def test_tabix_multi_ps_open(self): with open(self.tabix_ref,"rb") as fh1: with open(self.tabix_ref,"rb") as fh2: ps1 = pysam.tabix_file_iterator(fh1,pysam.asTuple()) ps2 = pysam.tabix_file_iterator(fh2,pysam.asTuple()) reader = MockReader(ps1,ps2,self.tabix_ref,tabix=True) for expected, found in zip(reader,self.bed_lines+self.bed_lines): self.assertEqual(expected.strip("\n"),found.strip("\n"))
def test_tabix_multi_ps_open(self): with open(self.tabix_ref, "rb") as fh1: with open(self.tabix_ref, "rb") as fh2: ps1 = pysam.tabix_file_iterator(fh1, pysam.asTuple()) ps2 = pysam.tabix_file_iterator(fh2, pysam.asTuple()) reader = MockReader(ps1, ps2, self.tabix_ref, tabix=True) for expected, found in zip(reader, self.bed_lines + self.bed_lines): self.assertEqual(expected.strip("\n"), found.strip("\n"))
def load_gap_intervals(gap_file): if gap_file is None: return [] logger.info("Loading the gaps in the genome from %s" % gap_file) with open(gap_file) as gap_file_fd: gap_intervals = [SVInterval(it.contig, it.start, it.end, it.name, "gap") for it in pysam.tabix_file_iterator(gap_file_fd, parser=pysam.asBed())] return merge_intervals(gap_intervals)
def _tabix_iteradaptor(stream): """Open `stream` as an iterator over a `tabix`_ file, returning raw strings from tabix data. Parameters ---------- streams : open file-like, :class:`pysam.ctabix.tabix_file_iterator` Returns ------- generator Generator of tab-delimited string records in `tabix`_ file """ if not isinstance(stream,(pysam.ctabix.tabix_generic_iterator, pysam.ctabix.tabix_file_iterator) ): stream = pysam.tabix_file_iterator(stream,pysam.asTuple()) return (str(X) for X in stream)
def test_iterator_file_uncompressed(): f = open("windows_small.bed") l = len( list( pysam.tabix_file_iterator( f, parser = pysam.asBed() )))
def iterate_file_uncompressed(fn): with open(fn) as f: return len(list(pysam.tabix_file_iterator(f, parser=pysam.asBed())))
def test_iterator_file_uncompressed(): f = open("windows_small.bed") l = len(list(pysam.tabix_file_iterator(f, parser=pysam.asBed())))