ó £žbc@€s…ddlmZddlZddlZddlZddlZyddlmZWn!ek rwddl mZnXyddl Z Wn!ek r«ddl m Z nXej ddkrÎddl Z nddlmZddlmZeejƒZd „Zd „Zd „Zd „Zed „Zd„Zd„Zd„Zd„Zd„Zd„Zdd„Z d„Z!d„Z"dS(iÿÿÿÿ(twith_statementN(t OrderedDict(tbz2ii(tqconfig(t get_loggercC€sd}tjj|ƒ\}}tj|tjƒsStjd|dtddƒn|dkrwt j |ddƒ}n–|dkr§t j |dd ƒ}t |ƒ}nf|dkrÁytj|dd ƒ}WnCtk rtjƒ\}}}tjd t|ƒddƒq X|jƒ}t|ƒdkrJtjd|ddƒnt|ƒdkrttjd|dƒny#|j |dƒ}t |ƒ}Wq tk r½tjdddƒq XnLyt |ƒ}Wn9tk r tjƒ\}}}tj|ddƒnX|S(NsPermission denied accessing t to_stderrtexit_with_codeis.gzs.gziptmodetrts.bz2s.bzip2trs.zipsCan't open zip file: is Reading %s: zip archive is emptys3Zip archive must contain exactly one file. Using %ss=Use python 2.6 or newer to work with contigs directly in zip.it exit_code(s.gzs.gzip(s.bz2s.bzip2(s.zip(tNonetostpathtsplitexttaccesstR_OKtloggerterrortTruetgziptopenRtBZ2Filet_read_compressed_filetzipfiletZipFilet Exceptiontsystexc_infotstrtnamelisttlentwarningtAttributeErrortIOErrort exception(tfpatht fasta_filet_texttzfiletexc_typet exc_valuetnames((sD/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/fastaparser.pyt_get_fasta_file_handler!s>     !   cC€s3tjddkr/tjtj|jƒƒƒS|S(Nii(Rt version_infotiot TextIOWrappertBytesIOtread(tcompressed_file((sD/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/fastaparser.pyRMscC€s/y|djƒdSWntk r*dSXdS(sk Extracts name from fasta entry line: ">chr1 length=100500; coverage=15;" ---> "chr1" iitN(tsplitt IndexError(tline((sD/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/fastaparser.pyt__get_entry_nameSs cC€såtƒ}d}d}t|ƒ}x©|D]¡}|jdƒdkrU|jdƒ}n |g}xh|D]`}|swqen|ddkr¯|r |||N( RR R,tfindR4R7Rtstriptclose(R$t chr_lengthstltchr_nameR%traw_linetlinesR6((sD/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/fastaparser.pytget_chr_lengths_from_fastafile^s(         c C€s©d}i}i}x‡t|ƒD]y\}}|jƒd}t|ƒ}||7}td„t|ƒDƒƒ||<|rŽ|t||ƒ8}n|||„s(t read_fastaR4Rtsett enumerate( t fasta_fpathtskip_nst genome_sizetreference_chromosomestns_by_chromosomestnametseqR>tchr_len((sD/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/fastaparser.pytget_genome_stats|s   c C€sÚd}d}d}d}|d}g}t|ƒ}x |D]}|jdƒdkrk|jdƒ} n |g} xË| D]Ã} | sq{n| ddkr |rê|j|||t| jƒƒt| ƒgƒ||7}d}d}nt| ƒ}|t| ƒ7}q{|s| } n|t| jƒƒ7}|t| ƒ7}q{Wq>WWdQX|j|||t| jƒƒt| ƒgƒt|dƒK} xA|D]9} | jdj g| D]}t |ƒ^q¬ƒdƒq“WWdQXdS( Nis.fais iÿÿÿÿR8tws s ( R RR9R4tappendRR:R7twritetjoinR(RIR=t total_offsett chr_offsetR>t fai_fpatht fai_fieldstin_fR?R@R6tchr_linetout_ftfieldstfs((sD/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/fastaparser.pytcreate_fai_file‹s<    .    . cC€sºtjj|ƒs"tj|ƒnd}xxt|ƒD]j}|ddkr‰|r^|jƒnttjj|t|ƒdƒdƒ}n|r5|j |ƒq5q5W|r¶|jƒndS(sñ Takes filename of FASTA-file and directory to output Creates separate FASTA-files for each sequence in FASTA-file Returns nothing Oops, similar to: pyfasta split --header "%(seqid)s.fasta" original.fasta iR8s.faRRN( R R tisdirtmkdirR RR;RUR7RT(R$toutput_dirpathtoutFileR6((sD/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/fastaparser.pyt split_fasta®s +cc€sçt}g}d}t|ƒ}x•|D]}|jdƒ}xu|D]m}|sSqAn|ddkr›|s€|dj|ƒfVnt}t|ƒ}g}qA|j|jƒƒqAWq%W|sÂ|rÙ|dj|ƒfVn|jƒdS(sH Generator that returns FASTA entries in tuples (name, seq) R3s iR8N( RR,R4RUtFalseR7RSR:R;(R$tfirstRORNR%R?R@R6((sD/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/fastaparser.pyRFÃs&      cC€s:g}x-t|ƒD]\}}|j||fƒqW|S(sB Returns list of FASTA entries (in tuples: name, seq) (RFRS(R$tlist_seqRNRO((sD/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/fastaparser.pytread_fasta_one_timeâscC€s’t|ƒ}g}x`|D]X}|jdƒ}x@|D]8}|sGq5n|ddkr5|j|jƒƒq5q5WqW|jƒdj|ƒ}|S(s Returns string s iR8R3(R,R4RSR:R;RU(R$R%RgR?R@R6t fasta_str((sD/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/fastaparser.pytread_fasta_strìs    cC€sWxP|D]H\}}d|GHx0tdt|ƒdƒD]}|||d!GHq5WqWdS(Ns>%sii<(trangeR(tfastaRNROti((sD/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/fastaparser.pyt print_fastas RRcC€s„t||ƒ}xd|D]\\}}|jd|ƒx<tdt|ƒdƒD]"}|j|||d!dƒqLWqW|jƒdS(Ns>%s ii<s (RRTRkRR;(R$RlRtoutfileRNRORm((sD/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/fastaparser.pyt write_fastas $cC€s1idd6dd6dd6dd6dd6|jƒS(NtTtAtGtCRB(tupper(tletter((sD/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/fastaparser.pytcompsc€s8ttddƒƒ‰dj‡fd†t|ƒDƒƒS(Nt ATCGNatcgnt TAGCNtagcnR3c3€s!|]}ˆj|dƒVqdS(R3N(tget(RCt nucleotide(tc(sD/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/fastaparser.pys s(tdicttzipRUtreversed(RO((R|sD/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/fastaparser.pytrev_comps(#t __future__RR RRRt collectionsRt ImportErrort%quast_libs.site_packages.ordered_dictRtquast_libs.site_packagesR-R.t quast_libsRtquast_libs.logRtLOGGER_DEFAULT_NAMERR,RR7RAReRQR_RdRFRhRjRnRpRwR€(((sD/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/fastaparser.pyts>       ,    #