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Sample an alignment to a fixed length#

Let’s load in an alignment of rodents to use in the examples.

from cogent3 import get_app

loader = get_app("load_aligned", moltype="protein", format="phylip")
aln = loader("data/abglobin_aa.phylip")
aln

NotCompleted(type=ERROR, origin=load_aligned, source="abglobin_aa.phylip", message="Traceback (most recent call last):
  File "/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/app/composable.py", line 366, in _call
    result = self.main(val, *args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/app/io.py", line 306, in main
    return _load_seqs(path, ArrayAlignment, self._parser, self.moltype)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/app/io.py", line 278, in _load_seqs
    data = _read_it(path)
           ^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/functools.py", line 909, in wrapper
    return dispatch(args[0].__class__)(*args, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/app/io.py", line 274, in _
    return _read_it(Path(path))
           ^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/functools.py", line 909, in wrapper
    return dispatch(args[0].__class__)(*args, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/app/io.py", line 269, in _
    return path.read_text()
           ^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/pathlib.py", line 1027, in read_text
    with self.open(mode='r', encoding=encoding, errors=errors) as f:
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/pathlib.py", line 1013, in open
    return io.open(self, mode, buffering, encoding, errors, newline)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/home/runner/work/cogent3.github.io/cogent3.github.io/c3org/doc/data/abglobin_aa.phylip'
")

How to sample the first n positions of an alignment#

We can use the fixed_length app to sample an alignment to a fixed length. By default, it will sample from the beginning of an alignment, the argument length=20 specifies how many positions to sample.

from cogent3 import get_app

first_20 = get_app("fixed_length", length=20)
first_20(aln)

NotCompleted(type=ERROR, origin=load_aligned, source="abglobin_aa.phylip", message="Traceback (most recent call last):
  File "/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/app/composable.py", line 366, in _call
    result = self.main(val, *args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/app/io.py", line 306, in main
    return _load_seqs(path, ArrayAlignment, self._parser, self.moltype)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/app/io.py", line 278, in _load_seqs
    data = _read_it(path)
           ^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/functools.py", line 909, in wrapper
    return dispatch(args[0].__class__)(*args, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/app/io.py", line 274, in _
    return _read_it(Path(path))
           ^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/functools.py", line 909, in wrapper
    return dispatch(args[0].__class__)(*args, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/app/io.py", line 269, in _
    return path.read_text()
           ^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/pathlib.py", line 1027, in read_text
    with self.open(mode='r', encoding=encoding, errors=errors) as f:
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/pathlib.py", line 1013, in open
    return io.open(self, mode, buffering, encoding, errors, newline)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/home/runner/work/cogent3.github.io/cogent3.github.io/c3org/doc/data/abglobin_aa.phylip'
")

How to sample n positions from within an alignment#

Creating the fixed_length app with the argument start=x specifies that the sampled sequence should begin x positions into the alignment.

from cogent3 import get_app

skip_10_take_20 = get_app("fixed_length", length=20, start=10)
skip_10_take_20(aln)

NotCompleted(type=ERROR, origin=load_aligned, source="abglobin_aa.phylip", message="Traceback (most recent call last):
  File "/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/app/composable.py", line 366, in _call
    result = self.main(val, *args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/app/io.py", line 306, in main
    return _load_seqs(path, ArrayAlignment, self._parser, self.moltype)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/app/io.py", line 278, in _load_seqs
    data = _read_it(path)
           ^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/functools.py", line 909, in wrapper
    return dispatch(args[0].__class__)(*args, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/app/io.py", line 274, in _
    return _read_it(Path(path))
           ^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/functools.py", line 909, in wrapper
    return dispatch(args[0].__class__)(*args, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/app/io.py", line 269, in _
    return path.read_text()
           ^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/pathlib.py", line 1027, in read_text
    with self.open(mode='r', encoding=encoding, errors=errors) as f:
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/pathlib.py", line 1013, in open
    return io.open(self, mode, buffering, encoding, errors, newline)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/home/runner/work/cogent3.github.io/cogent3.github.io/c3org/doc/data/abglobin_aa.phylip'
")

How to sample n positions randomly from within an alignment#

The start position can be selected at random with random=True. An optional seed can be provided to ensure the same start position is used when the app is called.

from cogent3 import get_app

random_20 = get_app("fixed_length", length=20, random=True)
random_20(aln)

NotCompleted(type=ERROR, origin=load_aligned, source="abglobin_aa.phylip", message="Traceback (most recent call last):
  File "/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/app/composable.py", line 366, in _call
    result = self.main(val, *args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/app/io.py", line 306, in main
    return _load_seqs(path, ArrayAlignment, self._parser, self.moltype)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/app/io.py", line 278, in _load_seqs
    data = _read_it(path)
           ^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/functools.py", line 909, in wrapper
    return dispatch(args[0].__class__)(*args, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/app/io.py", line 274, in _
    return _read_it(Path(path))
           ^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/functools.py", line 909, in wrapper
    return dispatch(args[0].__class__)(*args, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/app/io.py", line 269, in _
    return path.read_text()
           ^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/pathlib.py", line 1027, in read_text
    with self.open(mode='r', encoding=encoding, errors=errors) as f:
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/pathlib.py", line 1013, in open
    return io.open(self, mode, buffering, encoding, errors, newline)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/home/runner/work/cogent3.github.io/cogent3.github.io/c3org/doc/data/abglobin_aa.phylip'
")
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