thoraxe.add_transcripts package

Submodules

thoraxe.add_transcripts.add_transcripts module

Functions to add user-defined transcript data from a CSV file to the previously downloaded Ensembl data.

class thoraxe.add_transcripts.add_transcripts.Paths(input, tsl, exontable, sequences)

property exontable

Alias for field number 2

property input

Alias for field number 0

property sequences

Alias for field number 3

property tsl

Alias for field number 1

thoraxe.add_transcripts.add_transcripts.add_sequences(input_df, seqrecords)

It modifies seqrecords by appending the new sequences.

thoraxe.add_transcripts.add_transcripts.add_to_exontable(input_df, exontable)

It adds the new exons and transcripts to the Ensembl’s exontable.

thoraxe.add_transcripts.add_transcripts.add_to_tsl(input_df, tsl_df)

It adds the new transcripts to the TSL table downloaded from Ensembl.

thoraxe.add_transcripts.add_transcripts.check_input(input_df, exontable)

It raises an error if there is a problem with the user-defined transcripts.

thoraxe.add_transcripts.add_transcripts.get_output_paths(args)

Return a Paths namedtuple containing the input and output paths for add_transcripts.

thoraxe.add_transcripts.add_transcripts.main()

Main script function to add user transcript data.

thoraxe.add_transcripts.add_transcripts.parse_command_line()

Parse command line.

It uses argparse to parse add_transcripts’ command line arguments and returns the argparse parser.

thoraxe.add_transcripts.add_transcripts.read_fasta(sequences_path)

Returns a list of SeqRecord`s for the fasta file at `sequences_path.

Module contents

add_transcripts: Add user-defined transcript data.

It adds the new transcripts to the data previously downloaded from Ensembl.