ó Y_Sc@@s•dZddlmZddlZddlTddlTddlTdZdZdZ ej d ƒZ ej d ƒZ dd„Zdd„Zd„ZdS(sNRead sequence information in MSF format. This is a file format for biological sequence data. The sequences are interweaved and each line is labeled with the sequence name. The MSF format can be identified in one or more of the following ways: 1. The word PileUp on the first line (optional) 2. the word !!AA_MULTIPLE_ALIGNMENT or !!NA_MULTIPLE_ALIGNMENT at the start of the file (optional) 3. the word MSF on the first line of the file, and the characters ".." at the end of this line (optional) 4. A header containing sequence information followed by a line with the characters "//" i(tabsolute_importNi(t*is3 PileUp MSF: 64 Type: P Check: 767 .. Name: Cow Len: 100 Check: 3761 Weight: 1.00 Name: Carp Len: 100 Check: 1550 Weight: 1.00 Name: Chicken Len: 100 Check: 2397 Weight: 1.00 Name: Human Len: 100 Check: 9021 Weight: 1.00 Name: Loach Len: 100 Check: 984 Weight: 1.00 Name: Mouse Len: 100 Check: 2993 Weight: 1.00 // Cow MAYPMQLGFQ DATSPIMEEL LHFHDHTLMI VFLISSLVLY IISLMLTTKL Carp MAHPTQLGFK DAAMPVMEEL LHFHDHALMI VLLISTLVLY IITAMVSTKL Chicken MANHSQLGFQ DASSPIMEEL VEFHDHALMV ALAICSLVLY LLTLMLMEKL Human MAHAAQVGLQ DATSPIMEEL ITFHDHALMI IFLICFLVLY ALFLTLTTKL Loach MAHPTQLGFQ DAASPVMEEL LHFHDHALMI VFLISALVLY VIITTVSTKL Mouse MAYPFQLGLQ DATSPIMEEL MNFHDHTLMI VFLISSLVLY IISLMLTTKL Cow THTSTMDAQE VETIWTILPA IILILIALPS LRILYMMDEI NNPSLTVKTM Carp TNKYILDSQE IEIVWTILPA VILVLIALPS LRILYLMDEI NDPHLTIKAM Chicken S.SNTVDAQE VELIWTILPA IVLVLLALPS LQILYMMDEI DEPDLTLKAI Human TNTNISDAQE METVWTILPA IILVLIALPS LRILYMTDEV NDPSLTIKSI Loach TNMYILDSQE IEIVWTVLPA LILILIALPS LRILYLMDEI NDPHLTIKAM Mouse THTSTMDAQE VETIWTILPA VILIMIALPS LRILYMMDEI NNPVLTVKTM tmsfsgcg-msftgcgtPileUps (//)(\s*)$s\s*(\S+)\s+([\S\s.?]+)$cC@stt||ƒƒS(s'Iterate over the sequences in the file.(titertread(tfintalphabet((s?/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/msf_io.pytiterseqWscC@sZt|ƒ}g}g}d}xÔt|ƒD]Æ}|jdkrId}q+|jdkrt|ƒ|krñ|j|jƒ|jgƒqñq+|jdkr+|j|jƒsÐtd|j||jfƒ‚n||j|jƒ|d7}q+q+W|gkrtdƒ‚ngt ||ƒD]*\}}t dj |ƒ|d |ƒ^q }t |ƒS( Nit begin_blocktseq_idtseqs.Character on line: %d not in alphabet: %s : %sis"Parse error, possible wrong formatttname( tAlphabett_line_isttypeoftlentappendtdatat alphabetict ValueErrortlinenotziptSeqtjointSeqList(RRtseq_idstseqst block_countttokentsti((s?/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/msf_io.pyR^s,   @c c@sºtdƒ\}}}tdƒV|}xt|ƒD]\}}||kr•|jƒr]q3ntj|ƒ}|dk r3tdƒV|}q3q•q3n||krÇ|jƒr³q3ntdƒV|}n||kr3|jƒrötdƒV|}q3ntj|ƒ}|dkr$td|ƒ‚n|j dƒj ƒrZ|j dƒj ƒj ƒrZq3ntd |j dƒj ƒƒV|j dƒ}d j |j ƒƒ}td |j ƒƒVq3q3WdS( Nitbegint end_headerR t end_blocksParse error on line: %diiR R R (trangetTokent enumeratetisspaceR#tmatchtNonetseq_lineRtgrouptisdigittstripRtsplit( RtheadertbodytblocktstatetLtlinetmR((s?/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/msf_io.pyRxs@             0(Rsgcg-msfRR(t__doc__t __future__RtreR tutilsR texampletnamest extensionstcompileR#R+R*R RR(((s?/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/msf_io.pyt#s    %