utils

This contains useful functions

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download_file

 download_file (url, save_path)

Checks if a file with the same name is already in the save_path. If not download it.

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is_gzipped_file

 is_gzipped_file (file_path)

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default_open_gz

 default_open_gz (gff_path)

If file is gzipped then opens it with gzip.open, otherwise opens it with open

# Example usage
file_url = 'https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_genomic.gff.gz'
human_genome_gff = 'GRCh38_latest_genomic.gff.gz'

download_file(file_url, human_genome_gff)
is_gzipped_file(human_genome_gff)
File already exists: GRCh38_latest_genomic.gff.gz
True

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extract_attribute

 extract_attribute (input_str:str, attr_name:str)

Extracts the attribute called attr_name from the GFF attributes string

Type Details
input_str str attribute string to parse
attr_name str name of the attribute to extract
Returns str 
input_str = 'ID=cds-ATV02827.1;Parent=gene-SaO11_00001;Dbxref=NCBI_GP:ATV02827.1;Name=ATV02827.1;gbkey=CDS;gene=dnaA;locus_tag=SaO11_00001;product=Chromosomal replication initiator protein DnaA;protein_id=ATV02827.1;transl_table=11'
extract_attribute(input_str,"gene")
'dnaA'

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extract_all_attributes

 extract_all_attributes (input_str:str)

Extracts all attributes from the GFF attributes column

extract_all_attributes(input_str)
defaultdict(None,
            {'locus_tag': 'SaO11_00001',
             'product': 'Chromosomal replication initiator protein DnaA',
             'protein_id': 'ATV02827.1',
             'transl_table': '11'})

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attributes_to_columns

 attributes_to_columns (features:pandas.core.frame.DataFrame)

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set_positions

 set_positions (annotation:pandas.core.frame.DataFrame)

Sets left and right as the position of the feature on the sequence, left is always lower than right. start and end represent the begining and end of the feature where start can be greater than end depending on the feature strand.

Type Details
annotation DataFrame an annotation DataFrame extracted from a gff file

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parse_gff

 parse_gff (gff_path:str, seq_id:str=None, bounds:tuple=None,
            feature_types:list=None)
Type Default Details
gff_path str path to the gff file
seq_id str None sequence id (first column of the gff)
bounds tuple None (left limit, right limit)
feature_types list None list of feature types to extract
Returns DataFrame 
df=parse_gff(human_genome_gff, 
             seq_id="NC_000001.11",
             bounds=(10000,50000))
df.head()
seq_id source type start end score strand phase attributes matchable_bases ... mol_type pseudo assembly_bases_seq pct_coverage bit_score genome pct_identity_gapopen_only left right middle
0 NC_000001.11 RefSeq region 1 248956422 . + . ID=NC_000001.11:1..248956422;Dbxref=taxon:9606... None ... genomic DNA None None None None chromosome None 1 248956422 124478211.5
1 NC_000001.11 BestRefSeq pseudogene 11874 14409 . + . ID=gene-DDX11L1;Dbxref=GeneID:100287102,HGNC:H... None ... None true None None None None None 11874 14409 13141.5
2 NC_000001.11 BestRefSeq transcript 11874 14409 . + . ID=rna-NR_046018.2;Parent=gene-DDX11L1;Dbxref=... None ... None true None None None None None 11874 14409 13141.5
3 NC_000001.11 BestRefSeq exon 11874 12227 . + . ID=exon-NR_046018.2-1;Parent=rna-NR_046018.2;D... None ... None true None None None None None 11874 12227 12050.5
4 NC_000001.11 BestRefSeq exon 12613 12721 . + . ID=exon-NR_046018.2-2;Parent=rna-NR_046018.2;D... None ... None true None None None None None 12613 12721 12667.0

5 rows × 56 columns

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available_feature_types

 available_feature_types (gff_path)
from genomenotebook.data import get_example_data_dir
import os
data_path = get_example_data_dir()
gff_path = os.path.join(data_path, "MG1655_U00096.gff3")
available_feature_types(gff_path)
{'CDS',
 'exon',
 'gene',
 'mobile_genetic_element',
 'ncRNA',
 'origin_of_replication',
 'pseudogene',
 'rRNA',
 'recombination_feature',
 'region',
 'repeat_region',
 'sequence_feature',
 'tRNA'}

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available_attributes

 available_attributes (gff_path)
available_attributes(gff_path)
Index(['seq_id', 'source', 'type', 'start', 'end', 'score', 'strand', 'phase',
       'attributes', 'protein_id', 'Parent', 'rpt_type', 'gene', 'Dbxref',
       'gene_synonym', 'orig_protein_id', 'exception', 'recombination_class',
       'mobile_element_type', 'transl_except', 'gene_biotype', 'gbkey',
       'Is_circular', 'strain', 'substrain', 'Name', 'product', 'ID', 'genome',
       'Note', 'mol_type', 'pseudo', 'locus_tag', 'orig_transcript_id', 'part',
       'transl_table', 'left', 'right', 'middle'],
      dtype='object')