CloneSet26


Clone Mass	Clones in CloneSet	Parameter Count	Clone Similarity	Syntax Category [Sequence Length]
28	3	1	0.998	compound_stmt

Clone Abstraction

Parameter Bindings

Clone Instance (Click to see clone)	Line Count	Source Line	Source File
1	27	1387	Bio/SeqIO/QualityIO.py
2	28	1556	Bio/SeqIO/QualityIO.py
3	28	1611	Bio/SeqIO/QualityIO.py

Clone Instance
1

Line Count
27

Source Line
1387

Source File

Bio/SeqIO/QualityIO.py

    def write_record(self,record): 
        "Write a single FASTQ record to the file." 
        assert self._header_written 
        assert not self._footer_written 
        self._record_written = True 
        #TODO - Is an empty sequence allowed in FASTQ format?
        if record.seq is None: 
             raise ValueError("No sequence for record %s"%record.id) 
        seq_str = str(record.seq) 
        qualities_str = _get_sanger_quality_str(record) 
        if len(qualities_str)!=len(seq_str):   
            raise ValueError("Record %s has sequence length %i but %i quality scores"%(record.id,len(seq_str),len(qualities_str))) 


        #FASTQ files can include a description, just like FASTA files
        #(at least, this is what the NCBI Short Read Archive does)
        id = self.clean(record.id) 
        description = self.clean(record.description) 
        if description and description.split(None,1)[0]==id: 
            #The description includes the id at the start
            title = description 
        elif description: 
            title = "%s %s"%(id,description) 
        else: 
            title = id 

        self.handle.write("""@%s
%s
+
%s
"""                       %(title,seq_str,qualities_str))

Clone Instance
2

Line Count
28

Source Line
1556

Source File

Bio/SeqIO/QualityIO.py

    def write_record(self,record): 
        "Write a single FASTQ record to the file." 
        assert self._header_written 
        assert not self._footer_written 
        self._record_written = True 

        #TODO - Is an empty sequence allowed in FASTQ format?
        if record.seq is None: 
             raise ValueError("No sequence for record %s"%record.id) 
        seq_str = str(record.seq) 
        qualities_str = _get_solexa_quality_str(record) 
        if len(qualities_str)!=len(seq_str):   
            raise ValueError("Record %s has sequence length %i but %i quality scores"%(record.id,len(seq_str),len(qualities_str))) 


        #FASTQ files can include a description, just like FASTA files
        #(at least, this is what the NCBI Short Read Archive does)
        id = self.clean(record.id) 
        description = self.clean(record.description) 
        if description and description.split(None,1)[0]==id: 
            #The description includes the id at the start
            title = description 
        elif description: 
            title = "%s %s"%(id,description) 
        else: 
            title = id 

        self.handle.write("""@%s
%s
+
%s
"""                       %(title,seq_str,qualities_str))

Clone Instance
3

Line Count
28

Source Line
1611

Source File

Bio/SeqIO/QualityIO.py

    def write_record(self,record): 
        "Write a single FASTQ record to the file." 
        assert self._header_written 
        assert not self._footer_written 
        self._record_written = True 

        #TODO - Is an empty sequence allowed in FASTQ format?
        if record.seq is None: 
             raise ValueError("No sequence for record %s"%record.id) 
        seq_str = str(record.seq) 
        qualities_str = _get_illumina_quality_str(record) 
        if len(qualities_str)!=len(seq_str):   
            raise ValueError("Record %s has sequence length %i but %i quality scores"%(record.id,len(seq_str),len(qualities_str))) 


        #FASTQ files can include a description, just like FASTA files
        #(at least, this is what the NCBI Short Read Archive does)
        id = self.clean(record.id) 
        description = self.clean(record.description) 
        if description and description.split(None,1)[0]==id: 
            #The description includes the id at the start
            title = description 
        elif description: 
            title = "%s %s"%(id,description) 
        else: 
            title = id 

        self.handle.write("""@%s
%s
+
%s
"""                       %(title,seq_str,qualities_str))

Clone Abstraction

Parameter Count: 1

Parameter Bindings

def write_record(self,record):
  "Write a single FASTQ record to the file." 
  assert self._header_written 
  assert not self._footer_written 
  self._record_written = True 
  #TODO - Is an empty sequence allowed in FASTQ format?
  if record.seq is None:
  
    raise ValueError("No sequence for record %s"%record.id) 
  seq_str = str(record.seq) 
  qualities_str = [[#variable7801e320]](record) 
  if len(qualities_str)!=len(seq_str):
  
    raise ValueError("Record %s has sequence length %i but %i quality scores"%(record.id,len(seq_str),len(qualities_str))) 
    #FASTQ files can include a description, just like FASTA files
    #(at least, this is what the NCBI Short Read Archive does)
  id = self.clean(record.id) 
  description = self.clean(record.description) 
  if description and description.split(None,1)[0]==id:
  
    #The description includes the id at the start
    title = description 
  elif description:
  
    title = "%s %s"%(id,description) 
  else:
  
    title = id 
  self.handle.write("""@%s
%s
+
%s
"""                 %(title,seq_str,qualities_str))

CloneAbstraction

Parameter Bindings
Parameter Index	Clone Instance	Parameter Name	Value
1	1	`[[#7801e320]]`	_get_illumina_quality_str
1	2	`[[#7801e320]]`	_get_solexa_quality_str
1	3	`[[#7801e320]]`	_get_sanger_quality_str