Loading an alignment from a file or url

Loading aligned sequences

The load functions record the origin of the data in the info attribute under a “source” key.

Note

The function load_aligned_seqs() returns an ArrayAlignment by default. If you set the argument array_align=False, you will get an Alignment. (That class can be annotated.)

Loading unaligned sequences

The load_unaligned_seqs() function returns a sequence collection.

Loading from a url

The cogent3 load functions support loading from a url. We load the above fasta file directly from GitHub.

Specifying the file format

The loading functions use the filename suffix to infer the file format. This can be overridden using the format argument.

Specifying the sequence molecular type

Simple case of loading a list of aligned amino acid sequences in FASTA format, with and without moltype specification. When moltype is not specified it defaults to BYTES for the ArrayAlignment class, ASCII for the Alignment class.

Note

This applies to both the load_* or make_* functions.

Making an alignment from standard python objects

From a dict of strings

From a series of strings

Stripping label characters on loading

Load a list of aligned nucleotide sequences, while specifying the DNA molecule type and stripping the comments from the label. In this example, stripping is accomplished by passing a function that removes everything after the first whitespace to the label_to_name parameter.

Making a sequence collection from standard python objects

This is done using make_unaligned_seqs(), which returns a SequenceCollection instance. The function arguments match those of make_aligned_seqs(). We demonstrate only for the case where the input data is a dict.

Loading sequences using format parsers

load_aligned_seqs() and load_unaligned_seqs() are just convenience interfaces to format parsers. It can sometimes be more effective to use the parsers directly, say when you don’t want to load everything into memory.

Loading FASTA sequences from an open file or list of lines

To load FASTA formatted sequences directly, you can use the MinimalFastaParser.

Note

This returns the sequences as strings.

Handling overloaded FASTA sequence labels

The FASTA label field is frequently overloaded, with different information fields present in the field and separated by some delimiter. This can be flexibly addressed using the LabelParser. By creating a custom label parser, we can decide which part we use as the sequence name. We show how to convert a field into something specific.

RichLabel objects have an Info object as an attribute, allowing specific reference to all the specified label fields.