ó ’;ïHc@s²dZy eZWn!ek r3ddlmZnXddlmZddlmZddl m Z m Z de fd„ƒYZ de fd „ƒYZ ed kr®d GHd Zdd lmZeeƒZdZx=e eƒD]/Zx&ejƒD]ZedZejGHqïWqÜWedks!t‚djddƒjddƒjƒZejjƒjddƒekslt‚dZdZeeƒZe e eƒƒZ!ej"ƒe#e!ƒdks¸t‚e#e!djƒƒdksÚt‚eeƒZe e eƒƒZ$ej"ƒe#e$ƒdkst‚e#e$djƒƒdks<t‚x{e%ddƒD]jZ&e!djƒe&je$djƒe&jke!djƒe&jjƒe$djƒe&jjƒkqLWdZ'dZ(dZ)ee'ƒZe e eƒƒZ*ej"ƒe#e*ƒdks t‚e#e*djƒƒdks.t‚ee(ƒZyUe e eƒƒZ+e#e+ƒdksgt‚e#e+djƒƒdks‰t‚dGHWne,k r§dGHnXej"ƒee)ƒZe e eƒƒZ+ej"ƒe#e+ƒdksòt‚e#e*djƒƒdkst‚dGHee'de'ƒZe#e e eƒƒƒdksQt‚eede'd eƒZe#e e eƒƒƒd!ks‘t‚d"GHd#GHeƒZe eƒj-e+ƒej.dƒe e eƒƒZ/e#e+ƒe#e/ƒksôt‚x¯e0e+e/ƒD]ž\Z1Z2e#e1jƒƒe#e2jƒƒks:t‚xee0e1jƒe2jƒƒD]H\Z3Z4e3je4jkszt‚e3jjƒe4jjƒksVt‚qVWqWd$GHnd%S(&sš AlignIO support for the "phylip" format used in Joe Felsenstein's PHYLIP 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). Note ==== In TREE_PUZZLE (Schmidt et al. 2003) and PHYML (Guindon and Gascuel 2003) a dot/period (".") in a sequence is interpreted as meaning the same character as in the first sequence. The PHYLIP 3.6 documentation says: "a period was also previously allowed but it is no longer allowed, because it sometimes is used in different senses in other programs" At the time of writing, we do nothing special with a dot/period. iÿÿÿÿ(tSet(tsingle_letter_alphabet(t Alignment(tAlignmentIteratortSequentialAlignmentWritert PhylipWritercBseZdZd„ZRS(sPhylip alignment writer.cCsVd}|jƒ}|j}t|ƒdkr<tdƒ‚n|jƒ}x2|D]*}|t|jƒkrOtdƒ‚qOqOW|dkr˜tdƒ‚nt|ƒttg|D]}|j| ^q®ƒƒkrßtdƒ‚n|jdt|ƒ|fƒd}xMt rQx|D] }|dkr–|jj ƒ} x dD]} | j | d ƒ} q:Wx d D]} | j | d ƒ} q]W|j| | j |ƒƒn|jd |ƒxht dd ƒD]W} |d| d} |jjƒ| | d!} |jd| ƒ| d|kr·Pq·q·W|jdƒqW|d}|d|krAPn|jdƒqWdS(sÞUse this to write (another) single alignment to an open file. This code will write interlaced alignments (when the sequences are longer than 50 characters). Note that record identifiers are strictly truncated at 10 characters. For more information on the file format, please see: http://evolution.genetics.washington.edu/phylip/doc/sequence.html http://evolution.genetics.washington.edu/phylip/doc/main.html#inputfiles i isMust have at least one sequences%Sequences must all be the same lengths Non-empty sequences are requireds/Repeated identifier, possibly due to truncations %i %s s[](),ts:;t|t ii2s %ss iN(t get_all_seqsthandletlent ValueErrortget_alignment_lengthtseqtsettidtwritetTruetstriptreplacetljusttrangettostring(tselft alignmentttruncatetrecordsR tlength_of_seqstrecordtrtblocktnametchartchunktit seq_segment((s‡/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/PhylipIO.pytwrite_alignment#sH      8      (t__name__t __module__t__doc__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/PhylipIO.pyR!stPhylipIteratorcBs eZdZd„Zd„ZRS(sÚReads a Phylip alignment file returning an Alignment object iterator. Record identifiers are limited to at most 10 characters. It only copes with interlaced phylip files! Sequential files won't work where the sequences are split over multiple lines. For more information on the file format, please see: http://evolution.genetics.washington.edu/phylip/doc/sequence.html http://evolution.genetics.washington.edu/phylip/doc/main.html#inputfiles cCsx|jƒ}td|jƒƒ}t|ƒdkr7tSy(t|dƒ}t|dƒ}tSWntk rstSXdS(Niii( RtfiltertNonetsplitR tFalsetintRR (Rtlinetpartstnumber_of_seqsR((s‡/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/PhylipIO.pyt _is_header‚s  c Cs`|j}y|j}|`Wntk r;|jƒ}nX|sFdS|jƒ}td|jƒƒ}t|ƒdkrˆt dƒ‚ny$t |dƒ}t |dƒ}Wnt k rËt dƒ‚nX|j |ƒsát ‚|j dk r|j |krt d||j fƒ‚ng}g}xftd|ƒD]U}|jƒjƒ}|j|d jƒƒ|j|djƒjddƒgƒq7Wd}xØtrpx,d|jƒkrÍ|jƒ}|s¢Pq¢q¢W|sØPn|j |ƒrô||_Pnxltd|ƒD][}||j|jƒjddƒƒ|jƒ}| r|d|krt d ƒ‚qqW|s™Pq™q™Wt|jƒ} xÙtd|ƒD]È}dj||ƒ} t| ƒ|krát d |dt| ƒ|fƒ‚n| j||| ƒ| jƒd } ||| jks1||| jks1t ‚||| _||| _||| _qW| S( Nis#First line should have two integersiis5Found %i records in this alignment, told to expect %ii RRsEnd of file mid-blocks)Sequence %i length %i, expected length %iiÿÿÿÿ(R t_headertAttributeErrortreadlineRR*R+R,R R R.R2tAssertionErrortrecords_per_alignmentRtrstriptappendRRRtalphabettjoint add_sequenceR Rt descriptionR ( RR R/R0R1RtidstseqsR#RRR((s‡/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/PhylipIO.pytnextŽsv      *   #  ,  (R&R'R(R2R@(((s‡/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/PhylipIO.pyR)us  t__main__sRunning short mini-tests# 8 286 V_Harveyi_ --MKNWIKVA VAAIA--LSA A--------- ---------T VQAATEVKVG B_subtilis MKMKKWTVLV VAALLAVLSA CG-------- ----NGNSSS KEDDNVLHVG B_subtilis MKKALLALFM VVSIAALAAC GAGNDNQSKD NAKDGDLWAS IKKKGVLTVG YA80_HAEIN MKKLLFTTAL LTGAIAFSTF ---------- -SHAGEIADR VEKTKTLLVG FLIY_ECOLI MKLAHLGRQA LMGVMAVALV AG---MSVKS FADEG-LLNK VKERGTLLVG E_coli_Gln --MKSVLKVS LAALTLAFAV S--------- ---------S HAADKKLVVA Deinococcu -MKKSLLSLK LSGLLVPSVL ALS------- -LSACSSPSS TLNQGTLKIA HISJ_E_COL MKKLVLSLSL VLAFSSATAA F--------- ---------- AAIPQNIRIG MSGRYFPFTF VKQ--DKLQG FEVDMWDEIG KRNDYKIEYV TANFSGLFGL ATGQSYPFAY KEN--GKLTG FDVEVMEAVA KKIDMKLDWK LLEFSGLMGE TEGTYEPFTY HDKDTDKLTG YDVEVITEVA KRLGLKVDFK ETQWGSMFAG TEGTYAPFTF HDK-SGKLTG FDVEVIRKVA EKLGLKVEFK ETQWDAMYAG LEGTYPPFSF QGD-DGKLTG FEVEFAQQLA KHLGVEASLK PTKWDGMLAS TDTAFVPFEF KQG--DKYVG FDVDLWAAIA KELKLDYELK PMDFSGIIPA MEGTYPPFTS KNE-QGELVG FDVDIAKAVA QKLNLKPEFV LTEWSGILAG TDPTYAPFES KNS-QGELVG FDIDLAKELC KRINTQCTFV ENPLDALIPS LETGRIDTIS NQITMTDARK AKYLFADPYV VDG-AQITVR KGNDSIQGVE LQTGKLDTIS NQVAVTDERK ETYNFTKPYA YAG-TQIVVK KDNTDIKSVD LNSKRFDVVA NQVG-KTDRE DKYDFSDKYT TSR-AVVVTK KDNNDIKSEA LNAKRFDVIA NQTNPSPERL KKYSFTTPYN YSG-GVIVTK SSDNSIKSFE LDSKRIDVVI NQVTISDERK KKYDFSTPYT ISGIQALVKK GNEGTIKTAD LQTKNVDLAL AGITITDERK KAIDFSDGYY KSG-LLVMVK ANNNDVKSVK LQANKYDVIV NQVGITPERQ NSIGFSQPYA YSRPEIIVAK NNTFNPQSLA LKAKKIDAIM SSLSITEKRQ QEIAFTDKLY AADSRLVVAK NSDIQP-TVE DLAGKTVAVN LGSNFEQLLR DYDKDGKINI KTYDT--GIE HDVALGRADA DLKGKTVAAV LGSNHAKNLE SKDPDKKINI KTYETQEGTL KDVAYGRVDA DVKGKTSAQS LTSNYNKLAT N----AGAKV EGVEGMAQAL QMIQQARVDM DLKGRKSAQS ATSNWGKDAK A----AGAQI LVVDGLAQSL ELIKQGRAEA DLKGKKVGVG LGTNYEEWLR QNV--QGVDV RTYDDDPTKY QDLRVGRIDA DLDGKVVAVK SGTGSVDYAK AN--IKTKDL RQFPNIDNAY MELGTNRADA DLKGKRVGST LGSNYEKQLI DTG---DIKI VTYPGAPEIL ADLVAGRIDA SLKGKRVGVL QGTTQETFGN EHWAPKGIEI VSYQGQDNIY SDLTAGRIDA FIMDRLSALE -LIKKT-GLP LQLAGEPFET I-----QNAW PFVDNEKGRK YVNSRTVLIA -QIKKT-GLP LKLAGDPIVY E-----QVAF PFAKDDAHDK TYNDKLAVLN -YLKTSGNKN VKIAFETGEP Q-----STYF TFRKGS--GE TINDKLAVLD -YFKQHPNSG LKIAYDRGDK T-----PTAF AFLQGE--DA ILVDRLAALD -LVKKT-NDT LAVTGEAFSR Q-----ESGV ALRKGN--ED VLHDTPNILY -FIKTAGNGQ FKAVGDSLEA Q-----QYGI AFPKGS--DE AYNDRLVVNY -IINDQ-KLP VRGAGQIGDA A-----PVGI ALKKGN--SA AFQDEVAASE GFLKQPVGKD YKFGGPSVKD EKLFGVGTGM GLRKED--NE LQAEVNKALA EMRADGTVEK ISVKWFGADI TK---- LRKKVNKALD ELRKDGTLKK LSEKYFNEDI TVEQKH VVDQVNKALK EMKEDGTLSK ISKKWFGEDV SK---- LITKFNQVLE ALRQDGTLKQ ISIEWFGYDI TQ---- LLKAVNDAIA EMQKDGTLQA LSEKWFGADV TK---- LRDKVNGALK TLRENGTYNE IYKKWFGTEP K----- LKDQIDKALT EMRSDGTFEK ISQKWFGQDV GQP--- LREALNKAFA EMRADGTYEK LAKKYFDFDV YGG--- (tStringIOiiis+mkklvlslsl vlafssataa faaipqniri gtdptyapfe sknsqgelvg fdidlakelc krintqctfv enpldalips lkakkidaim sslsitekrq qeiaftdkly aadsrlvvak nsdiqptves lkgkrvgvlq gttqetfgne hwapkgieiv syqgqdniys dltagridaafqdevaaseg flkqpvgkdy kfggpsvkde klfgvgtgmg lrkednelre alnkafaemradgtyeklak kyfdfdvyggRRs t-sw5 60 Tax1 CCATCTCACGGTCGGTACGATACACCTGCTTTTGGCAG Tax2 CCATCTCACGGTCAGTAAGATACACCTGCTTTTGGCGG Tax3 CCATCTCCCGCTCAGTAAGATACCCCTGCTGTTGGCGG Tax4 TCATCTCATGGTCAATAAGATACTCCTGCTTTTGGCGG Tax5 CCATCTCACGGTCGGTAAGATACACCTGCTTTTGGCGG GAAATGGTCAATATTACAAGGT GAAATGGTCAACATTAAAAGAT GAAATCGTCAATATTAAAAGGT GAAATGGTCAATCTTAAAAGGT GAAATGGTCAATATTAAAAGGTsq5 60 Tax1 CCATCTCACGGTCGGTACGATACACCTGCTTTTGGCAGGAAATGGTCAATATTACAAGGT Tax2 CCATCTCACGGTCAGTAAGATACACCTGCTTTTGGCGGGAAATGGTCAACATTAAAAGAT Tax3 CCATCTCCCGCTCAGTAAGATACCCCTGCTGTTGGCGGGAAATCGTCAATATTAAAAGGT Tax4 TCATCTCATGGTCAATAAGATACTCCTGCTTTTGGCGGGAAATGGTCAATCTTAAAAGGT Tax5 CCATCTCACGGTCGGTAAGATACACCTGCTTTTGGCGGGAAATGGTCAATATTAAAAGGTis' 5 42 Turkey AAGCTNGGGC ATTTCAGGGT Salmo gairAAGCCTTGGC AGTGCAGGGT H. SapiensACCGGTTGGC CGTTCAGGGT Chimp AAACCCTTGC CGTTACGCTT Gorilla AAACCCTTGC CGGTACGCTT GAGCCCGGGC AATACAGGGT AT GAGCCGTGGC CGGGCACGGT AT ACAGGTTGGC CGTTCAGGGT AA AAACCGAGGC CGGGACACTC AT AAACCATTGC CGGTACGCTT AAs& 5 42 Turkey AAGCTNGGGC ATTTCAGGGT GAGCCCGGGC AATACAGGGT AT Salmo gairAAGCCTTGGC AGTGCAGGGT GAGCCGTGGC CGGGCACGGT AT H. SapiensACCGGTTGGC CGTTCAGGGT ACAGGTTGGC CGTTCAGGGT AA Chimp AAACCCTTGC CGTTACGCTT AAACCGAGGC CGGGACACTC AT Gorilla AAACCCTTGC CGGTACGCTT AAACCATTGC CGGTACGCTT AAs& 5 42 Turkey AAGCTNGGGC ATTTCAGGGT GAGCCCGGGC AATACAGGGT AT Salmo gairAAGCCTTGGC AGTGCAGGGT GAGCCGTGGC CGGGCACGGT AT H. SapiensACCGGTTGGC CGTTCAGGGT ACAGGTTGGC CGTTCAGGGT AA Chimp AAACCCTTGC CGTTACGCTT AAACCGAGGC CGGGACACTC AT Gorilla AAACCCTTGC CGGTACGCTT AAACCATTGC CGGTACGCTT AAsThat should have failed...s8Evil multiline non-interlaced example failed as expectedt Concatenationis itOKsChecking write/readtDoneN(5R(Rt NameErrortsetsRt Bio.AlphabetRtBio.Align.GenericRt InterfacesRRRR)R&t phylip_textt cStringIORBR tcountRR RRR6RtuppertexpectedRRt phylip_text2t phylip_text3tlisttlist2tcloseR tlist3RR#t phylip_text4t phylip_text5t phylip_text5atlist4tlist5R t write_filetseektlist6tzipta1ta2tr1tr2(((s‡/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/AlignIO/PhylipIO.pytsš  Te 8  $'  "  ",<  " "      "$$  *(,