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| Clone Mass | Clones in CloneSet | Parameter Count | Clone Similarity | Syntax Category [Sequence Length] |
|---|---|---|---|---|
| 38 | 2 | 1 | 0.995 | compound_stmt |
| Clone Abstraction | Parameter Bindings |
| Clone Instance (Click to see clone) | Line Count | Source Line | Source File |
|---|---|---|---|
| 1 | 38 | 72 | Bio/SeqIO/FastaIO.py |
| 2 | 27 | 1437 | Bio/SeqIO/QualityIO.py |
| ||||
def __init__(self,handle,wrap = 60,record2title = None):
'''Create a Fasta writer.
handle - Handle to an output file, e.g. as returned
by open(filename, "w")
wrap - Optional line length used to wrap sequence lines.
Defaults to wrapping the sequence at 60 characters
Use zero (or None) for no wrapping, giving a single
long line for the sequence.
record2title - Optional function to return the text to be
used for the title line of each record. By default the
a combination of the record.id and record.description
is used. If the record.description starts with the
record.id, then just the record.description is used.
You can either use:
myWriter = FastaWriter(open(filename,"w"))
writer.write_file(myRecords)
Or, follow the sequential file writer system, for example:
myWriter = FastaWriter(open(filename,"w"))
writer.write_header() # does nothing for Fasta files
...
Multiple calls to writer.write_record() and/or writer.write_records()
...
writer.write_footer() # does nothing for Fasta files
writer.close()
'''
SequentialSequenceWriter.__init__(self,handle)
#self.handle = handle
self.wrap = None
if wrap:
if wrap<1:
raise ValueError
self.wrap = wrap
self.record2title = record2title
|
| ||||
def __init__(self,handle,wrap = 60,record2title = None):
'''Create a QUAL writer.
Arguments:
- handle - Handle to an output file, e.g. as returned
by open(filename, "w")
- wrap - Optional line length used to wrap sequence lines.
Defaults to wrapping the sequence at 60 characters
Use zero (or None) for no wrapping, giving a single
long line for the sequence.
- record2title - Optional function to return the text to be
used for the title line of each record. By default
a combination of the record.id and record.description
is used. If the record.description starts with the
record.id, then just the record.description is used.
The record2title argument is present for consistency with the
Bio.SeqIO.FastaIO writer class.
'''
SequentialSequenceWriter.__init__(self,handle)
#self.handle = handle
self.wrap = None
if wrap:
if wrap<1:
raise ValueError
self.wrap = wrap
self.record2title = record2title
|
| |||
def __init__(self,handle,wrap = 60,record2title = None):
[[#variable5d78dfa0]]
SequentialSequenceWriter.__init__(self,handle)
#self.handle = handle
self.wrap = None
if wrap:
if wrap<1:
raise ValueError
self.wrap = wrap
self.record2title = record2title
|
| CloneAbstraction |
| Parameter Index | Clone Instance | Parameter Name | Value |
|---|---|---|---|
| 1 | 1 | [[#5d78dfa0]] | '''Create a Fasta writer.
handle - Handle to an output file, e.g. as returned
by open(filename, "w")
wrap - Optional line length used to wrap sequence lines.
Defaults to wrapping the sequence at 60 characters
Use zero (or None) for no wrapping, giving a single
long line for the sequence.
record2title - Optional function to return the text to be
used for the title line of each record. By default the
a combination of the record.id and record.description
is used. If the record.description starts with the
record.id, then just the record.description is used.
You can either use:
myWriter = FastaWriter(open(filename,"w"))
writer.write_file(myRecords)
Or, follow the sequential file writer system, for example:
myWriter = FastaWriter(open(filename,"w"))
writer.write_header() # does nothing for Fasta files
...
Multiple calls to writer.write_record() and/or writer.write_records()
...
writer.write_footer() # does nothing for Fasta files
writer.close()
''' |
| 1 | 2 | [[#5d78dfa0]] | '''Create a QUAL writer.
Arguments:
- handle - Handle to an output file, e.g. as returned
by open(filename, "w")
- wrap - Optional line length used to wrap sequence lines.
Defaults to wrapping the sequence at 60 characters
Use zero (or None) for no wrapping, giving a single
long line for the sequence.
- record2title - Optional function to return the text to be
used for the title line of each record. By default
a combination of the record.id and record.description
is used. If the record.description starts with the
record.id, then just the record.description is used.
The record2title argument is present for consistency with the
Bio.SeqIO.FastaIO writer class.
''' |