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a/docs/.doctrees/formats/meta/samples.doctree and b/docs/.doctrees/formats/meta/samples.doctree differ diff --git a/docs/.doctrees/formats/meta/sections.doctree b/docs/.doctrees/formats/meta/sections.doctree index 5b4e42e7..958a82cb 100644 Binary files a/docs/.doctrees/formats/meta/sections.doctree and b/docs/.doctrees/formats/meta/sections.doctree differ diff --git a/docs/.doctrees/howto/run/mask.doctree b/docs/.doctrees/howto/run/mask.doctree index 520b3c4d..c4f8cf2a 100644 Binary files a/docs/.doctrees/howto/run/mask.doctree and b/docs/.doctrees/howto/run/mask.doctree differ diff --git a/docs/_sources/api/seismicrna.lists.rst.txt b/docs/_sources/api/seismicrna.lists.rst.txt new file mode 100644 index 00000000..5e192274 --- /dev/null +++ b/docs/_sources/api/seismicrna.lists.rst.txt @@ -0,0 +1,22 @@ +seismicrna.lists package +======================== + +.. automodule:: seismicrna.lists + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + + +.. automodule:: seismicrna.lists.listpos + :members: + :undoc-members: + :show-inheritance: + + +.. automodule:: seismicrna.lists.lists + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/_sources/api/seismicrna.rst.txt b/docs/_sources/api/seismicrna.rst.txt index df222676..f31d12e5 100644 --- a/docs/_sources/api/seismicrna.rst.txt +++ b/docs/_sources/api/seismicrna.rst.txt @@ -21,6 +21,7 @@ Subpackages seismicrna.fold seismicrna.graph seismicrna.join + seismicrna.lists seismicrna.mask seismicrna.pool seismicrna.relate diff --git a/docs/_sources/formats/index.rst.txt b/docs/_sources/formats/index.rst.txt index 710e0321..3896d11f 100644 --- a/docs/_sources/formats/index.rst.txt +++ b/docs/_sources/formats/index.rst.txt @@ -6,6 +6,7 @@ File Formats .. toctree:: :maxdepth: 2 - report/index data/index + list/index meta/index + report/index diff --git a/docs/_sources/formats/list/index.rst.txt b/docs/_sources/formats/list/index.rst.txt new file mode 100644 index 00000000..a4ecebab --- /dev/null +++ b/docs/_sources/formats/list/index.rst.txt @@ -0,0 +1,16 @@ + +List Formats +================================================================================ + +Using list files, one can list positions and reads that meet certain criteria, +as well as provide them to other commands. +All list files are in comma-separated values (CSV) format, which is advantageous +because it is both human-readable and widely supported by software including +Microsoft Excel and Python. +An example in CSV format is given for each type of list file. + + +.. toctree:: + :maxdepth: 2 + + listpos diff --git a/docs/_sources/formats/list/listpos.rst.txt b/docs/_sources/formats/list/listpos.rst.txt new file mode 100644 index 00000000..ed8c08ff --- /dev/null +++ b/docs/_sources/formats/list/listpos.rst.txt @@ -0,0 +1,58 @@ + +List of Positions +-------------------------------------------------------------------------------- + +List of Positions: Fields +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +========= ==== ========================================================= ======== +Name Type Description Required +========= ==== ========================================================= ======== +Reference str Name of the reference sequence yes +Position int Position in the reference sequence yes +... n/a Additional field (ignored) no +========= ==== ========================================================= ======== + +List of Positions file: Uses +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +List of Positions as input file +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +- The ``mask`` command accepts a List of Positions file via ``--exclude-file``. + +List of Positions as output file +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +- The ``+listpos`` command outputs a List of Positions file for each table file. + +Example List of Positions +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +List of Positions as a pretty table +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +========= ======== +Reference Position +========= ======== +refA 11 +refA 16 +refA 20 +refB 11 +refB 46 +refB 83 +========= ======== + +List of Positions as plain text +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" +:: + + Reference,Position + refA,11 + refA,16 + refA,20 + refB,11 + refB,46 + refB,83 + +This text can be copied into a new CSV file. diff --git a/docs/_sources/formats/meta/index.rst.txt b/docs/_sources/formats/meta/index.rst.txt index 5be575f4..9c0b8eca 100644 --- a/docs/_sources/formats/meta/index.rst.txt +++ b/docs/_sources/formats/meta/index.rst.txt @@ -1,12 +1,12 @@ Metadata Formats -======================================================================== +================================================================================ Using metadata files, information can be given about samples, reference sequences, and sections. -All metadata files must be in comma-separated values (CSV) format, which -is advantageous because it is both human-readable and widely supported -by software including Microsoft Excel and Python. +All metadata files are in comma-separated values (CSV) format, which is +advantageous because it is both human-readable and widely supported by software +including Microsoft Excel and Python. An example in CSV format is given for each type of metadata file. diff --git a/docs/_sources/formats/meta/joined.rst.txt b/docs/_sources/formats/meta/joined.rst.txt index 948ac87d..4022fb0c 100644 --- a/docs/_sources/formats/meta/joined.rst.txt +++ b/docs/_sources/formats/meta/joined.rst.txt @@ -40,12 +40,6 @@ joined cluster in the joined clusters metadata file. of ways to join those sections is *k*\ :sup:`n`. -Commands that use metadata for sections -"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" - -- ``seismic wf`` -- ``seismic join`` - Fields of metadata for joined clusters ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ diff --git a/docs/_sources/formats/meta/refs.rst.txt b/docs/_sources/formats/meta/refs.rst.txt index 5856580d..b23b6716 100644 --- a/docs/_sources/formats/meta/refs.rst.txt +++ b/docs/_sources/formats/meta/refs.rst.txt @@ -7,15 +7,10 @@ About metadata for references Purpose of metadata for references """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + Define metadata about reference sequences, such as the coordinates at which barcodes are located. -Commands that use metadata for references -"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" - -- ``seismic export`` - - Fields of metadata for references ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ @@ -33,7 +28,6 @@ Notes about metadata for references - Additional fields with arbitrary names can be given. Their data types will be inferred as strings, integers, or floats. - Example metadata for references ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ diff --git a/docs/_sources/formats/meta/samples.rst.txt b/docs/_sources/formats/meta/samples.rst.txt index e893589b..e4496cef 100644 --- a/docs/_sources/formats/meta/samples.rst.txt +++ b/docs/_sources/formats/meta/samples.rst.txt @@ -12,11 +12,6 @@ Define metadata about samples, such as the cell line or buffer in which the RNA was probed, the type and concentration of the chemical probe, and the temperature during chemical probing. -Commands that use metadata for samples -"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" - -- ``seismic export`` - Fields of metadata for samples ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ diff --git a/docs/_sources/formats/meta/sections.rst.txt b/docs/_sources/formats/meta/sections.rst.txt index 129efebd..4ae147c3 100644 --- a/docs/_sources/formats/meta/sections.rst.txt +++ b/docs/_sources/formats/meta/sections.rst.txt @@ -14,13 +14,6 @@ and traceable to define the sections in a file than on the command line, using the option ``--sections-file`` (``-s``). The sections file additionally permits giving each section a name. -Commands that use metadata for sections -"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" - -- ``seismic wf`` -- ``seismic mask`` -- ``seismic fold`` - Fields of metadata for sections ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ diff --git a/docs/_sources/howto/run/mask.rst.txt b/docs/_sources/howto/run/mask.rst.txt index bea0e7be..cfe9a379 100644 --- a/docs/_sources/howto/run/mask.rst.txt +++ b/docs/_sources/howto/run/mask.rst.txt @@ -101,10 +101,8 @@ Exclude arbitary positions You can also exclude any arbitary positions from any reference sequence. A common reason to exclude a position is if the base is modified endogenously in a way that causes mutations during reverse transcription. -To exclude an arbitrary position, use ``--exclude-pos`` followed by the name of -the reference and the position to exclude. -For example, ``--exclude-pos lititz 48`` would exclude positions 48 from the -reference "lititz". +To exclude an arbitrary position, use ``--exclude-file`` followed by a file of +all positions to exclude, in :doc:`../../formats/list/listpos` format. Mask setting: Filter reads """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" diff --git a/docs/api/seismicrna.align.html b/docs/api/seismicrna.align.html index 6fafeda3..69d68b90 100644 --- a/docs/api/seismicrna.align.html +++ b/docs/api/seismicrna.align.html @@ -66,6 +66,7 @@
  • seismicrna.fold package
  • seismicrna.graph package
  • seismicrna.join package
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • diff --git a/docs/api/seismicrna.align.tests.html b/docs/api/seismicrna.align.tests.html index 71d0a140..0683d9a7 100644 --- a/docs/api/seismicrna.align.tests.html +++ b/docs/api/seismicrna.align.tests.html @@ -66,6 +66,7 @@
  • seismicrna.fold package
  • seismicrna.graph package
  • seismicrna.join package
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • diff --git a/docs/api/seismicrna.cleanfa.html b/docs/api/seismicrna.cleanfa.html index 2c21aa36..ede137f9 100644 --- a/docs/api/seismicrna.cleanfa.html +++ b/docs/api/seismicrna.cleanfa.html @@ -65,6 +65,7 @@
  • seismicrna.fold package
  • seismicrna.graph package
  • seismicrna.join package
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • diff --git a/docs/api/seismicrna.cluster.html b/docs/api/seismicrna.cluster.html index cb60c0bd..bc0b9e5b 100644 --- a/docs/api/seismicrna.cluster.html +++ b/docs/api/seismicrna.cluster.html @@ -65,6 +65,7 @@
  • seismicrna.fold package
  • seismicrna.graph package
  • seismicrna.join package
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • diff --git a/docs/api/seismicrna.core.arg.html b/docs/api/seismicrna.core.arg.html index bc9807c5..6f9a7de4 100644 --- a/docs/api/seismicrna.core.arg.html +++ b/docs/api/seismicrna.core.arg.html @@ -66,6 +66,7 @@
  • seismicrna.fold package
  • seismicrna.graph package
  • seismicrna.join package
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • diff --git a/docs/api/seismicrna.core.batch.html b/docs/api/seismicrna.core.batch.html index 6cd21472..b67d2cde 100644 --- a/docs/api/seismicrna.core.batch.html +++ b/docs/api/seismicrna.core.batch.html @@ -66,6 +66,7 @@
  • seismicrna.fold package
  • seismicrna.graph package
  • seismicrna.join package
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • diff --git a/docs/api/seismicrna.core.extern.html b/docs/api/seismicrna.core.extern.html index a98969dd..9890d826 100644 --- a/docs/api/seismicrna.core.extern.html +++ b/docs/api/seismicrna.core.extern.html @@ -66,6 +66,7 @@
  • seismicrna.fold package
  • seismicrna.graph package
  • seismicrna.join package
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • diff --git a/docs/api/seismicrna.core.html b/docs/api/seismicrna.core.html index 26add992..fa297419 100644 --- a/docs/api/seismicrna.core.html +++ b/docs/api/seismicrna.core.html @@ -66,6 +66,7 @@
  • seismicrna.fold package
  • seismicrna.graph package
  • seismicrna.join package
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • @@ -2104,12 +2105,12 @@

    Purpose

    Version information for SEISMIC-RNA

    -seismicrna.core.version.format_version(major: int = 0, minor: int = 13, patch: int = 1)
    +seismicrna.core.version.format_version(major: int = 0, minor: int = 14, patch: int = 0)
    -seismicrna.core.version.parse_version(version: str = '0.13.1')
    +seismicrna.core.version.parse_version(version: str = '0.14.0')
    diff --git a/docs/api/seismicrna.core.io.html b/docs/api/seismicrna.core.io.html index 19fb3980..998748a1 100644 --- a/docs/api/seismicrna.core.io.html +++ b/docs/api/seismicrna.core.io.html @@ -66,6 +66,7 @@
  • seismicrna.fold package
  • seismicrna.graph package
  • seismicrna.join package
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • diff --git a/docs/api/seismicrna.core.io.tests.html b/docs/api/seismicrna.core.io.tests.html index b708efd2..93765c28 100644 --- a/docs/api/seismicrna.core.io.tests.html +++ b/docs/api/seismicrna.core.io.tests.html @@ -66,6 +66,7 @@
  • seismicrna.fold package
  • seismicrna.graph package
  • seismicrna.join package
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • diff --git a/docs/api/seismicrna.core.mu.html b/docs/api/seismicrna.core.mu.html index c0453557..6ae3001d 100644 --- a/docs/api/seismicrna.core.mu.html +++ b/docs/api/seismicrna.core.mu.html @@ -66,6 +66,7 @@
  • seismicrna.fold package
  • seismicrna.graph package
  • seismicrna.join package
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • diff --git a/docs/api/seismicrna.core.mu.tests.html b/docs/api/seismicrna.core.mu.tests.html index cc60ea91..9757719f 100644 --- a/docs/api/seismicrna.core.mu.tests.html +++ b/docs/api/seismicrna.core.mu.tests.html @@ -66,6 +66,7 @@
  • seismicrna.fold package
  • seismicrna.graph package
  • seismicrna.join package
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • diff --git a/docs/api/seismicrna.core.mu.unbias.html b/docs/api/seismicrna.core.mu.unbias.html index b4607afa..b1d86e87 100644 --- a/docs/api/seismicrna.core.mu.unbias.html +++ b/docs/api/seismicrna.core.mu.unbias.html @@ -66,6 +66,7 @@
  • seismicrna.fold package
  • seismicrna.graph package
  • seismicrna.join package
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • diff --git a/docs/api/seismicrna.core.mu.unbias.tests.html b/docs/api/seismicrna.core.mu.unbias.tests.html index d41a3da0..de7f761d 100644 --- a/docs/api/seismicrna.core.mu.unbias.tests.html +++ b/docs/api/seismicrna.core.mu.unbias.tests.html @@ -66,6 +66,7 @@
  • seismicrna.fold package
  • seismicrna.graph package
  • seismicrna.join package
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • diff --git a/docs/api/seismicrna.core.ngs.html b/docs/api/seismicrna.core.ngs.html index 0e94633e..85c639a0 100644 --- a/docs/api/seismicrna.core.ngs.html +++ b/docs/api/seismicrna.core.ngs.html @@ -66,6 +66,7 @@
  • seismicrna.fold package
  • seismicrna.graph package
  • seismicrna.join package
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • diff --git a/docs/api/seismicrna.core.ngs.tests.html b/docs/api/seismicrna.core.ngs.tests.html index cbd7c3cc..8ac84256 100644 --- a/docs/api/seismicrna.core.ngs.tests.html +++ b/docs/api/seismicrna.core.ngs.tests.html @@ -66,6 +66,7 @@
  • seismicrna.fold package
  • seismicrna.graph package
  • seismicrna.join package
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • diff --git a/docs/api/seismicrna.core.parallel.html b/docs/api/seismicrna.core.parallel.html index b0adc4ca..7cbee0eb 100644 --- a/docs/api/seismicrna.core.parallel.html +++ b/docs/api/seismicrna.core.parallel.html @@ -66,6 +66,7 @@
  • seismicrna.fold package
  • seismicrna.graph package
  • seismicrna.join package
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • diff --git a/docs/api/seismicrna.core.parallel.tests.html b/docs/api/seismicrna.core.parallel.tests.html index d96854e1..f453f32c 100644 --- a/docs/api/seismicrna.core.parallel.tests.html +++ b/docs/api/seismicrna.core.parallel.tests.html @@ -66,6 +66,7 @@
  • seismicrna.fold package
  • seismicrna.graph package
  • seismicrna.join package
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • diff --git a/docs/api/seismicrna.core.rel.html b/docs/api/seismicrna.core.rel.html index b3603d9e..176e891d 100644 --- a/docs/api/seismicrna.core.rel.html +++ b/docs/api/seismicrna.core.rel.html @@ -66,6 +66,7 @@
  • seismicrna.fold package
  • seismicrna.graph package
  • seismicrna.join package
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • diff --git a/docs/api/seismicrna.core.rel.tests.html b/docs/api/seismicrna.core.rel.tests.html index da430487..a8356472 100644 --- a/docs/api/seismicrna.core.rel.tests.html +++ b/docs/api/seismicrna.core.rel.tests.html @@ -66,6 +66,7 @@
  • seismicrna.fold package
  • seismicrna.graph package
  • seismicrna.join package
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • diff --git a/docs/api/seismicrna.core.rna.html b/docs/api/seismicrna.core.rna.html index 8d451c3f..58972853 100644 --- a/docs/api/seismicrna.core.rna.html +++ b/docs/api/seismicrna.core.rna.html @@ -66,6 +66,7 @@
  • seismicrna.fold package
  • seismicrna.graph package
  • seismicrna.join package
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • diff --git a/docs/api/seismicrna.core.seq.html b/docs/api/seismicrna.core.seq.html index 26b5bce0..b3e1d2b8 100644 --- a/docs/api/seismicrna.core.seq.html +++ b/docs/api/seismicrna.core.seq.html @@ -66,6 +66,7 @@
  • seismicrna.fold package
  • seismicrna.graph package
  • seismicrna.join package
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • @@ -243,15 +244,15 @@

    Subpackages
    -add_mask(name: str, mask_pos: Iterable[int], invert: bool = False)
    +add_mask(name: str, mask_pos: Iterable[int], complement: bool = False)

    Mask the integer positions in the array mask_pos.

    Parameters

    • name (str) – Name of the mask.

    • mask_pos (Iterable[int]) – Positions to mask (1-indexed).

      • -

    • invert (bool = False) – If invert is False, then mask out the positions in mask_pos. -If True, then mask out all but the given positions.

      • +

    • complement (bool = False) – If False, then remove the positions in mask_pos. Otherwise, +remove all but those positions.

    @@ -263,6 +264,12 @@

    Subpackages +
    +copy()
    +

    Return an identical section.

    +

    +
    get_mask(name: str)
    diff --git a/docs/api/seismicrna.core.seq.tests.html b/docs/api/seismicrna.core.seq.tests.html index 32082a15..60ac7895 100644 --- a/docs/api/seismicrna.core.seq.tests.html +++ b/docs/api/seismicrna.core.seq.tests.html @@ -66,6 +66,7 @@
  • seismicrna.fold package
  • seismicrna.graph package
  • seismicrna.join package
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • @@ -609,6 +610,83 @@
    +
    +
    +class seismicrna.core.seq.tests.section_test.TestSectionCopy(methodName='runTest')
    +

    Bases: unittest.case.TestCase

    +
    +
    +test_copy()
    +
    + +
    + +
    +
    +class seismicrna.core.seq.tests.section_test.TestSectionEqual(methodName='runTest')
    +

    Bases: unittest.case.TestCase

    +
    +
    +test_diff_end3()
    +
    + +
    +
    +test_diff_end5()
    +
    + +
    +
    +test_diff_full()
    +
    + +
    +
    +test_diff_mask_name()
    +
    + +
    +
    +test_diff_mask_pos()
    +
    + +
    +
    +test_diff_name()
    +
    + +
    +
    +test_diff_ref()
    +
    + +
    +
    +test_diff_seq()
    +
    + +
    +
    +test_diff_seq5()
    +
    + +
    +
    +test_equal_full()
    +
    + +
    +
    +test_equal_mask()
    +
    + +
    +
    +test_equal_part()
    +
    + +
    +
    class seismicrna.core.seq.tests.section_test.TestSectionInit(methodName='runTest')
    diff --git a/docs/api/seismicrna.core.tests.html b/docs/api/seismicrna.core.tests.html index bcd2cf84..b9167bd5 100644 --- a/docs/api/seismicrna.core.tests.html +++ b/docs/api/seismicrna.core.tests.html @@ -66,6 +66,7 @@
  • seismicrna.fold package
  • seismicrna.graph package
  • seismicrna.join package
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • diff --git a/docs/api/seismicrna.demult.html b/docs/api/seismicrna.demult.html index b31f6e5f..d0581aef 100644 --- a/docs/api/seismicrna.demult.html +++ b/docs/api/seismicrna.demult.html @@ -65,6 +65,7 @@
  • seismicrna.fold package
  • seismicrna.graph package
  • seismicrna.join package
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • diff --git a/docs/api/seismicrna.export.html b/docs/api/seismicrna.export.html index 8899211f..c89d2671 100644 --- a/docs/api/seismicrna.export.html +++ b/docs/api/seismicrna.export.html @@ -65,6 +65,7 @@
  • seismicrna.fold package
  • seismicrna.graph package
  • seismicrna.join package
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • diff --git a/docs/api/seismicrna.fold.html b/docs/api/seismicrna.fold.html index d4567215..6b0b0502 100644 --- a/docs/api/seismicrna.fold.html +++ b/docs/api/seismicrna.fold.html @@ -65,6 +65,7 @@
  • seismicrna.graph package
  • seismicrna.join package
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • diff --git a/docs/api/seismicrna.graph.html b/docs/api/seismicrna.graph.html index 79ae2194..12825920 100644 --- a/docs/api/seismicrna.graph.html +++ b/docs/api/seismicrna.graph.html @@ -65,6 +65,7 @@
  • seismicrna.join package
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • diff --git a/docs/api/seismicrna.html b/docs/api/seismicrna.html index 6e6186c5..932cff3a 100644 --- a/docs/api/seismicrna.html +++ b/docs/api/seismicrna.html @@ -62,6 +62,7 @@
  • seismicrna.fold package
  • seismicrna.graph package
  • seismicrna.join package
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • @@ -237,6 +238,10 @@

    SubpackagesSubmodules +
  • seismicrna.lists package +
  • seismicrna.mask package diff --git a/docs/api/seismicrna.join.html b/docs/api/seismicrna.join.html index b3a67e54..1a152d5c 100644 --- a/docs/api/seismicrna.join.html +++ b/docs/api/seismicrna.join.html @@ -19,7 +19,7 @@ - + @@ -65,6 +65,7 @@
  • Submodules
    • +
  • seismicrna.lists package
  • seismicrna.mask package
  • seismicrna.pool package
  • seismicrna.relate package
    • @@ -319,7 +320,7 @@