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Clone Mass | Clones in CloneSet | Parameter Count | Clone Similarity | Syntax Category [Sequence Length] |
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13 | 6 | 6 | 0.956 | stmt_list[4] |
Clone Abstraction | Parameter Bindings |
Clone Instance (Click to see clone) | Line Count | Source Line | Source File |
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1 | 13 | 603 | Bio/SeqIO/QualityIO.py |
2 | 15 | 624 | Bio/SeqIO/QualityIO.py |
3 | 13 | 667 | Bio/SeqIO/QualityIO.py |
4 | 15 | 688 | Bio/SeqIO/QualityIO.py |
5 | 13 | 731 | Bio/SeqIO/QualityIO.py |
6 | 17 | 752 | Bio/SeqIO/QualityIO.py |
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try : return "".join([_phred_to_sanger_quality_str[qp] for qp in qualities]) except KeyError: #Could be a float, or a None in the list, or a high value. pass if None in qualities: raise TypeError("A quality value of None was found") if max(qualities)>=93.5: warnings.warn("Data loss - max PHRED quality 93 in Sanger FASTQ") #This will apply the truncation at 93, giving max ASCII 126 return "".join([chr(min(126,int(round(qp))+SANGER_SCORE_OFFSET)) for qp in qualities]) |
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try : return "".join([_solexa_to_sanger_quality_str[qs] for qs in qualities]) except KeyError: #Either no PHRED scores, or something odd like a float or None pass if None in qualities: raise TypeError("A quality value of None was found") #Must do this the slow way, first converting the PHRED scores into #Solexa scores: if max(qualities)>=93.5: warnings.warn("Data loss - max PHRED quality 93 in Sanger FASTQ") #This will apply the truncation at 93, giving max ASCII 126 return "".join([chr(min(126,int(round(phred_quality_from_solexa(qs)))+SANGER_SCORE_OFFSET)) for qs in qualities]) |
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try : return "".join([_phred_to_illumina_quality_str[qp] for qp in qualities]) except KeyError: #Could be a float, or a None in the list, or a high value. pass if None in qualities: raise TypeError("A quality value of None was found") if max(qualities)>=62.5: warnings.warn("Data loss - max PHRED quality 62 in Illumina FASTQ") #This will apply the truncation at 62, giving max ASCII 126 return "".join([chr(min(126,int(round(qp))+SOLEXA_SCORE_OFFSET)) for qp in qualities]) |
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try : return "".join([_solexa_to_illumina_quality_str[qs] for qs in qualities]) except KeyError: #Either no PHRED scores, or something odd like a float or None pass if None in qualities: raise TypeError("A quality value of None was found") #Must do this the slow way, first converting the PHRED scores into #Solexa scores: if max(qualities)>=62.5: warnings.warn("Data loss - max PHRED quality 62 in Illumina FASTQ") #This will apply the truncation at 62, giving max ASCII 126 return "".join([chr(min(126,int(round(phred_quality_from_solexa(qs)))+SOLEXA_SCORE_OFFSET)) for qs in qualities]) |
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try : return "".join([_solexa_to_solexa_quality_str[qs] for qs in qualities]) except KeyError: #Could be a float, or a None in the list, or a high value. pass if None in qualities: raise TypeError("A quality value of None was found") if max(qualities)>=62.5: warnings.warn("Data loss - max Solexa quality 62 in Solexa FASTQ") #This will apply the truncation at 62, giving max ASCII 126 return "".join([chr(min(126,int(round(qs))+SOLEXA_SCORE_OFFSET)) for qs in qualities]) |
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try : return "".join([_phred_to_solexa_quality_str[qp] for qp in qualities]) except KeyError: #Either no PHRED scores, or something odd like a float or None #or too big to be in the cache pass if None in qualities: raise TypeError("A quality value of None was found") #Must do this the slow way, first converting the PHRED scores into #Solexa scores: if max(qualities)>=62.5: warnings.warn("Data loss - max Solexa quality 62 in Solexa FASTQ") return "".join([chr(min(126,int(round(solexa_quality_from_phred(qp)))+SOLEXA_SCORE_OFFSET)) for qp in qualities]) |
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try : return "".join([ [[#variable1676d460]][ [[#variable167bf400]]] for [[#variable167bf400]]in qualities]) except KeyError: #Could be a float, or a None in the list, or a high value. #Either no PHRED scores, or something odd like a float or None #or too big to be in the cache pass if None in qualities: raise TypeError("A quality value of None was found") #Must do this the slow way, first converting the PHRED scores into #Solexa scores: if max(qualities)>= [[#variable1683fea0]]: warnings.warn( [[#variable1661cec0]]) #This will apply the truncation at 93, giving max ASCII 126 #This will apply the truncation at 62, giving max ASCII 126 return "".join([chr(min(126,int(round( [[#variable167626c0]]))+ [[#variable16778bc0]])) for [[#variable167bf400]]in qualities]) |
CloneAbstraction |
Parameter Index | Clone Instance | Parameter Name | Value |
---|---|---|---|
1 | 1 | [[#1676d460]] | _phred_to_sanger_quality_str |
1 | 2 | [[#1676d460]] | _solexa_to_sanger_quality_str |
1 | 3 | [[#1676d460]] | _phred_to_illumina_quality_str |
1 | 4 | [[#1676d460]] | _solexa_to_illumina_quality_str |
1 | 5 | [[#1676d460]] | _solexa_to_solexa_quality_str |
1 | 6 | [[#1676d460]] | _phred_to_solexa_quality_str |
2 | 1 | [[#167bf400]] | qp |
2 | 2 | [[#167bf400]] | qs |
2 | 3 | [[#167bf400]] | qp |
2 | 4 | [[#167bf400]] | qs |
2 | 5 | [[#167bf400]] | qs |
2 | 6 | [[#167bf400]] | qp |
3 | 1 | [[#1683fea0]] | 93.5 |
3 | 2 | [[#1683fea0]] | 93.5 |
3 | 3 | [[#1683fea0]] | 62.5 |
3 | 4 | [[#1683fea0]] | 62.5 |
3 | 5 | [[#1683fea0]] | 62.5 |
3 | 6 | [[#1683fea0]] | 62.5 |
4 | 1 | [[#1661cec0]] | "Data loss - max PHRED quality 93 in Sanger FASTQ" |
4 | 2 | [[#1661cec0]] | "Data loss - max PHRED quality 93 in Sanger FASTQ" |
4 | 3 | [[#1661cec0]] | "Data loss - max PHRED quality 62 in Illumina FASTQ" |
4 | 4 | [[#1661cec0]] | "Data loss - max PHRED quality 62 in Illumina FASTQ" |
4 | 5 | [[#1661cec0]] | "Data loss - max Solexa quality 62 in Solexa FASTQ" |
4 | 6 | [[#1661cec0]] | "Data loss - max Solexa quality 62 in Solexa FASTQ" |
5 | 1 | [[#167626c0]] | qp |
5 | 2 | [[#167626c0]] | phred_quality_from_solexa(qs) |
5 | 3 | [[#167626c0]] | qp |
5 | 4 | [[#167626c0]] | phred_quality_from_solexa(qs) |
5 | 5 | [[#167626c0]] | qs |
5 | 6 | [[#167626c0]] | solexa_quality_from_phred(qp) |
6 | 1 | [[#16778bc0]] | SANGER_SCORE_OFFSET |
6 | 2 | [[#16778bc0]] | SANGER_SCORE_OFFSET |
6 | 3 | [[#16778bc0]] | SOLEXA_SCORE_OFFSET |
6 | 4 | [[#16778bc0]] | SOLEXA_SCORE_OFFSET |
6 | 5 | [[#16778bc0]] | SOLEXA_SCORE_OFFSET |
6 | 6 | [[#16778bc0]] | SOLEXA_SCORE_OFFSET |