CloneSet21


Clone Mass	Clones in CloneSet	Parameter Count	Clone Similarity	Syntax Category [Sequence Length]
13	6	6	0.956	stmt_list[4]

Clone Abstraction

Parameter Bindings


Bio/SeqIO/QualityIO.py
Bio/SeqIO/QualityIO.py
Bio/SeqIO/QualityIO.py
Bio/SeqIO/QualityIO.py
Bio/SeqIO/QualityIO.py
Bio/SeqIO/QualityIO.py

Clone Instance (Click to see clone)	Line Count	Source Line	Source File
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

Clone Instance
1

Line Count
13

Source Line
603

Source File

Bio/SeqIO/QualityIO.py

        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])

Clone Instance
2

Line Count
15

Source Line
624

Source File

Bio/SeqIO/QualityIO.py

    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])

Clone Instance
3

Line Count
13

Source Line
667

Source File

Bio/SeqIO/QualityIO.py

        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])

Clone Instance
4

Line Count
15

Source Line
688

Source File

Bio/SeqIO/QualityIO.py

    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])

Clone Instance
5

Line Count
13

Source Line
731

Source File

Bio/SeqIO/QualityIO.py

        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])

Clone Instance
6

Line Count
17

Source Line
752

Source File

Bio/SeqIO/QualityIO.py

    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])

Clone Abstraction

Parameter Count: 6

Parameter Bindings

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 Bindings
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