U H$xe@sdZddlmZmZddlmZddlmZGdddeZGdd d eZ Gd d d eZ Gd d d eZ GdddeZ GdddeZ GdddeZGdddeZGdddeZdS)z! Filtering criteria (predicates) )ABCabstractmethod)expected_errors)ModificationInfoc@s2eZdZeeedddZeedddZ dS) Predicate)inforeturncCsdS)zA Return True if the filtering criterion matches. Nselfreadrr r 2lib/python3.8/site-packages/cutadapt/predicates.pytest szPredicate.test)r cCsddd|jDddS)z Return a short name for this predicate based on the class name such as "too_long", "too_many_expected_errors". This is used as identifier in the JSON report. css&|]}|rd|n|VqdS)_N)isupperlower).0Zchr r r sz3Predicate.descriptive_identifier..rN)join__name__)clsr r rdescriptive_identifiers  z Predicate.descriptive_identifierN) r __module__ __qualname__rrboolr classmethodstrrr r r rr src@s4eZdZdZedddZddZeddd Zd S) TooShortz?Select reads that are shorter than the specified minimum lengthminimum_lengthcCs ||_dSNr )r r!r r r__init__ szTooShort.__init__cCsd|jdS)NzTooShort(minimum_length=)r r r r r__repr__#szTooShort.__repr__rcCst||jkSr")lenr!r r r rr&sz TooShort.testN rrr__doc__intr#r&rrr r r rrsrc@s4eZdZdZedddZddZeddd Zd S) TooLongz>Select reads that are longer than the specified maximum lengthmaximum_lengthcCs ||_dSr"r-)r r.r r rr#-szTooLong.__init__cCsd|jdS)NzTooLong(maximum_length=r$r-r%r r rr&0szTooLong.__repr__r'cCst||jkSr")r(r.r r r rr3sz TooLong.testNr)r r r rr,*sr,c@s4eZdZdZedddZddZeddd Zd S) TooManyExpectedErrorsz Select reads whose expected number of errors, according to the quality values, exceeds a threshold. The idea comes from usearch's -fastq_maxee parameter (http://drive5.com/usearch/).  max_errorscCs ||_dSr"r0)r r1r r rr#@szTooManyExpectedErrors.__init__cCsd|jdS)Nz!TooManyExpectedErrors(max_errors=r$r0r%r r rr&CszTooManyExpectedErrors.__repr__r'cCst|j|jkSr")r qualitiesr1r r r rrFszTooManyExpectedErrors.testN rrrr*floatr#r&rrr r r rr/7sr/c@s4eZdZdZedddZddZeddd Zd S) TooHighAverageErrorRatez Select reads that have an average error rate above the threshold. This works better than TooManyExpectedErrors for reads that are expected to have varying lengths, such as for long read sequencing technologies. max_error_ratecCs0d|krdks&ntd|d||_dS)Ng?z0max_error_rate must be between 0.0 and 1.0, got .) ValueErrorr7)r r7r r rr#Qs  z TooHighAverageErrorRate.__init__cCs d|jS)Nz'TooHighAverageErrorRate(max_error_rate=r6r%r r rr&Xsz TooHighAverageErrorRate.__repr__r'cCst|jt||jkSr")rr2r(r7r r r rr[szTooHighAverageErrorRate.testNr3r r r rr5Jsr5c@s4eZdZdZedddZddZeddd Zd S) TooManyNz Select reads that have too many 'N' bases. Both a raw count or a proportion (relative to the sequence length) can be used. )countcCs |dks t|dk|_||_dS)z count -- if it is below 1.0, it will be considered a proportion, and above and equal to 1 will be considered as discarding reads with a number of N's greater than this cutoff. rr8N)AssertionError is_proportioncutoff)r r<r r rr#fs  zTooManyN.__init__cCsd|jd|jdS)NzTooManyN(cutoff=z, is_proportion=r$)r?r>r%r r rr&oszTooManyN.__repr__r'cCsF|jd}|jr8t|dkr&dS|t||jkS||jkSdS)NnrF)Zsequencerr<r>r(r?)r r rZn_countr r rrrs  z TooManyN.testNr3r r r rr;_s r;c@s&eZdZdZddZedddZdS)CasavaFiltereda Select reads that have failed the CASAVA filter according to the read header. The headers look like ``xxxx x:Y:x:x`` (with a ``Y``). Reads that pass the filter have an ``N`` instead of ``Y``. Reads with unrecognized headers are not selected. cCsdS)NzCasavaFiltered()r r%r r rr&szCasavaFiltered.__repr__r'cCs"|jd\}}}|dddkS)N rz:Y:)name partition)r r rrrightr r rrszCasavaFiltered.testNrrrr*r&rrr r r rrA|srAc@s&eZdZdZddZedddZdS)DiscardUntrimmedz; Select reads for which no adapter match was found cCsdS)NzDiscardUntrimmed()r r%r r rr&szDiscardUntrimmed.__repr__r'cCs|j Sr")matchesr r r rrszDiscardUntrimmed.testNrGr r r rrHsrHc@s&eZdZdZddZedddZdS)DiscardTrimmedzE Select reads for which at least one adapter match was found cCsdS)NzDiscardTrimmed()r r%r r rr&szDiscardTrimmed.__repr__r'cCs t|jSr")rrIr r r rrszDiscardTrimmed.testNrGr r r rrJsrJN)r*abcrrZqualtrimrZ modifiersrrrr,r/r5r;rArHrJr r r rs