ó ™62Pc@s8dZddlTdZd Zdd„Zdd„ZdS( sÂReads Sequences in interleaved Phylip format (not sequential) and returns a list of sequences. Phylip is a very common phylogeny generating sequence type that has the following traits: 1) First line contains number of species and number of characters in a species' sequence. Options may follow, and they can be spaced or unspaced. Options are simply letters such as A and W after the number of characters. 2) Options don't have to contain U in order for a usertree to appear. 3) If there are options then options appear first, then the sequences. For the first iteration of sequences the first ten spaces are reserved for names of options and species, the rest is for sequences. 4) For the second and following iterations the names are removed, only sequence appears 4) At end of file a usertree may appear. First there is a number that indicts the number of lines the usertree will take, and then the usertrees follow. Examples: 6 50 W W 0101001111 0101110101 01011 dmras1 GTCGTCGTTG GACCTGGAGG CGTGG hschras GTGGTGGTGG GCGCCGGCCG TGTGG ddrasa GTTATTGTTG GTGGTGGTGG TGTCG spras GTAGTTGTAG GAGATGGTGG TGTTG scras1 GTAGTTGTCG GTGGAGGTGG CGTTG scras2 GTCGTCGTTG GTGGTGGTGG TGTTG 0101001111 0101110101 01011 GTCGTCGTTG GACCTGGAGG CGTGG GTGGTGGTGG GCGCCGGCCG TGTGG GTTATTGTTG GTGGTGGTGG TGTCG GTAGTTGTAG GAGATGGTGG TGTTG GTAGTTGTCG GTGGAGGTGG CGTTG GTCGTCGTTG GTGGTGGTGG TGTTG 1 ((dmras1,ddrasa),((hschras,spras),(scras1,scras2))); iÿÿÿÿ(t*tphyliptphycCstt||ƒƒS(s'Iterate over the sequences in the file.(titertread(tfintalphabet((sN/home/CIBIV/huy/public_html/EpiSpeller/weblogo-3.2/corebio/seq_io/phylip_io.pytiterseqGscCs£g}g}d}d}d}d}d}d} |jƒ} xµ| ró| jƒ} | gkr`n„| djƒr½t| ƒdkr½t|ƒ|kr½t|dƒ|kr½t| dƒ}n'| dkrt|ƒ|kr | dd|krü| d8} qtdƒ‚qä| d8} nÌ|dkrZt||dƒ|krK|d8}qätdƒ‚nŠ| djƒrt| ƒdkròt|ƒdkròt| dƒ}t| dƒ}t| ƒdkrþdj| dƒ}t|ƒ|jdƒ} qþqätdƒ‚nã| dkrä|dkr(td ƒ‚qä||krä|t|ƒkr|jdj| d jƒƒƒ|j| dd !j ƒƒ|d7}n#||cdj| ƒ7<|d7}||krád}t|ƒ|jdƒ} qáqän|jƒ} q?Wt|ƒt|ƒkst|ƒ|kr-td ƒ‚ng} xct dt|ƒƒD]L} t|| ƒ|kr‰| jt || ||| ƒƒqItd ƒ‚qIWt | ƒS( Nitis#Not an option, but it should be onesUser Tree in Wrong PlaceitUs parse errors"Empty File, or possibly wrong filei s#Number of different sequences wrongsextra sequence in list( treadlinetsplittisdigittlentintt ValueErrortjointcounttappendtstriptrangetSeqtSeqList(RRtsequencetidentstnum_seqt num_total_seqttrackertusertree_trackertoptionst num_optionstlinets_linetseqsti((sN/home/CIBIV/huy/public_html/EpiSpeller/weblogo-3.2/corebio/seq_io/phylip_io.pyRNsv    J     $       "*$N(R(R(t__doc__t corebio.seqtnamest extensionstNoneRR(((sN/home/CIBIV/huy/public_html/EpiSpeller/weblogo-3.2/corebio/seq_io/phylip_io.pyt@s