CloneSet21


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Clone
Mass
Clones in
CloneSet
Parameter
Count
Clone
Similarity
Syntax Category
[Sequence Length]
13660.956stmt_list[4]
Clone AbstractionParameter Bindings
Clone Instance
(Click to see clone)
Line CountSource Line
Source File
113603
Bio/SeqIO/QualityIO.py
215624
Bio/SeqIO/QualityIO.py
313667
Bio/SeqIO/QualityIO.py
415688
Bio/SeqIO/QualityIO.py
513731
Bio/SeqIO/QualityIO.py
617752
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 AbstractionParameter Count: 6Parameter 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
11[[#1676d460]]
_phred_to_sanger_quality_str 
12[[#1676d460]]
_solexa_to_sanger_quality_str 
13[[#1676d460]]
_phred_to_illumina_quality_str 
14[[#1676d460]]
_solexa_to_illumina_quality_str 
15[[#1676d460]]
_solexa_to_solexa_quality_str 
16[[#1676d460]]
_phred_to_solexa_quality_str 
21[[#167bf400]]
qp 
22[[#167bf400]]
qs 
23[[#167bf400]]
qp 
24[[#167bf400]]
qs 
25[[#167bf400]]
qs 
26[[#167bf400]]
qp 
31[[#1683fea0]]
93.5 
32[[#1683fea0]]
93.5 
33[[#1683fea0]]
62.5 
34[[#1683fea0]]
62.5 
35[[#1683fea0]]
62.5 
36[[#1683fea0]]
62.5 
41[[#1661cec0]]
"Data loss - max PHRED quality 93 in Sanger FASTQ" 
42[[#1661cec0]]
"Data loss - max PHRED quality 93 in Sanger FASTQ" 
43[[#1661cec0]]
"Data loss - max PHRED quality 62 in Illumina FASTQ" 
44[[#1661cec0]]
"Data loss - max PHRED quality 62 in Illumina FASTQ" 
45[[#1661cec0]]
"Data loss - max Solexa quality 62 in Solexa FASTQ" 
46[[#1661cec0]]
"Data loss - max Solexa quality 62 in Solexa FASTQ" 
51[[#167626c0]]
qp 
52[[#167626c0]]
phred_quality_from_solexa(qs) 
53[[#167626c0]]
qp 
54[[#167626c0]]
phred_quality_from_solexa(qs) 
55[[#167626c0]]
qs 
56[[#167626c0]]
solexa_quality_from_phred(qp) 
61[[#16778bc0]]
SANGER_SCORE_OFFSET 
62[[#16778bc0]]
SANGER_SCORE_OFFSET 
63[[#16778bc0]]
SOLEXA_SCORE_OFFSET 
64[[#16778bc0]]
SOLEXA_SCORE_OFFSET 
65[[#16778bc0]]
SOLEXA_SCORE_OFFSET 
66[[#16778bc0]]
SOLEXA_SCORE_OFFSET