manifest
ensembl.io.genomio.manifest
¶
Manifest files handling module.
StatsLengths = dict[str, int]
module-attribute
¶
ArgumentParser
¶
Bases: ArgumentParser
Extends argparse.ArgumentParser
with additional methods and functionality.
The default behaviour of the help text will be to display the default values on every non-required
argument, i.e. optional arguments with required=False
.
Source code in ensembl/utils/argparse.py
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|
formatter_class = argparse.ArgumentDefaultsHelpFormatter
instance-attribute
¶
add_argument(*args, **kwargs)
¶
Extends the parent function by excluding the default value in the help text when not provided.
Only applied to required arguments without a default value, i.e. positional arguments or optional
arguments with required=True
.
Source code in ensembl/utils/argparse.py
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|
add_argument_dst_path(*args, exists_ok=True, **kwargs)
¶
Adds pathlib.Path
argument, checking if it is writable at parsing time.
If "metavar" is not defined it is added with "PATH" as value to improve help text readability.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
exists_ok
|
bool
|
Do not raise an error if the destination path already exists. |
True
|
Source code in ensembl/utils/argparse.py
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|
add_argument_src_path(*args, **kwargs)
¶
Adds pathlib.Path
argument, checking if it exists and it is readable at parsing time.
If "metavar" is not defined, it is added with "PATH" as value to improve help text readability.
Source code in ensembl/utils/argparse.py
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|
add_argument_url(*args, **kwargs)
¶
Adds sqlalchemy.engine.URL
argument.
If "metavar" is not defined it is added with "URI" as value to improve help text readability.
Source code in ensembl/utils/argparse.py
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|
add_log_arguments(add_log_file=False)
¶
Adds the usual set of arguments required to set and initialise a logging system.
The current set includes a mutually exclusive group for the default logging level: --verbose
,
--debug
or --log LEVEL
.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
add_log_file
|
bool
|
Add arguments to allow storing messages into a file, i.e. |
False
|
Source code in ensembl/utils/argparse.py
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|
add_numeric_argument(*args, type=float, min_value=None, max_value=None, **kwargs)
¶
Adds a numeric argument with constrains on its type and its minimum or maximum value.
Note that the default value (if defined) is not checked unless the argument is an optional argument and no value is provided in the command line.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
type
|
Callable[[str], int | float]
|
Type to convert the argument value to when parsing. |
float
|
min_value
|
int | float | None
|
Minimum value constrain. If |
None
|
max_value
|
int | float | None
|
Maximum value constrain. If |
None
|
Source code in ensembl/utils/argparse.py
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|
add_server_arguments(prefix='', include_database=False, help=None)
¶
Adds the usual set of arguments needed to connect to a server, i.e. --host
, --port
, --user
and --password
(optional).
Note that the parser will assume this is a MySQL server.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
prefix
|
str
|
Prefix to add the each argument, e.g. if prefix is |
''
|
include_database
|
bool
|
Include |
False
|
help
|
str | None
|
Description message to include for this set of arguments. |
None
|
Source code in ensembl/utils/argparse.py
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|
parse_args(*args, **kwargs)
¶
Extends the parent function by adding a new URL argument for every server group added.
The type of this new argument will be sqlalchemy.engine.URL
. It also logs all the parsed
arguments for debugging purposes when logging arguments have been added.
Source code in ensembl/utils/argparse.py
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|
BiotypeCounter
¶
A counter for a given biotype, given a list of features.
Source code in src/python/ensembl/io/genomio/manifest/compute_stats.py
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|
count = count
instance-attribute
¶
example = example
instance-attribute
¶
ids = ids
instance-attribute
¶
add_id(feature_id)
¶
Add a feature to the counter.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
feature_id
|
str
|
Feature id to add. |
required |
Source code in src/python/ensembl/io/genomio/manifest/compute_stats.py
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|
unique_count()
¶
Total number feature ids added to the counter so far.
Returns:
Name | Type | Description |
---|---|---|
int |
int
|
number of features in the counter. |
Source code in src/python/ensembl/io/genomio/manifest/compute_stats.py
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|
IntegrityTool
¶
Check the integrity of sequence and annotation files in the genome
Source code in src/python/ensembl/io/genomio/manifest/check_integrity.py
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|
errors = []
instance-attribute
¶
ignore_final_stops = False
instance-attribute
¶
manifest = ManifestStats(manifest_file)
instance-attribute
¶
no_fail = no_fail
instance-attribute
¶
add_errors(errors)
¶
Store the given errors (list or single string) in the list of all errors.
Source code in src/python/ensembl/io/genomio/manifest/check_integrity.py
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|
check_ids(list1, list2, name)
¶
Compare the ids in list1 and list2.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
list1
|
dict[str, Any]
|
Sequence IDs retrieved from |
required |
list2
|
dict[str, Any]
|
Sequence IDs retrieved from the GFF3 file. |
required |
name
|
str
|
Source name. |
required |
Return
List of message errors of sequence IDs found only in one of the lists provided.
Source code in src/python/ensembl/io/genomio/manifest/check_integrity.py
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|
check_integrity()
¶
Load files listed in the manifest.json and check the integrity. Check if the files are correct by verifying the MD5 hash. Check if translation, functional annotation and sequence region ids and lengths are consistent with the information in gff. Compare sequence length from fasta_dna file to seq_region.json metadata.
Source code in src/python/ensembl/io/genomio/manifest/check_integrity.py
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|
check_lengths(list1, list2, name, *, allowed_len_diff=None, special_diff=False)
¶
Check the difference in ids and length between list1 and list2. There are a few special cases here where we allow a certain asymmetry by changing the values of the arguments.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
list1
|
dict[str, int]
|
dict containing length and id of the sequence from fasta files. |
required |
list2
|
dict[str, int]
|
dict containing length and id in the retrieved from the gff. |
required |
name
|
str
|
string |
required |
None to to not accept differences in length between list1 and list2.
The value can be changed based on how much difference in sequence length we are wanting to accept.
set as False when no special length difference is expected between the lists.
This can be changed if we want to report common sequences with 1 BP difference.
Returns:
Type | Description |
---|---|
list[str]
|
Error if there is a difference in length or ids between the lists. |
Source code in src/python/ensembl/io/genomio/manifest/check_integrity.py
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|
check_seq_region_lengths(seqrs, feats, name, circular=None)
¶
Check the integrity of seq_region.json file by comparing the length of the sequence to fasta files and the gff.
Seq_region file is in json format containing the metadata of the sequence.
It contains sequence id, length, location and the synonyms for the sequence name
from different sources.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
seqs
|
Sequence name and length retrieved from seq_region.json file. |
required | |
feats
|
dict[str, Any] | None
|
Sequence name and length retrieved from the fasta and gff file. |
required |
name
|
str
|
Name of the check to show in the logs. |
required |
circular
|
dict[str, Any] | None
|
Whether any sequence is circular. |
None
|
Returns:
Type | Description |
---|---|
None
|
Error if there are common sequences with difference in ids |
None
|
and if the sequences are not consistent in the files. |
Source code in src/python/ensembl/io/genomio/manifest/check_integrity.py
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|
set_ignore_final_stops(ignore_final_stops)
¶
Set ignore_final_stops (when calculating peptide length) for this tool and the manifest.
Source code in src/python/ensembl/io/genomio/manifest/check_integrity.py
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|
InvalidIntegrityError
¶
Bases: Exception
When a file integrity check fails
Source code in src/python/ensembl/io/genomio/manifest/manifest_stats.py
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|
Manifest
¶
Records of a manifest file and its files and md5 checksums.
Source code in src/python/ensembl/io/genomio/manifest/manifest.py
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|
file_path = manifest_dir / 'manifest.json'
instance-attribute
¶
files = {}
instance-attribute
¶
multi_files = {'agp'}
class-attribute
instance-attribute
¶
names = {None: _same_names_dict, None: _alias_names}
class-attribute
instance-attribute
¶
root_dir = manifest_dir
instance-attribute
¶
create()
¶
Creates a manifest file from the files in a directory.
Source code in src/python/ensembl/io/genomio/manifest/manifest.py
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|
get_files_checksums()
¶
Records all the files in the directory with their checksum.
Source code in src/python/ensembl/io/genomio/manifest/manifest.py
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|
load()
¶
Load the content of an existing manifest file.
Source code in src/python/ensembl/io/genomio/manifest/manifest.py
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|
ManifestStats
¶
Representation of the main stats of the files in a manifest for comparison.
The stats in question are: - lengths of sequences (DNA, genes and peptides) - sequences and features IDs - sequences circularity
Source code in src/python/ensembl/io/genomio/manifest/manifest_stats.py
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|
circular = {'seq_regions': {}}
instance-attribute
¶
errors = []
instance-attribute
¶
genome = {}
instance-attribute
¶
ignore_final_stops = ignore_final_stops
instance-attribute
¶
lengths = {'dna_sequences': {}, 'peptide_sequences': {}, 'seq_region_levels': {}, 'annotations': {}, 'agp': {}, 'gff3_seq_regions': {}, 'gff3_genes': {}, 'gff3_translations': {}, 'gff3_all_translations': {}, 'gff3_transposable_elements': {}, 'ann_genes': {}, 'ann_translations': {}, 'ann_transposable_elements': {}, 'seq_regions': {}}
instance-attribute
¶
manifest_files = self._get_manifest(manifest_path)
instance-attribute
¶
add_error(error)
¶
Record an error.
Source code in src/python/ensembl/io/genomio/manifest/manifest_stats.py
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|
get_circular(name)
¶
Returns a dict associating IDs with their is_circular flag from a given file name.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
name
|
str
|
Name for the circular data to get. |
required |
Raises:
Type | Description |
---|---|
KeyError
|
If the name is not supported. |
Source code in src/python/ensembl/io/genomio/manifest/manifest_stats.py
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|
get_lengths(name)
¶
Returns a dict associating IDs with their length from a given file name.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
name
|
str
|
Name for the lengths to get. |
required |
Raises:
Type | Description |
---|---|
KeyError
|
If the name is not supported. |
Source code in src/python/ensembl/io/genomio/manifest/manifest_stats.py
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|
has_lengths(name)
¶
Check if a given name has lengths records.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
name
|
str
|
Name for the lengths to check. |
required |
Raises:
Type | Description |
---|---|
KeyError
|
If the name is not supported. |
Source code in src/python/ensembl/io/genomio/manifest/manifest_stats.py
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|
load_agp_seq_regions(agp_dict)
¶
AGP files describe the assembly of larger sequence objects using smaller objects.
E.g. describes the assembly of scaffolds from contigs.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
agp_dict
|
dict | None
|
Dict containing the information about the sequence. |
required |
Note
AGP file is only used in the older builds, not used for current processing.
Source code in src/python/ensembl/io/genomio/manifest/manifest_stats.py
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|
load_dna_fasta_lengths()
¶
Retrieve DNA sequences lengths from their FASTA file.
Source code in src/python/ensembl/io/genomio/manifest/manifest_stats.py
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|
load_functional_annotation()
¶
Load the functional annotation file to retrieve the gene_id and translation id.
The functional annotation file is stored in a JSON format containing the description, id and object type, eg: "gene", "transcript", "translation".
Source code in src/python/ensembl/io/genomio/manifest/manifest_stats.py
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|
load_genome()
¶
Load the genome data.
Source code in src/python/ensembl/io/genomio/manifest/manifest_stats.py
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|
load_gff3()
¶
A GFF3 parser is used to retrieve information in the GFF3 file such as gene and CDS ids and their corresponding lengths.
Source code in src/python/ensembl/io/genomio/manifest/manifest_stats.py
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|
load_peptides_fasta_lengths()
¶
Retrieve peptides sequences lengths from their FASTA file.
Source code in src/python/ensembl/io/genomio/manifest/manifest_stats.py
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|
load_seq_regions()
¶
Retrieve seq_regions lengths and circular information from the seq_region JSON file.
Source code in src/python/ensembl/io/genomio/manifest/manifest_stats.py
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|
prepare_integrity_data()
¶
Read all the files and keep a record (IDs and their lengths) for each case to be compared later.
Source code in src/python/ensembl/io/genomio/manifest/manifest_stats.py
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|
StatsError
¶
Bases: Exception
Raised when stats could not be computed.
Source code in src/python/ensembl/io/genomio/manifest/compute_stats.py
69 70 |
|
manifest_stats
¶
Representation of the statistics of the set of files listed in the manifest file provided.
Source code in src/python/ensembl/io/genomio/manifest/compute_stats.py
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|
accession = accession
instance-attribute
¶
check_ncbi = False
instance-attribute
¶
datasets_bin = datasets_bin
instance-attribute
¶
errors = []
instance-attribute
¶
errors_file = Path(manifest_dir) / 'stats_diff.log'
instance-attribute
¶
manifest = f'{manifest_dir}/manifest.json'
instance-attribute
¶
manifest_parent = manifest_dir
instance-attribute
¶
biotypes_stats(biotypes)
¶
Prepare biotype stats in order of their name.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
biotypes
|
Dict[str, BiotypeCounter]
|
Biotypes counters. |
required |
Returns:
Type | Description |
---|---|
List[str]
|
A list with the computed statistics in a printable format. |
Source code in src/python/ensembl/io/genomio/manifest/compute_stats.py
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|
check_ncbi_stats(biotypes)
¶
Use the dataset tool from NCBI to get stats and compare with what we have
Source code in src/python/ensembl/io/genomio/manifest/compute_stats.py
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|
compare_ncbi_counts(biotypes, ncbi)
¶
Compare specific gene stats from NCBI
Source code in src/python/ensembl/io/genomio/manifest/compute_stats.py
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|
coord_systems_stats(coord_systems)
¶
For each coord_system compute various stats
- number of sequences
- sequence length sum, minimum, maximum, mean
Parameters:
Name | Type | Description | Default |
---|---|---|---|
coord_systems
|
Dict[str, List[int]]
|
Coordinate system dictionary of lengths. |
required |
Returns:
Type | Description |
---|---|
List[str]
|
A list with the computed statistics in a printable format. |
Source code in src/python/ensembl/io/genomio/manifest/compute_stats.py
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|
count_biotypes(gff3_path)
¶
Count the biotypes in a GFF3 file.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
gff3_path
|
Path
|
Path to the GFF3 file. |
required |
Returns:
Type | Description |
---|---|
Dict[str, BiotypeCounter]
|
Dictionary of biotype counters. |
Source code in src/python/ensembl/io/genomio/manifest/compute_stats.py
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|
get_gff3_stats(gff3_path)
¶
Extract the gene models from the GFF3 file and compute stats.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
gff3_path
|
Path
|
the GFF3 file. |
required |
Returns:
Name | Type | Description |
---|---|---|
List |
List[str]
|
Stats from the gene model. |
Source code in src/python/ensembl/io/genomio/manifest/compute_stats.py
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|
get_manifest()
¶
Get the files metadata from the manifest json file.
Returns:
Name | Type | Description |
---|---|---|
Dict |
Dict
|
A representation of the manifest json data. |
Source code in src/python/ensembl/io/genomio/manifest/compute_stats.py
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|
get_seq_region_stats(seq_region_path)
¶
Compute stats from the seq_region json file.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
seq_region_path
|
Path
|
the seq_region json file. |
required |
Returns:
Type | Description |
---|---|
List[str]
|
List[str]: Stats from the seq_regions. |
Source code in src/python/ensembl/io/genomio/manifest/compute_stats.py
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increment_biotype(biotypes, feature_id, feature_biotype)
staticmethod
¶
Add the feature to their respective biotype counter.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
biotypes
|
Dict[str, BiotypeCounter]
|
All current biotypes, with their counter. |
required |
feature_id
|
str
|
Feature id to be counted. |
required |
feature_biotype
|
str
|
The biotype of the feature. |
required |
Source code in src/python/ensembl/io/genomio/manifest/compute_stats.py
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|
run(stats_path)
¶
Compute stats in the files and output a stats.txt file in the same folder.
Raises:
Type | Description |
---|---|
StatsError
|
Could not compute some stats. |
Source code in src/python/ensembl/io/genomio/manifest/compute_stats.py
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|
seq_region_special_stats(circular=0, locations=None, codon_tables=None)
¶
Prepare stats in case there are circular regions, specific locations and codon_tables. stats.append(f"{count: 9f} {name}")
Parameters:
Name | Type | Description | Default |
---|---|---|---|
circular
|
int
|
Number of circular regions. Defaults to 0. |
0
|
locations
|
Optional[List[str]]
|
The regions and their location. Defaults to None. |
None
|
codon_tables
|
Optional[List[str]]
|
The regions and their codon_table. Defaults to None. |
None
|
Returns:
Type | Description |
---|---|
List[str]
|
A list with the computed statistics in a printable format. |
Source code in src/python/ensembl/io/genomio/manifest/compute_stats.py
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|
init_logging_with_args(args)
¶
Processes the Namespace object provided to call init_logging()
with the correct arguments.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
args
|
Namespace
|
Namespace populated by an argument parser. |
required |
Source code in ensembl/utils/logging.py
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|
main()
¶
Main entrypoint.
Source code in src/python/ensembl/io/genomio/manifest/generate.py
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|