plastid.readers.bowtie module

This module contains a parser for bowtie’s legacy output format. Functions in this module are are seldom used on their own, and rather are accessed by GenomeArray or SparseGenomeArray when importing from bowtie files.

See also

GenomeArray and SparseGenomeArray
Array-like objects that store and index quantitative data over genomes
http://bowtie-bio.sourceforge.net/manual.shtml#default-bowtie-output
Detailed description of bowtie output format
plastid.test.unit.genomics.test_genome_array
for integrative tests of these functions
class plastid.readers.bowtie.BowtieReader(stream)[source]

Bases: plastid.util.io.filters.AbstractReader

Read alignments from bowtie files line-by-line into SegmentChains. The following attributes are defined and stored in the attr dict of each returned SegmentChain

seq_as_aligned
the sequence in the direction it aligns, NOT necessarily the read in the direction it was sequenced
qualstr_phred
a quality string, phred encoded
total_alignments
the number of total alignments found

See description of bowtie legacy format at http://bowtie-bio.sourceforge.net/manual.shtml

Parameters:
stream : file-like

Stream of alignments in bowtie’s legacy output format

Yields:
|SegmentChain|

A read alignment

Attributes:
closed

Methods

close() Close stream
filter(line) Parse a read alignment as SegmentChain from a line of bowtie output
flush Flush write buffers, if applicable.
read() Similar to file.read().
readline() Process a single line of data, assuming it is string-like next(self) is more likely to behave as expected.
readlines() Similar to file.readlines().
seek Change stream position.
tell Return current stream position.
truncate Truncate file to size bytes.
fileno  
isatty  
next  
readable  
seekable  
writable  
writelines  
close()

Close stream

fileno()

Returns underlying file descriptor if one exists.

An IOError is raised if the IO object does not use a file descriptor.

filter(line)[source]

Parse a read alignment as SegmentChain from a line of bowtie output

flush()

Flush write buffers, if applicable.

This is not implemented for read-only and non-blocking streams.

isatty()

Return whether this is an ‘interactive’ stream.

Return False if it can’t be determined.

next() → the next value, or raise StopIteration
read()

Similar to file.read(). Process all units of data, assuming it is string-like

Returns:
str
readable()

Return whether object was opened for reading.

If False, read() will raise IOError.

readline()

Process a single line of data, assuming it is string-like next(self) is more likely to behave as expected.

Returns:
object

a unit of processed data

readlines()

Similar to file.readlines().

Returns:
list

processed data

seek()

Change stream position.

Change the stream position to the given byte offset. The offset is interpreted relative to the position indicated by whence. Values for whence are:

  • 0 – start of stream (the default); offset should be zero or positive
  • 1 – current stream position; offset may be negative
  • 2 – end of stream; offset is usually negative

Return the new absolute position.

seekable()

Return whether object supports random access.

If False, seek(), tell() and truncate() will raise IOError. This method may need to do a test seek().

tell()

Return current stream position.

truncate()

Truncate file to size bytes.

File pointer is left unchanged. Size defaults to the current IO position as reported by tell(). Returns the new size.

writable()

Return whether object was opened for writing.

If False, read() will raise IOError.

writelines()
closed