Loading unaligned sequence data#
We can load unaligned sequence data using the load_unaligned
app, this will return a SequenceCollection
.
Loading unaligned DNA sequences from a single fasta file#
In this example, we load unaligned DNA sequences from a single fasta file using the load_unaligned
app. We specify the molecular type (moltype="protein")
and the file format (format="fasta")
.
from cogent3 import get_app
load_unaligned_app = get_app("load_unaligned", format="fasta", moltype="protein")
seqs = load_unaligned_app("data/inseqs_protein.fasta")
seqs
0 | |
1091044_fragment | IPLDFDKEFRDKTVVIVAIPGAFTPT |
13541053_fragment | KKKNTEVISVSEDTVYVHKAWVQYD |
15605725_fragment | FEILAINMDPENLTGFLKNNP |
3 x {min=21, median=25, max=26} protein sequence collection
Loading unaligned DNA sequences from multiple fasta files#
To load unaligned DNA sequences from multiple fasta files, we need two things, a data store that identifies the files we are interested in and a process composed of our apps of interest.
1. A data store that identifies the files we are interested in#
Here we open a read-only (mode="r"
) data store that identifies all fasta files in the data directory, limiting the data store to two members as a minimum example.
from cogent3 import get_app, open_data_store
fasta_seq_dstore = open_data_store("data", suffix="fasta", mode="r", limit=2)
2. A composed process that defines our workflow#
In this example, our process loads the unaligned sequences using load_unaligned
, then applies jaccard_dist
to estimate a kmer-based genetic distance, which we write out to a data store using write_tabular
.
Note
Apps that are “writers” require a data store to write to, learn more about writers here!.
out_dstore = open_data_store(path_to_dir, suffix="tsv", mode="w")
load_unaligned_app = get_app("load_unaligned", format="fasta", moltype="dna")
jdist = get_app("jaccard_dist")
writer = get_app("write_tabular", out_dstore, format="tsv")
process = load_unaligned_app + jdist + writer
Tip
When running this code on your machine, remember to replace path_to_dir
with an actual directory path.
Now we’re good to go! We can apply process
to our data store of fasta sequences. result
is a data store, which you can index to see individual data members. We can inspect a given data member using the .read()
on data members.
result = process.apply_to(fasta_seq_dstore)
print(result[1].read())
{"type": "cogent3.app.composable.NotCompleted", "not_completed_construction": {"args": ["ERROR", "load_unaligned", "Traceback (most recent call last):\n File \"/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/app/composable.py\", line 401, in _call\n result = self.main(val, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/app/io.py\", line 355, in main\n seqs = _load_seqs(path, cogent3.make_unaligned_seqs, self._parser, self.moltype)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/app/io.py\", line 290, in _load_seqs\n return coll_maker(data=data, moltype=moltype, source=unique_id)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/__init__.py\", line 201, in make_unaligned_seqs\n return _make_seq_container(\n ^^^^^^^^^^^^^^^^^^^^\n File \"/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/__init__.py\", line 144, in _make_seq_container\n return klass(\n ^^^^^^\n File \"/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/core/alignment.py\", line 1855, in __init__\n super().__init__(*args, **kwargs)\n File \"/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/core/alignment.py\", line 444, in __init__\n seqs, names = conversion_f(\n ^^^^^^^^^^^^^\n File \"/opt/hostedtoolcache/Python/3.12.9/x64/lib/python3.12/functools.py\", line 912, in wrapper\n return dispatch(args[0].__class__)(*args, **kw)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/core/alignment.py\", line 5585, in _\n return _coerce_to_unaligned_seqs(\n ^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/opt/hostedtoolcache/Python/3.12.9/x64/lib/python3.12/functools.py\", line 912, in wrapper\n return dispatch(args[0].__class__)(*args, **kw)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/core/alignment.py\", line 5566, in _coerce_to_unaligned_seqs\n seq = _construct_unaligned_seq(data[name], name=name, moltype=moltype)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/opt/hostedtoolcache/Python/3.12.9/x64/lib/python3.12/functools.py\", line 912, in wrapper\n return dispatch(args[0].__class__)(*args, **kw)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/core/alignment.py\", line 5868, in _\n return moltype.make_seq(seq=data, name=name, preserve_case=False)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/core/moltype.py\", line 766, in make_seq\n return self._make_seq(seq=self.coerce_str(seq), name=name, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/core/sequence.py\", line 839, in __init__\n self._seq = _coerce_to_seqview(\n ^^^^^^^^^^^^^^^^^^^\n File \"/opt/hostedtoolcache/Python/3.12.9/x64/lib/python3.12/functools.py\", line 912, in wrapper\n return dispatch(args[0].__class__)(*args, **kw)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/core/sequence.py\", line 3179, in _\n checker(data)\n File \"/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/core/sequence.py\", line 834, in <lambda>\n (lambda x: self.moltype.verify_sequence(x, gaps_allowed, wildcards_allowed))\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/home/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.12/site-packages/cogent3/core/moltype.py\", line 811, in verify_sequence\n raise AlphabetError(msg)\ncogent3.core.alphabet.AlphabetError: 'I'\n"], "kwargs": {"source": "inseqs_protein.fasta"}}, "version": "2025.3.22a2"}