B h}\G @sZddlZddlZddlZddlZddlZddlmZddl Z ddl m Z ddl m Z mZeddZddd d d d d d ZddddddddZde je je jdZiZx,e jD]Ze jeededd<qWdddddddd d!d"d# ZGd$d%d%eZd&d'Zd(d)Z d*d+Z!d,d-Z"d5d.d/Z#gdfd0d1Z$e%d2krVd3d4l&m'Z'e'#dS)6N)StringIO)Template) ColorScheme SymbolColorcCs*ddl}|j|j||}t|S)Nr)ospathjoindirnameopenread)resourceZ basefilenamerfnrV/home/fristb/BIRCH/lib-linux-x86_64/python/lib/python3.7/site-packages/weblogo/_cgi.pyresource_stringAsrzapplication/postscriptzapplication/pdfz image/svg+xmlz image/pngz text/plainz image/jpeg)epspdfsvgpng png_printlogodatajpegrrrrtxtr)rrrrrrr) alphabet_autoalphabet_protein alphabet_rna alphabet_dnaZcolor_ _noneautoZ equiprobable percentCGz C. eleganszD. melanogasterzE. coliz H. sapiensz M. musculusz S. cerevisiae) comp_none comp_autocomp_equiprobablecomp_CG comp_Celeganscomp_Dmelanogaster comp_Ecoli comp_Hsapienscomp_Mmusculuscomp_Scerevisiaec@s"eZdZdZdddZddZdS) Fieldz( A representation of an HTML form field.NIllegal value.cCs(||_||_||_||_||_||_dS)N)namedefaultvalue conversionoptionserrmsg)selfr.r/r1r2r3rrr__init__us zField.__init__cCsn|jr&|j|jkr&tt|j|jf|jrdy ||jStk r`tt|j|jfYqjXn|jSdS)N)r2r0 ValueErrorstrr.r3r1)r4rrr get_value}s  zField.get_value)NNNr-)__name__ __module__ __qualname____doc__r5r8rrrrr,rs r,cCs|dks|dkrdSt|S)Nr )r7)r0rrrstring_or_nonesr=cCs|dkr dSt|S)NtrueT)bool)r0rrrtruthsr@cCs$|dks|dks|dkrdSt|S)Nr )int)r0rrr int_or_nonesrCcCs$|dks|dks|dkrdSt|S)NrAr )float)r0rrr float_or_nonesrEc",Cst}tddtddtddtjjddddd d d gd d td|jtddtddtjjdddgdd tddtjddddgdd tdddddd d!d"gd#td$d%t td&dt td'dt td(d)t jd*d)d+d,d-d.d/d0d1d2g d3d td4dt d5dtd6d7t td8|j td9|jtd:d7t td;|jtd|jt d?dtd@|jt tdAd7t tdBd7t tdCdDtjtdEd tdFdtdGdtdHdtdIdtdJdtdKdtdLdtdMdtdNdtdOdtdPdtdQdtdRdtdSdtdTdtdUd7t tdVd7t g)}i}x|D]}|||j<qWt}t|dWksDdX|kr|j|d6_|j|d:_|j|d<_|j|dA_|j|dB_|j |dV_t!||dYdSx |D]}|"|j|j#|_qWdddddd$d&d'd(d6d8d9d:d;dd@dAdBdVg}g}xf|D]^}y&||$} | dk rt%||| Wn0t&k rP} z|'| j(Wdd} ~ XYnXqWt)} xt*dWdZD]} |d[| $} |d\| $}|d]| $}| rjy| j+'t,|| |Wn,t&k r|'d[| d^| fYnXqjW|dCjd_kr| |_-nDy|dC$|_-Wn0t&k rJ} z|'| j(Wdd} ~ XYnXd}d`|krd|.d`}|d$}|d$}d}d}|r|s|r|'dan |}t/|}n|r|r|'dbn8dc}t||kr|'ddtdd|dW<n |}t/|}nj|rbd%del0m1}y ||}Wn>t&k r@|'dfYn t2k r^|'dgYnXn |'dh|s|di|krt!|||dSy|d($}|d4$}dU|k}|d4krt3|dj}d%dkl4m5}y4|j6||j7dl}t8||j7}tj9:|j7||}WnDt&k rHtj;||j7|dm}t8||j7}tj9<||}YnXt=||}|dj} tj| ||}!Wnt&k r} z|'| j(Wdd} ~ XYn^t2k r} z|'| j(Wdd} ~ XYn0t>k r} z|'| j(Wdd} ~ XYnX|sdn|kr t!|||dSt?dot@| dp|krJt?dqtA| nt?drtA| t?tBjCdWdskrtBjDjEF|!n tBjDF|!dS)tN sequencesrA sequences_urlformatrrrrrrrzUnknown format option.)r2r3stacks_per_linez"Invalid number of stacks per line.)r3Z stack_widthZmediumZsmallZlargezInvalid logo size.alphabetrrrrzUnknown sequence type.Z unit_namebitsZ probabilityZnatsZkTzkJ/molzkcal/mol)r2Z first_indexZ logo_startZlogo_end compositionr#r"r$r%r&r'r(r)r*r+zIllegal sequence composition.r!zInvalid CG percentage.show_errorbarsF logo_title logo_label show_xaxis xaxis_label show_yaxis yaxis_label yaxis_scalez*The yaxis scale must be a positive number.yaxis_tic_interval show_endsshow_fineprint color_schemeZ color_autozUnknown color schemeZcolor0Zsymbols0Zdesc0Zcolor1Zsymbols1Zdesc1Zcolor2Zsymbols2Zdesc2Zcolor3Zsymbols3Zdesc3Zcolor4Zsymbols4Zdesc4ignore_lower_case scale_widthrZ cmd_reset)htdocs_directoryzcolor%dz symbols%dzdesc%dzInvalid color: %s color_customsequences_file)r_z'Cannot upload, sequence source conflict)rFz'Cannot upload, sequence source conflicti)rFz@Sequence data too large for text input. Use file upload instead.)_from_URL_fileopen)rGzCannot parse URL)rGzCannot load sequences from URL)rFzXPlease enter a multiple-sequence alignment in the box above, or select a file to upload.Zcmd_editd)Motif)rJ)rJrZZ cmd_validatez Content-Type:downloadz3Content-Disposition: attachment; filename="logo.%s"z/Content-Disposition: inline; filename="logo.%s")GweblogoZ LogoOptionsr,Z formattersgetrIrBZ std_sizes alphabetsrCrMrEr@rOrPrRrTr=rUrV color_schemeskeysr.cgilibZ FieldStoragelenrNr0rQrSrWrXr[ send_formZgetfirstr/r8setattrr6appendargsrrangeZrulesrrYgetvaluerrAr`IOErrorr7ZmatrixrbZ read_transfacrJZ parse_priorZLogoDataZ from_countsZ read_seq_dataZ from_seqsZ LogoFormat RuntimeErrorprint mime_type extensionsys version_infostdoutbufferwrite)"r\Z logooptionscontrolsZformcZ form_valuesZoptions_from_formerrorsoptnamer0errZcustomiZcolorsymbolsdescZsequences_from_fileZsequences_from_textfieldrGrFZseq_fileZSEQUENCES_MAXLENGTHr`compr!rZrbZmotifZpriordataZseqsZ logoformatrHZlogorrrmains`                                   $"                         rc Cs&|dkrtjtjtd}i}tj|d<d|d<x|D]}|jrxx|jD]}d||dd<qLWd||j dd<n\|j }|dkrd}|d krd ||j <n6t |t kr|rd ||j <qd||j <nt |||j <d||j d <q:Wd|d <td dkr>tddkr>d|d<d|d<d|d<d|d<d|d<d|d<tddkrVd|d<|rt|tjdg}xj|D]b}t |t kr|} n0t|dkrd||dd <|d} n|d} |d7}|| 7}|d7}qtW|d7}d||d <nd|d <td!|} t| |} td"t| dS)#NZhtdocsversionrAr^/rselectedr r>checkedZ_errZlogo_range_errZgsz gswin32c.exezdisabled="disabled"rrrrrzselected="selected"rZpdf2svg)filez class='error'rrLzERROR: z
ze error_messagezcreate_html_template.htmlzContent-Type: text/html )rrrr __file__reZrelease_descriptionr2replacer0r.typer?r7shutilwhichrtrwstderrrkrrsafe_substitute) r|r~r\Z substitutionsr}optr0remsgtemplatehtmlrrrrlsj           rl__main__rL)_cli)N)(cgirjZcgitbos.pathrrwriorrestringrZweblogo.colorschemerrenablerrurvZunambiguous_protein_alphabetZunambiguous_rna_alphabetZunambiguous_dna_alphabetrgrhZstd_color_schemesrikrrMobjectr,r=r@rCrErrlr9rArrrrr'sh     {S