U H$xe@sdZddlZddlmZddlmZddlmZmZm Z m Z m Z m Z m Z ddlmZmZddlZddlmZdd lmZmZmZmZmZmZdd lmZmZeZGd d d Z Gd dde!Z"GdddeZ#ddZ$GdddZ%GdddeZ&Gddde&eZ'Gddde'Z(Gddde'Z)Gddde&Z*Gdd d e&Z+Gd!d"d"eZ,Gd#d$d$e,eZ-Gd%d&d&e-Z.Gd'd(d(e-Z/dgfe0d)d*d+Z1Gd,d-d-eZ2Gd.d/d/e2eZ3Gd0d1d1e3eZ4Gd2d3d3e4Z5Gd4d5d5e5Z6Gd6d7d7e4Z7Gd8d9d9e4Z8Gd:d;d;e5Z9Gdd?d?e9Z;Gd@dAdAe:ZGdFdGdGe2Z?GdHdIdIe2eZ@GdJdKdKe@ZAGdLdMdMe@ZBdNdOZCe e,eeDeDfdPdQdRZEdS)Sz Adapter finding and trimming classes The ...Adapter classes are responsible for finding adapters. The ...Match classes trim the reads. 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"REFERENCE" is the adapter sequence, "QUERY" is the read sequence N)rr r!__doc__rZ QUERY_STARTZ QUERY_STOPZ REFERENCE_ENDBACKZREFERENCE_STARTFRONTPREFIXSUFFIXFRONT_NOT_INTERNALBACK_NOT_INTERNALZ SEMIGLOBALANYWHERErrrrr$&s  r$cCsttSN)rintrrrrreturns_defaultdict_int7sr/c@sTeZdZdZddddZddZedd d Zed d Z e e e d ddZ dS) EndStatisticsz!Statistics about the 5' or 3' end SingleAdapteradaptercCsf|j|_|j|_|j|_|j|_|j|_||_|j|_t t |_ dddddd|_ t |t|_dS)NrACGT)max_error_ratereffective_lengthadapter_wildcards has_wildcardsindelsdescriptive_identifierZ adapter_typeallows_partial_matchesrr/errorsadjacent_bases isinstance FrontAdapter_remove_prefixrr3rrr__init__As  zEndStatistics.__init__cCs&dd|jD}d|j||jS)NcSsi|]\}}|t|qSr)dict).0kvrrr Psz*EndStatistics.__repr__..z>EndStatistics(max_error_rate={}, errors={}, adjacent_bases={}))rAitemsformatr:rB)rrArrr__repr__Os zEndStatistics.__repr__othercCst||jstd|j|jksD|j|jksD|j|jksD|j|jkrLtddD]}|j||j|7<qP|j D]2\}}|D]$}|j |||j ||7<qqx|S)NzCannot comparez+Incompatible EndStatistics, cannot be addedr4) rC __class__ ValueErrorr:rr;r> RuntimeErrorrBrArM)rrQbaselengthZ error_dictrArrr__iadd__Ws"     $zEndStatistics.__iadd__cCsdd|jD}|S)NcSsi|]\}}|t|qSr)sumvalues)rIrVrArrrrLjsz)EndStatistics.lengths..)rArM)rdrrrlengthshszEndStatistics.lengths) gc_contentreturncCsd|krdksnt|j}|jr4|ddd}|jr>dnd}d}|g}t|D]8\}}||krr||d9}n|d|d9}||qT|S)a Estimate probabilities that this adapter end matches a random sequence. 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Returns a list p, where p[i] is the probability that i bases of this adapter match a random sequence with GC content gc_content. gg?NZ CGRYSKMBDHVNZGCg@)AssertionErrorrrEr= enumerateappend)rr\seqZ allowed_basespZ probabilitiesicrrrrandom_match_probabilitiesms  z(EndStatistics.random_match_probabilitiesN) rr r!r%rGrOrrWpropertyr[floatr rfrrrrr0>s r0c@sjeZdZUdZeed<eed<ded<eddZee e e e e fdd d Z ed dd d Z d S)AdapterStatisticsrreverse_complementednameAdapterr3cCsdSr-rrrQrrrrWszAdapterStatistics.__iadd__r]cCsdSr-rrrrrend_statisticssz AdapterStatistics.end_statisticsNcCsdSr-rrmatchrrr add_matchszAdapterStatistics.add_match)rr r!rjr.__annotations__r"r rWrrr0rprsrrrrris    ric@s4eZdZdZddddZddZddd d Zd S) SingleAdapterStatisticszx Statistics about a 5' or 3' adapter, where we only need to keep track of sequences removed from one "end". r1r2cCs|j|_||_t||_dSr-)rkr3r0endrFrrrrGsz SingleAdapterStatistics.__init__cCsd|jd|jdS)NzSingleAdapterStatistics(name=z, end=))rkrvrorrrrOsz SingleAdapterStatistics.__repr__rPcCs8t||jstd|j|j7_|j|j7_|SNz Cannot iadd)rCrRrSrvrjrmrrrrWs  z SingleAdapterStatistics.__iadd__N)rr r!r%rGrOrWrrrrrusruc@s8eZdZddddZeeeeefdddZdS) FrontAdapterStatisticsRemoveBeforeMatchrrcCs"|jj||jd7<dSNr )rvrAremoved_sequence_lengthrqrrrrssz FrontAdapterStatistics.add_matchrncCs |jdfSr-rvrorrrrpsz%FrontAdapterStatistics.end_statisticsNrr r!rsrrr0rprrrrrysryc@s8eZdZddddZeeeeefdddZdS) BackAdapterStatisticsRemoveAfterMatchr{cCsl|}|jj||jd7<z|jj|d7<Wn(tk rf|jjdd7<YnXdSNr r9) adjacent_baservrAr}rBKeyErrorrrrrrrrrss zBackAdapterStatistics.add_matchrncCs d|jfSr-r~rorrrrpsz$BackAdapterStatistics.end_statisticsNrrrrrrsrc@sdeZdZdZddddddZddZdd d d Zd d ddZee e e e fdddZ dS)LinkedAdapterStatistics@ Statistics about sequences removed by a lined adapter. LinkedAdapterr1)r3frontbackcCs,|j|_||_t||_t||_d|_dSNrrkr3r0rrrj)rr3rrrrrrGs   z LinkedAdapterStatistics.__init__cCsd|jd|jd|jdS)NzLinkedAdapterStatistics(name=, front=, back=rwrkrrrorrrrOsz LinkedAdapterStatistics.__repr__rPcCsHt||jstd|j|j7_|j|j7_|j|j7_|Srx)rCrRrSrrrjrmrrrrWs  z LinkedAdapterStatistics.__iadd__ LinkedMatchr{cCs|jr(|jj|j|jjd7<|jr|j}|jj|j|jjd7<z|jj|d7<Wn(tk r|jjdd7<YnXdSr) front_matchrrAr} back_matchrrrBrrrrrrss" z!LinkedAdapterStatistics.add_matchrncCs |j|jfSr-rrrorrrrpsz&LinkedAdapterStatistics.end_statisticsN) rr r!r%rGrOrWrsrrr0rprrrrrs rc@sfeZdZdZddddZddZddd d Zed d d ddZe e e e e fdddZ d S)AnywhereAdapterStatisticsrAnywhereAdapterr2cCs,|j|_||_t||_t||_d|_dSrrrFrrrrGs   z"AnywhereAdapterStatistics.__init__cCsd|jd|jd|jdS)NzAnywhereAdapterStatistics(name=rrrwrrorrrrOsz"AnywhereAdapterStatistics.__repr__rPcCsFt|tstd|j|j7_|j|j7_|j|j7_|S)Nz Cannot add)rCrrSrrrjrmrrrrWs  z"AnywhereAdapterStatistics.__iadd__)rzrN)rrr]cCst|tr*|jj||jd7<nh|}|jj||jd7<z|jj|d7<Wn(tk r|jjdd7<YnXdSr) rCrzrrAr}rrrBrrrrrrs s  z#AnywhereAdapterStatistics.add_matchrncCs |j|jfSr-rrorrrrpsz(AnywhereAdapterStatistics.end_statistics) rr r!r%rGrOrWr rsrrr0rprrrrrs  rc@sxeZdZUded<eeeefdddZeeeefdddZee e ddd Z ed d Z ed d Z dS)Matchrlr3rncCsdSr-rrorrrremainder_intervalszMatch.remainder_intervalcCsdSr-rrorrrretained_adapter_interval"szMatch.retained_adapter_intervalcCsdSr-rrreadrrrget_info_records&szMatch.get_info_recordscCsdSr-rrrrrtrimmed*sz Match.trimmedcCsdSr-rrorrrmatch_sequence.szMatch.match_sequenceN) rr r!rtr rr.rrr rrrrrrrrs  rc @seZdZdZdddddddd d d g Zeeeeeed ed ddZddZe dddZ d eedddZ e e dddZ ddZeedddZdS)! SingleMatchzG Representation of a single adapter matched to a single string astartastoprstartrstopscorerAr3rrVrr1rrrrrrAr3rc Cs>||_||_||_||_||_||_||_||_|||_dSr-) rrrrrrAr3rrV) rrrrrrrAr3rrrrrGEs zSingleMatch.__init__cCs>|jjd|jd|jd|jd|jd|jd|jdS)Nz(astart=z, astop=z , rstart=z, rstop=z, score=z , errors=rw)rRrrrrrrrArorrrrO]s}jjj|krj|tjkrjj|qSr)r3rrrlen)rIrdrrrr zsz)SingleMatch.wildcards..r9)rangerVjoin)rr wildcardsrrrrqs zSingleMatch.wildcardsc Cs|j}|j}d|j|j|j|d|j||j|j||jd|jjg}|r~||d|j||j|j||jdg7}n|dddg7}|gS)Nr9r)r qualitiesrArrr3rk)rrrbrinforrrrs&     zSingleMatch.get_info_recordscCs|j|j|jSr-)rrrrorrrrszSingleMatch.match_sequencecCsdSr-rrorrrr}sz#SingleMatch.removed_sequence_lengthN)r)rr r!r% __slots__r.r"rGrOboolrrr rrr r}rrrrr3s8  rc@sheZdZdZedddZeeefdddZeeefdddZ d d Z d d Z edd dZ dS)rzz.A match that removes sequence before the matchrncCs|jd|jSz Return the part of the read before this match if this is a 'front' (5') adapter, return the part after the match if this is not a 'front' adapter (3'). 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NrrrorrrrestszRemoveBeforeMatch.restcCs|jt|jfS) Return an interval (start, stop) that describes the part of the read that would remain after trimming )rrrrorrrrsz$RemoveBeforeMatch.remainder_intervalcCs|jt|jfSr-)rrrrorrrrsz+RemoveBeforeMatch.retained_adapter_intervalcCs t|jdSr-)slicerrorrr trim_sliceszRemoveBeforeMatch.trim_slicecCs||jdSr-rrrrrrszRemoveBeforeMatch.trimmedcCs|jSr-rrorrrr}sz)RemoveBeforeMatch.removed_sequence_lengthN) rr r!r%r"rrr.rrrrr}rrrrrzs rzc@sveZdZdZedddZeeefdddZeeefdddZ d d Z d d Z edd dZ edddZ dS)rz-A match that removes sequence after the matchrncCs|j|jdSr)rrrorrrrszRemoveAfterMatch.restcCs d|jfS)rrrrorrrrsz#RemoveAfterMatch.remainder_intervalcCs d|jfSrrrorrrrsz*RemoveAfterMatch.retained_adapter_intervalcCs td|jSr-)rrrorrrrszRemoveAfterMatch.trim_slicecCs|d|jSr-rrrrrrszRemoveAfterMatch.trimmedcCs|j|jd|jSr|rrorrrrszRemoveAfterMatch.adjacent_basecCst|j|jSr-)rrrrorrrr}sz(RemoveAfterMatch.removed_sequence_lengthN)rr r!r%r"rrr.rrrrrr}rrrrrs rrncCs t|d}|dd7<|S)Nrr )r")Z_startrkrrr_generate_adapter_names rc@s@eZdZdZeedddZeddZeeddd Z d S) Matchablez'Something that has a match_to() method.rkcOs ||_dSr-r)rrkargskwargsrrrrGszMatchable.__init__cCsdSr-rrorrr enable_debugszMatchable.enable_debugrcCsdSr-rrrrrmatch_toszMatchable.match_toN) rr r!r%rr"rGr rrrrrrrs  rc@sFeZdZdZeedddZeedddZeedddZ d S) rlzadapter with one componentrncCsdS)z,Return string representation of this adapterNrrorrrspecsz Adapter.speccCsdSr-rrorrrcreate_statisticsszAdapter.create_statisticscCsdSr-rrorrrr?szAdapter.descriptive_identifierN) rr r! descriptionr r"rrirr?rrrrrlsrlc seZdZUdZdZeed<d!eee eee eedfd d Z ee e d d d Z d"eeeeedddZddZee dddZddddZeddZeddZeedddZe ddd ZZS)#r1a This class is used to find a single adapter characterized by sequence, error rate, type etc. within reads. Arguments: sequence (str): The adapter sequence. Will be converted to uppercase. Also, Us will be converted to Ts. max_errors: Maximum allowed errors (non-negative float). If the values is less than 1, this is interpreted as a rate and passed to the aligner. If it is 1 or greater, the value is converted to a rate by dividing it by the number of non-N characters in the sequence. The error rate is the number of errors in the alignment divided by the length of the part of the alignment that matches the adapter. min_overlap: Report a match only if at least this number of bases of the adapter are aligned to the read. read_wildcards: Whether IUPAC wildcards in the read are allowed. adapter_wildcards: Whether IUPAC wildcards in the adapter are allowed. name: Optional name of the adapter. If not provided, the name is set to a unique number. indels: Whether indels are allowed in the alignment. Tr@皙?FN)r max_errors min_overlapread_wildcardsr<rkr>c s$|dkrtn||_t|jd|_|dddd|_|jsPtd|dkr|j dt |jkr|t |j|j d}||_ t |t |j|_ td}|rt|j|ks|jD]$} | |krtd | d |jd q|ot|jtd k |_||_||_||_||_dS) NFUr8IrzAdapter sequence is emptyr ZABCDGHKMNRSTUVWXYz Character 'z' in adapter sequence 'zF' is not a valid IUPAC code. Use only characters 'ABCDGHIKMNRSTUVWXY'.ZACGT)rrksuperrG_debugupperreplacerrScountrr:minr frozensetsetr#r<rr>_aligneraligner _kmer_finder kmer_finder) rrrrrr<rkr>ZiupacrerRrrrG+s4   zSingleAdapter.__init__)rflagsr]c Cs,|jr dnd}t||j||j|j||jdS)Nr i)r wildcard_refwildcard_query indel_costr)r>rr:r<rr)rrrrrrr _make_alignerPszSingleAdapter._make_aligner)r back_adapter front_adapterinternalr]cCs8t||j|j|||}|jr(tt|t||j|jSr-) rrr:rprintrrr<r)rrrrrZpositions_and_kmersrrr_make_kmer_finder_s zSingleAdapter._make_kmer_findercCsdjfd|jjit|S)Nz<{cls}(name={name!r}, sequence={sequence!r}, max_error_rate={max_error_rate}, min_overlap={min_overlap}, read_wildcards={read_wildcards}, adapter_wildcards={adapter_wildcards}, indels={indels})>cls)rNrRrvarsrorrrrOts zSingleAdapter.__repr__rncCs|jjSr-)rr;rorrrr;}szSingleAdapter.effective_lengthcCsd|_|jdS)zg Print out the dynamic programming matrix after matching a read to an adapter. 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Nr3r)rrrlocaterrdpmatrixrzrr alignmentrrrrs  zFrontAdapter.match_tocCs |jdSN...rrorrrrszFrontAdapter.speccCst|Sr-)ryrorrrrszFrontAdapter.create_statistics)rr r!r%rrGr"r?rrrrrryrrrrrrrDs rDc@sTeZdZdZdZedddZedddZdd Z ed d d Z edd dZ dS)RightmostFrontAdapterz+A 5' adapter that prefers rightmost matchesz rightmost 5'rncCsdS)NZrightmost_five_primerrorrrr?sz,RightmostFrontAdapter.descriptive_identifiercCs.||jddd|jr tjjntjj}|S)Nr^rrrr$r,rr&)rrrrrrs zRightmostFrontAdapter._alignercCs"|j|jdddd|jd}|S)Nr^Trr)rrrrrrs z"RightmostFrontAdapter._kmer_finderrc Cs|ddd}|j|sdS|j|}|jrdS|ddkr\t|||d}nt |||d}|S)rNrr) rrrrrrrrrzr)rrrrrrrrrOs   zAnywhereAdapter.match_tocCsd|jdSrrrorrrreszAnywhereAdapter.speccCst|Sr-)rrorrrrhsz!AnywhereAdapter.create_statisticsN) rr r!r%rr"r?rrrrrrrrrrr<src@sNeZdZdZdZedddZddZdd Zed d d Z edd dZ dS)NonInternalFrontAdapterzA non-internal 5' adapterznon-internal 5'rncCsdS)NZnoninternal_five_primerrorrrr?qsz.NonInternalFrontAdapter.descriptive_identifiercCs||jtjjSr-)rrr$r*rrorrrrtsz NonInternalFrontAdapter._alignercCs|j|jd|jddS)NTF)rrrrrorrrrws z$NonInternalFrontAdapter._kmer_finderrcCsd|j|sdS|j|}|jrHzt|jjWntk rFYnX|dkrTdSt|||dSNr) rrrrrrrAttributeErrorrzrrrrrs  z NonInternalFrontAdapter.match_tocCsd|jdS)NXrrrorrrrszNonInternalFrontAdapter.specN rr r!r%rr"r?rrrrrrrrrlsrc@sNeZdZdZdZedddZddZdd Zed d d Z edd dZ dS)NonInternalBackAdapterzA non-internal 3' adapterznon-internal 3'rncCsdS)NZnoninternal_three_primerrorrrr?sz-NonInternalBackAdapter.descriptive_identifiercCs||jtjjSr-)rrr$r+rrorrrrszNonInternalBackAdapter._alignercCs|j|jd|jddS)NTF)rrrrrorrrrs z#NonInternalBackAdapter._kmer_finderrcCsd|j|sdS|j|}|jrHzt|jjWntk rFYnX|dkrTdSt|||dSr) rrrrrrrrrrrrrrs  zNonInternalBackAdapter.match_tocCs |jdS)NrrrorrrrszNonInternalBackAdapter.specNrrrrrrsrcs^eZdZdZdZdZedfdd Zeddd Zd d Z fd d Z edddZ Z S) PrefixAdapterzAn anchored 5' adapterz anchored 5'Frcs$t||d<tj|f||dSNrrrrGrrrrrrrrGs zPrefixAdapter.__init__rncCsdS)NZanchored_five_primerrorrrr?sz$PrefixAdapter.descriptive_identifiercCs8|js"t|j|j|j|j|jdS||jtj j SdSN)rrr) r>rrr:r<rrrr$r(rrorrrrszPrefixAdapter._alignercs t|jtrtStSdSr-)rCrrrrrrorrrrs zPrefixAdapter._kmer_findercCsd|jdS)N^rrrorrrrszPrefixAdapter.spec rr r!r%rr@r"rGr?rrrrrrrrrs rcs^eZdZdZdZdZedfdd Zeddd Zd d Z fd d Z edddZ Z S) SuffixAdapterzAn anchored 3' adapterz anchored 3'Frcs$t||d<tj|f||dSrrrrrrrGs zSuffixAdapter.__init__rncCsdS)NZanchored_three_primerrorrrr?sz$SuffixAdapter.descriptive_identifiercCs8|js"t|j|j|j|j|jdS||jtj j SdSr) r>rrr:r<rrrr$r)rrorrrrszSuffixAdapter._alignercs t|jtrtStSdSr-)rCrrrrrrorrrrs zSuffixAdapter._kmer_findercCs |jdS)N$rrorrrrszSuffixAdapter.specr rrrrr s r c@seZdZdZeeddddZddZedd Z ed d Z d d Z e e e fdddZe e e fdddZeedddZddZdS)rz. 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Return either a Match instance or None if there are no matches. N)rrrrA)rrZ best_matchr3rrrrrrs     zMultipleAdapters.match_to)rr r!r%rrrGrr!rr"rrrrrrrrrs rcseZdZdZeeeeeeffZ fddZ ddZ edddZ e d d Ze ed d d ZeddZeddZeeedfd ddZeddZedddZedddZddZddZZS)IndexedAdaptersa Represent multiple adapters of the same type at once and use an index data structure to speed up matching. This acts like a "normal" Adapter as it provides a match_to method, but is faster with lots of adapters. There are quite a few restrictions: - the error rate allows at most 2 mismatches - wildcards in the adapter are not allowed - wildcards in the read are not allowed Use the is_acceptable() method to check individual adapters. cstjdd|std|D]}||q||_t||_|\|_|_ t dt |jddt |jdkr|jd|_|j|_n|j|_||_d S) z+All given adapters must be of the same typeZindexed_adaptersrzAdapter list is emptyzString lengths in the index: %sTreverser rN)rrGrS_acceptrrZ_multiple_adapters _make_index_lengths_indexloggerdebugsortedr_length_match_to_one_lengthr_match_to_multiple_lengths_get_make_affix _make_affix)rrr3rrrrGs"     zIndexedAdapters.__init__cCs|jjd|jdS)Nz (adapters=rw)rRrrrorrrrOszIndexedAdapters.__repr__rcCsdS)z4Never called because it gets overwritten in __init__NrrrrrrszIndexedAdapters.match_tocCsdSr-rrorrrr/szIndexedAdapters._get_make_affixrncCsdSr-r)rr3rVrrArrrr _make_matchszIndexedAdapters._make_matchcCsB|jrtd|jrtdtt||j}|dkr>tddS)z3Raise a ValueError if the adapter is not acceptablez#Wildcards in the read not supportedz&Wildcards in the adapter not supportedrzError rate too highN)rrSr<r.rr:)rr3rJrrrr%szIndexedAdapters._acceptcCs*z||Wntk r$YdSXdS)z Return whether this adapter is acceptable for being used in an index Adapters are not acceptable if they allow wildcards, allow too many errors, or would lead to a very large index. FT)r%rSrr3rrr is_acceptables zIndexedAdapters.is_acceptable AdapterIndexc Cst}tdt|jt}t}d}|jD],}|j}t|j t|}|j rt ||D]h\}} } ||kr||\} } } | | krq^| | kr|s| || ||| d}|| | f||<| t|q^q0t|}t|dD]t} t|| D]d}|| } ||krB||\} } } | | krq| | krB|sB| || ||| d}|| | f||<qq| |q0t|}tdt||t|dd|fS)Nz!Building index of %s adapters ...FTr z/Built an index containing %s strings in %.1f s.r#)timer)rrrrHrrr.r:r>r _warn_similaraddrrr+)rZ start_timeindexr[Z has_warnedr3rrJr rAr other_adapterZ other_errorsZ other_matchesnelapsedrrrr& sZ      zIndexedAdapters._make_indexc Cs$td|j|j|j|j|||dS)NzAdapters %s %r and %s %r are very similar. At %s allowed errors, the sequence %r cannot be assigned uniquely because the number of matches is %s compared to both adapters.)r)warningrkr)r3r9rJr rrrrr69szIndexedAdapters._warn_similarcCs||||j}d|kr<||}|dkr0dS|\}}}n,z|j|\}}}Wntk rfYdSX|||j|||S)z Match a query string against all adapters and return a Match that represents the best match or None if no match was found rN)r0rr,_lookup_with_nr(rr1)rraffixresultr3r mrrrr-Hs  z$IndexedAdapters._match_to_one_lengthc Cs|}d}d}d}d}|jD]}||kr.q|||}d|krb||}|dkrVq|\} } } n.z|j|\} } } Wntk rYqYnX| |ks| |kr| |kr| }| }| }|}q|dkrdS||||||SdS)z Match the adapters against a string and return a Match that represents the best match or None if no match was found Nrr^ir)rr'r0r=r(rr1) rrr>Z best_adapterZ best_lengthZbest_mZbest_erVr?r3r r@rrrr.Zs4     z*IndexedAdapters._match_to_multiple_lengthscCs^|dd}z|j|}Wntk r0YdSX|d}||}|dkrPdS||j|jfS)Nrr5r)rr(rrrAr)rr>Zaffix_without_nr?r3rrrrrr=s  zIndexedAdapters._lookup_with_ncCsdSr-rrorrrrszIndexedAdapters.enable_debug)rr r!r%rr"rr1r.r4rGrOrr r/rr1 classmethodr%r3r r& staticmethodr6r-r.r=rrrrrrr"s(     , +r"cs<eZdZefddZddZddZeddZZ S) IndexedPrefixAdapterscst|tstdt|S)Nz%Only 5' anchored adapters are allowed)rCrrSrr%r2rrrr%s zIndexedPrefixAdapters._acceptc Cstdt|jd|||||dSNrr)rzrrrr3rVrrArrrrr1sz!IndexedPrefixAdapters._make_matchcCs|jSr-) _make_prefixrorrrr/sz%IndexedPrefixAdapters._get_make_affixcCs |d|Sr-rr r:rrrrFsz"IndexedPrefixAdapters._make_prefix) rr r!rAr%r1r/rBrFrrrrrrCs  rCcs<eZdZefddZddZddZeddZZ S) IndexedSuffixAdapterscst|tstdt|S)Nz%Only anchored 3' adapters are allowed)rCr rSrr%r2rrrr%s zIndexedSuffixAdapters._acceptc Cs*tdt|jt||t|||||dSrD)rrrrErrrr1s z!IndexedSuffixAdapters._make_matchcCs|jSr-) _make_suffixrorrrr/sz%IndexedSuffixAdapters._get_make_affixcCs|| dSr-rrGrrrrIsz"IndexedSuffixAdapters._make_suffix) rr r!rAr%r1r/rBrIrrrrrrHs  rHcCsDt}|D]4}|j|jf}||kr4td|j|j|j||<q dS)NzZAdapter %r (%s) was specified multiple times! Please make sure that this is what you want.)rHrRrr)r<rrk)rrZr3keyrrrwarn_duplicate_adapterss rK)rr]cCsB|s tdd}|D]}|\}}||7}q||}|||fS)z Determine which section of the read would not be trimmed. Return a tuple (start, stop) that gives the interval of the untrimmed part relative to the original read. matches must be non-empty zmatches must not be emptyr)rSr)rrrrZ match_startZ match_stoprVrrrrs  r)Fr%Zloggingenumr collectionsrtypingrrrrrr r abcr r r5rrZalignrrrrrrZkmer_heuristicrrZ getLoggerr)r Exceptionr#r$r/r0riruryrrrrrrzrr"rrrlr1rDrrrrrrr rrrr"rCrHrKr.rrrrrs^  $  I 0'o!$1;10%%%%Y>+Z