API¶

metacov.compat¶

metacov.pileup¶

metacov.scan¶

class metacov.scan.AlignmentFileIterator¶: Iterates over all reads of a BAM/SAM/CRAM file

class metacov.scan.ByFlag(processor, list flags)¶

get_rows(self, int i)¶

class metacov.scan.FastQFileIterator¶: Iterates over all reads of a fq/fg.gz file

class metacov.scan.ReadIterator¶: Abstract Base Class for iterating over reads

class metacov.scan.ReadProcessor¶

Base class for read stats accumulators

set_max_readlen(self, int rlen) → void¶

class metacov.scan.ReadProcessorList(list processors)¶

Container class multiplexing over several read stats accumulators

get_rows(self, int i)¶

set_max_readlen(self, int rlen) → void¶

metacov.scan.kmer_base2_to_ascii(uint32_t kmer, int l) → str¶

metacov.scan.scan_reads(infile, fasta, counters, int progress_interval=10000000, progress_cb=None, maxreads=0) → long¶

metacov.simulate¶

metacov.blast¶

class metacov.blast.blast_parser[source]¶: Base class for BLAST parsers

class metacov.blast.fmt7_parser(fileobj)[source]¶: Parses BLAST results in fmt7 (CSV with comments)

metacov.util¶

class metacov.util.Region(qacc, sacc, sstart, send)¶

qacc¶: Alias for field number 0

sacc¶: Alias for field number 1

send¶: Alias for field number 3

sstart¶: Alias for field number 2

metacov.util.get_regions_from_bam(bamfile)[source]¶: Yields Region tuples directly from BAM file

metacov.util.get_regions_from_blast7(regionfile)[source]¶: Yields Region tuples from BLAST file

metacov.util.get_regions_from_csv(regionfile)[source]¶

Yields Region tuples from CSV file

The column containing the contig name must be ‘sacc’ or ‘sequence_id’. The column containing the start offset must be ‘sstart’ or ‘start’. The column containing the end offset must be ‘end’ or ‘send’.

metacov.cli¶

metacov.pyfq¶

class metacov.pyfq.FastQFile(str filename, int max_linelen=1000)¶

FastQ File Class (read only)

filename¶: filename: str

pos¶: Position in file in kb

rlen¶: Length of current read

seq¶: List of bases of current read (ACGTN->01234)

size¶: Size of file in kb

class metacov.pyfq.FastQFilePair(str read1, str read2, int max_linelen=1000)¶

FastQ File Pair Class

Essentially zip(FastQFile, FastQFile)

read1¶: read1: metacov.pyfq.FastQFile

read2¶: read2: metacov.pyfq.FastQFile

class metacov.pyfq.FastQWriter(fileobj)¶

FastQ File Writer

write(self, read)¶