seqan package

Subpackages

• seqan.io package
  • Submodules
  • seqan.io.graphtool module
  • seqan.io.pgf module
  • Module contents
• seqan.test package
  • Submodules
  • seqan.test.test_build_index module
  • seqan.test.test_graphtool module
  • seqan.test.test_index module
  • seqan.test.test_iterator module
  • seqan.test.test_property_map module
  • seqan.test.test_read_fasta module
  • seqan.test.test_simple_types module
  • seqan.test.test_small_index module
  • seqan.test.test_strings module
  • seqan.test.test_write_pgf module
  • Module contents

Submodules

seqan.traverse module

Code to traverse indexes.

seqan.traverse.depthfirsttraversal(index, visitvertex)

Visit the vertexes of index in a depth-first traversal. The traversal is abandoned if visitvertex(it) returns False for any vertex.

seqan.traverse.depthpredicate(maxdepth)

Create a predicate that only descends the tree to a maximum depth.

seqan.traverse.suffixpredicate(suffix)

Create a predicate that only descends the part of the tree that matches the suffix.

seqan.traverse.topdowncopytraversal(it, visitvertex)

Visit the vertexes beneath the iterator in a top-down manner. visitvertex(it) is called for each vertex. If this method returns False, the top-down descent is truncated. Note this method copies the iterator once per vertex, so it is suitable for top-down iterators but not top-down-history iterators.

seqan.traverse.topdownhistorytraversal(it, visitvertex)

Visit the vertexes beneath the iterator in a top-down manner. visitvertex(it) is called for each vertex. If this method returns False, the top-down descent is truncated. Note this method uses it.goUp(), so it is suitable for top-down-history iterators but not top-down iterators.

seqan.traverse.topdownparalleltraversal(primit, secit, visitvertex, stillsynced=True)

Descends two top-down-history iterators (primary and secondary) in parallel.

Each vertex in the primary index is visited and the corresponding vertices (or closest vertices) in the secondary are simultaneously visited. The two iterators are called synchronised if and only if the representative of the primary iterator matches the start of the representative of the secondary iterator.

Module contents

pyseqan

A python interface to the the C++ SeqAn sequence analysis library

SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. SeqAn applies a unique generic design that guarantees high performance, generality, extensibility, and integration with other libraries. SeqAn is easy to use and simplifies the development of new software tools with a minimal loss of performance.

seqan.findsuffixes(it, callback)

Counts all complete suffixes below the vertex represented by the iterator. Calls the callback(it, count) whenever the count > 0.

seqan.property_map_for(index, dtype=None)

Create a sparse matrix suitable for use as a property map for the index. The data type will be an unsigned int unless specified.

seqan.version_string()

Return the release and git id as a string.