN(tAlphabet(tIUPAC(tSeq(t FreqTableg?g?t SummaryInfocBseZdZdZdddddZdddddZdZgdZd Z d Z gd Z dgd Z d Z ddddgdZdZdZdZRS(sCalculate summary info about the alignment. This class should be used to caclculate information summarizing the results of an alignment. This may either be straight consensus info or more complicated things. cCs||_i|_dS(sInitialize with the alignment to calculate information on. ic_vector attribute. A dictionary. Keys: column numbers. Values: N(t alignmentt ic_vector(tselfR((s4C:\Python27\Lib\site-packages\Bio\Align\AlignInfo.pyt__init__!s gffffff?tXicCsd}|jj}xt|D]}}i}d} x|jjD]} |t| jkrA| j|dkr| j|dkr| j||krd|| j|tbase_dictionaryRTt first_lettert second_letter((s4C:\Python27\Lib\site-packages\Bio\Align\AlignInfo.pyR8Cs     c Cs|j}|stt|ts6tdnt|jjtjrg|j |jjj nx |D]}|j |d}qnW|r|}t ||jj kstn |j}g}xtt |D]}|j|}x|jjD]} y| j|} Wntk r1d} nX| r| |kr| jjdd} y|| c| 7   $     cCs%i}x|D]}d|| sn  FD %    !