VNc@syddlmZWnddlmZnXddlZddlTddlmZejdruejdZ ndZ ddd d d d d dddddddddddgZ dddddddd d d d d ddddddgZ iZ iZ iZiZiZiZiZiZiZiZiZdZddZdfdYZidZdid d!Zx4e D],Zd"eZedUed#ee e %d and start < %d) or (stop > %d and stop < %d)) Rmiii(RlR_RKRf(RWR`tradiusRGRgRcRXRhRiR7RkRjRbRrtrstarttrstopt thelength((sV/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/__init__.pytleftGeneDistances.   !      cCsA|}|j||}|dkr=|\}}}} } ||krZ|} |}| }nd|||||||f} |j| dt}x|D]} t| d}t| d}||kr|} |}| }n||}||dkr|||kr||}n|dkr||kr|}qqWn|S(NR/sSELECT name, start, stop, length, orientation from gene_entries where chromosome = '%s' and ((start > %d and start < %d) or (stop > %d and stop < %d)) Rmiii(RlR_RKRf(RWR`RtRGRgRcRXRhRiR7RkRjRbRrRuRvRw((sV/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/__init__.pytrightGeneDistances.   !      cCs|\}}g}||jkr%tSd|}|j|dt}t|dkr{x"|D]}|j|dq]Wn|S(Ns9SELECT description from gene_annotation where name = '%s'Rmi(RERVR_RKR0Rn(RWR`RERaRgRbRcRr((sV/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/__init__.pyt annotInfo s   cCs|\}}g}||jkr%tSd|}|j|dt}t|dkrx*|D]}|jtj|dq]Wn|S(Ns[SELECT GOID, objType, objName, isNot, GOterm, evidence from gene_ontology where name = '%s'Rmis (RERVR_RKR0RntstringR3(RWR`RERaRgRbRcRr((sV/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/__init__.pytgoInfo/s    cCs\|dkr'|jdkr'|j}nd|}|j|}d|d|df}|S(NR/sDSELECT sequenceName, storageType from chromosomes where name = '%s' s%s %sii(RFR_(RWRXRbRcRg((sV/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/__init__.pyt chromInfo>s   cCsGg}d}|j|dt}x|D]}|j|dq(W|S(s* returns [ list of all orf names] s&SELECT distinct name from gene_entriesRmi(R_RKRn(RWRgRbRcRr((sV/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/__init__.pytallGIDsIs  cCsKg}d|}|j|dt}x|D]}|j|dq,W|S(sG returns [ list of all orf names] that match a particular GOID s:SELECT distinct name from gene_ontology where GOID = '%s' Rmi(R_RKRn(RWtGOIDRgRbRcRr((sV/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/__init__.pyt allGIDsbyGOIDUs   cCsGg}d}|j|dt}x|D]}|j|dq(W|S(s2 returns the list of GOID's in the genome s'SELECT distinct GOID from gene_ontologyRmi(R_RKRn(RWRgRbRcRr((sV/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/__init__.pytallGOIDsas  cCsTi}d}|j|dt}x,|D]$}t|d|t|d %d %s order by startRmsselect chromosome, start, stop, orientation, name, version, type from sequence_features where chromosome = "%s" and stop >= %d and stop <= %d %s order by startschromosome, start, stop, orientation, name, version, type from sequence_features where chromosome = "%s" and start >= %d and start <= %d %s order by start(RVRKR0R_Rn(RWRXtqstarttqlengthRRRtqstopRRbRcRrRFRhRiRkRoRGR((sV/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/__init__.pytgetFeaturesIntersectings8      & !) !)c Csg}||}d}d|||f}|j|dt}xH|D]@} | \} } } } }}|j||| | | | |fqEWd|||f}|j|dt}xi|D]a} | \} } } } }}||| | | | f|kr|j||| | | | |fqqWd|||f}|j|dt}xi|D]a} | \} } } } }}||| | | | f|krL|j||| | | | |fqLqLW|S(s Return features that are on a ptarticular stretch of the genome. Can optionally limit by feature type; the wild-card % can be used to search feature substrings. tmodelsselect chromosome, start, stop, orientation, name, version from sequence_features where chromosome = "%s" and start < %d and stop > %d order by startRmsselect chromosome, start, stop, orientation, name, version from sequence_features where chromosome = "%s" and stop >= %d and stop <= %d order by startsselect chromosome, start, stop, orientation, name, version from sequence_features where chromosome = "%s" and start >= %d and start <= %d order by start(R_RKRn(RWRXRRRRRRbRcRrRFRhRiRkRoRG((sV/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/__init__.pytgetGenesIntersecting?s*  & ) )cCsad}|dkr-|jdkr-|j}nd|}|j|}|d} |d} | dkrd| }|j|}|d|||!}d}n{tdt| fd} t| jdd t} t| j| jd t} | j|| j |}| j |r||d} t |}|j |||d }x|D]}|\}}}}}}}||kr|}n|| kr| }n||}||d}x&t ||D]}d |||t tableDictR[Rb((sV/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/__init__.pyRQs   cCsi dd6dd6dd6dd 6dd 6dd 6dd6dd6dd6}xJ|jD]<}||\}}d|||f}|j|d|qRWdS( NR?Rot nameIndex1R@t nameIndex2RAt nameIndex3Rt goidIndexRBt nameIndex4RCt nameIndex5RDs name, typet geneIDIndexschromosome, start, stop, typetposIndexRt typeIndexsCREATE INDEX %s on %s(%s)R(s gene_entriessname(sgene_annotationsname(s gene_ontologysname(s gene_ontologysGOID(s sequencessname(s chromosomessname(ssequence_featuress name, type(ssequence_featuresschromosome, start, stop, type(ssequence_featuresstype(RR(RWR>t indexDictt indexNamet tableNametfieldsRb((sV/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/__init__.pyRUs  g?c Csk|\}} ttt|t|d} d| t||||| ||f} |j| dS(Nisinsert into gene_entries(ID, name, version, chromosome, start, stop, length, orientation, feature) values (NULL, '%s', '%s', '%s', '%s', '%s', '%s', '%s', '%s') (RtabsRfR( RWR`RXRhRiRktfeatureRGRERaR7Rb((sV/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/__init__.pyt addGeneEntrys &(c Cse|\}} ttt|t|d} d|| |||| ||f} |j| dS(Nisinsert into sequence_features(ID, name, geneID, chromosome, start, stop, length, orientation, type) values (NULL, '%s', '%s', '%s', '%s', '%s', '%s', '%s', '%s') (RRRfR( RWRoR`RXRhRiRkRRERaR7Rb((sV/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/__init__.pytaddFeatureEntrys &"cCs-|\}}d||f}|j|dS(NsMinsert into gene_annotation(ID, name, description) values (NULL, '%s', '%s') (R(RWR`t descriptionRERaRb((sV/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/__init__.pyt addAnnotations c CsE|\} } d| t|||||||f} |j| dS(Nsinsert into gene_ontology(ID, name, GOID, objType, objName, isNot, GOterm, evidence, other) values (NULL, '%s', '%s', '%s', '%s', '%s', '%s', '%s', '%s') (RR( RWR`RtobjTypetobjNametisNottGOtermtevidencetotherRERaRb((sV/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/__init__.pyt addGoInfos (s-1cCs`|\}}t|dkr3tt|}nd|t|||f}|j|dS(Nisminsert into sequences(ID, name, sequenceLength, sequenceType, sequence) values (NULL, '%s', '%s', '%s', '%s')(RfRR0R(RWR`RRtseqLenRERaRb((sV/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/__init__.pyt addSequences  cCs$d|||f}|j|dS(Ns]insert into chromosomes(ID, name, sequenceName, storageType) values (NULL, '%s', '%s', '%s')(R(RWtchromoRt storageTypeRb((sV/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/__init__.pytaddChromosomeEntrysc Csg}d}xr|D]j}|\}}}} |\} } t| dkr^tt|} n|j| t| ||fqW|j||dS(Nsainsert into sequences(ID, name, sequenceLength, sequenceType, sequence) values (NULL, ?, ?, ?, ?)i(RfRR0Rnt writeBatchDB( RWt entryArrayR>t stmtArrayRbRrR`RRRRERa((sV/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/__init__.pytaddSequenceBatchs  #cCs d}|j||d|dS(NsTinsert into chromosomes(ID, name, sequenceName, storageType) values (NULL, ?, ?, ?)R(R(RWRR>Rb((sV/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/__init__.pytaddChromosomeEntryBatch$sc Csg}d}x|D]~}|\}}}} } } } |\} }ttt|t| d}|j|t| ||| || | fqW|j||d|dS(Nsinsert into gene_entries(ID, name, version, chromosome, start, stop, length, orientation, feature) values (NULL, ?, ?, ?, ?, ?, ?, ?, ?) iR(RRRfRnR(RWRR>RRbRrR`RXRhRiRkRRGRERaR7((sV/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/__init__.pytaddGeneEntryBatch)s  &/c Csg}d}x|D]}|\}}}} } } } |\} }ttt| t| d}|j|||t| t| || | fqW|j||d|dS(Nsinsert into sequence_features(ID, name, version, chromosome, start, stop, length, orientation, type) values (NULL, ?, ?, ?, ?, ?, ?, ?, ?) iR(RRRfRnR(RWRR>RRbRrR`RGRXRhRiRkRRERaR7((sV/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/__init__.pytaddFeatureEntryBatch5s  &5c Csbg}d}x9|D]1}|\}}|\}} |j| |fqW|j||d|dS(NsGinsert into gene_annotation(ID, name, description) values (NULL, ?, ?) R(RnR( RWRR>RRbRrR`RRERa((sV/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/__init__.pytaddAnnotationBatchAs   c Csg}d}xc|D][}|\}}}} } } } } |\}}|j|t||| | | | | fqW|j||d|dS(Nsinsert into gene_ontology(ID, name, GOID, objType, objName, isNot, GOterm, evidence, other) values (NULL, ?, ?, ?, ?, ?, ?, ?, ?) R(RnRR(RWRR>RRbRrR`RRRRRRRRERa((sV/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/__init__.pytaddGoInfoBatchLs  /t cistematicc Csg}g}d}d}d}d} d} d} idd6dd6dd6} t|} |dkrx| D]4}|d d krqjn|jj}|dkr|d }|d } t|d }| |d } n|d |krI|j|j|f| ||| ddf|d }|d } t|d }| |d } nt|d }t|d}|d} |j|j|fd| ||| | fqjWn|dkrx|| D]^}|d d krqn|jd}t|d}|djd}|djd}|d d } | |d } t|dd}t|dd}d|df}xt|D]}t||d}t||d}||kr||kr|j|d| ||| dfqz||kr1| dkrd}nd}|j|d| ||| |fqz||kr}| dkrRd}nd}|j|d| ||| |fqz||kr||kr| dkrd}nd}|j|d| ||| df|j|d| |d|| |fqz||kry||kry| dkr(d}nd}|j|d| ||d| |f|j|d| ||| dfqz| dkrd}d}n d}d}|j|d| ||d| |f|j|d| ||| df|j|d| |d|d| |fqzWqWndGH| jdS| j|tkro|j dd t|j d!d tn|j |d"t|j |d"tdS(#NR/itFt+Rt-t.Rit#iiit TranscriptReiitUCSCs ii t,i iitgenericRt5UTRt3UTRs%s format not supported yetsdelete from sequence_featuresRsdelete from gene_entriesR>( RtstriptsplitRfRnRER5RTRKR_RR(RWt featureFiletfileTypetreplacet geneEntryListtgeneFeatureListt currentGenetgstarttgstoptgchromtgsenseRt senseArraytfeatfiletlineRtlstartt geneFieldstexonNumt exonStartst exonStopsR`R;testarttestoptfTypetfType1tfType2((sV/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/__init__.pytextendFeaturesWs        +   2  %   %   %  ")  &%  &"5   cCs|s|jr|j}ntj|jdd}|j}|j||ra|j}n |j}|j |p|js|j n|S(Nttimeouti<( RMRPRNRORHRRRSRmtfetchoneRT(RWRbRmRRRZR((sV/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/__init__.pyR_s      cCsn|r|j}ntj|jdd}|j}|j||j|j|sj|jndS(NRi<(RPRNRORHRRRStcommitRT(RWRbRRRZ((sV/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/__init__.pyRs     cCs|r|j}ntj|jdd}|j}y|j||Wnd|GHnX|j|j|s|jndS(NRi<swriteBatchDB: problem with %s(RPRNRORHRRt executemanyRRT(RWRbRRRRZ((sV/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/__init__.pyRs     (9t__name__t __module__RERFRGRHRVRLtoldStyletcustomAnnotationsR\R]R^RdRlRsRxRyRzR|R}R~RRRRRRRRRRRRRRR6RRRQRURRRRRRRRRRRRRR_RR(((sV/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/genomes/__init__.pyR=lsl&            + * !4        p c Csi}t|}d}xd|kr9|j}qqW|j}|d}|ikrd|dsP       (/