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Clone Mass | Clones in CloneSet | Parameter Count | Clone Similarity | Syntax Category [Sequence Length] |
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28 | 3 | 1 | 0.998 | compound_stmt |
Clone Abstraction | Parameter Bindings |
Clone Instance (Click to see clone) | Line Count | Source Line | Source File |
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1 | 27 | 1387 | Bio/SeqIO/QualityIO.py |
2 | 28 | 1556 | Bio/SeqIO/QualityIO.py |
3 | 28 | 1611 | Bio/SeqIO/QualityIO.py |
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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)) |
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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)) |
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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)) |
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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 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 |