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-rw-r--r--gn3/computations/correlations.py3
-rw-r--r--gn3/computations/correlations2.py37
-rw-r--r--gn3/computations/slink.py97
-rw-r--r--gn3/db/traits.py159
4 files changed, 244 insertions, 52 deletions
diff --git a/gn3/computations/correlations.py b/gn3/computations/correlations.py
index bc738a7..56f483c 100644
--- a/gn3/computations/correlations.py
+++ b/gn3/computations/correlations.py
@@ -1,4 +1,5 @@
"""module contains code for correlations"""
+import math
import multiprocessing
from typing import List
@@ -90,7 +91,7 @@ def compute_sample_r_correlation(trait_name, corr_method, trait_vals,
target_values=sanitized_target_vals,
corr_method=corr_method)
- if corr_coefficient is not None:
+ if corr_coefficient is not None and not math.isnan(corr_coefficient):
return (trait_name, corr_coefficient, p_value, num_overlap)
return None
diff --git a/gn3/computations/correlations2.py b/gn3/computations/correlations2.py
index 6c456db..93db3fa 100644
--- a/gn3/computations/correlations2.py
+++ b/gn3/computations/correlations2.py
@@ -1,15 +1,25 @@
+"""
+DESCRIPTION:
+ TODO: Add a description for the module
+
+FUNCTIONS:
+compute_correlation:
+ TODO: Describe what the function does..."""
+
from math import sqrt
from functools import reduce
## From GN1: mostly for clustering and heatmap generation
-def items_with_values(dbdata, userdata):
+def __items_with_values(dbdata, userdata):
"""Retains only corresponding items in the data items that are not `None` values.
-This should probably be renamed to something sensible"""
+ This should probably be renamed to something sensible"""
def both_not_none(item1, item2):
+ """Check that both items are not the value `None`."""
if (item1 is not None) and (item2 is not None):
return (item1, item2)
return None
def split_lists(accumulator, item):
+ """Separate the 'x' and 'y' items."""
return [accumulator[0] + [item[0]], accumulator[1] + [item[1]]]
return reduce(
split_lists,
@@ -17,19 +27,24 @@ This should probably be renamed to something sensible"""
[[], []])
def compute_correlation(dbdata, userdata):
- x, y = items_with_values(dbdata, userdata)
- if len(x) < 6:
- return (0.0, len(x))
- meanx = sum(x)/len(x)
- meany = sum(y)/len(y)
+ """Compute some form of correlation.
+
+ This is extracted from
+ https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/utility/webqtlUtil.py#L622-L647
+ """
+ x_items, y_items = __items_with_values(dbdata, userdata)
+ if len(x_items) < 6:
+ return (0.0, len(x_items))
+ meanx = sum(x_items)/len(x_items)
+ meany = sum(y_items)/len(y_items)
def cal_corr_vals(acc, item):
xitem, yitem = item
return [
acc[0] + ((xitem - meanx) * (yitem - meany)),
acc[1] + ((xitem - meanx) * (xitem - meanx)),
acc[2] + ((yitem - meany) * (yitem - meany))]
- xyd, sxd, syd = reduce(cal_corr_vals, zip(x, y), [0.0, 0.0, 0.0])
+ xyd, sxd, syd = reduce(cal_corr_vals, zip(x_items, y_items), [0.0, 0.0, 0.0])
try:
- return ((xyd/(sqrt(sxd)*sqrt(syd))), len(x))
- except ZeroDivisionError as zde:
- return(0, len(x))
+ return ((xyd/(sqrt(sxd)*sqrt(syd))), len(x_items))
+ except ZeroDivisionError:
+ return(0, len(x_items))
diff --git a/gn3/computations/slink.py b/gn3/computations/slink.py
index 8d51f29..23d3d88 100644
--- a/gn3/computations/slink.py
+++ b/gn3/computations/slink.py
@@ -7,13 +7,18 @@ slink:
TODO: Describe what the function does...
"""
import logging
-from functools import partial
+from typing import List, Tuple, Union, Sequence
+
+NumType = Union[int, float]
+SeqOfNums = Sequence[NumType]
class LengthError(BaseException):
- pass
+ """Raised whenever child lists/tuples are not the same length as the parent
+ list of tuple."""
class MirrorError(BaseException):
- pass
+ """Raised if the distance from child A to child B is not the same as the
+ distance from child B to child A."""
def __is_list_or_tuple(item):
return type(item) in [list, tuple]
@@ -50,19 +55,20 @@ def __raise_valueerror_if_child_list_distance_from_itself_is_not_zero(lists):
def __raise_mirrorerror_of_distances_one_way_are_not_same_other_way(lists):
"""Check that the distance from A to B, is the same as the distance from B to A.
If the two distances are different, throw an exception."""
- for i in range(len(lists)):
- for j in range(len(lists)):
- if lists[i][j] != lists[j][i]:
- raise MirrorError(
- ("Distance from one child({}) to the other ({}) "
- "should be the same in both directions.").format(
- lists[i][j], lists[j][i]))
+ inner_coords = range(len(lists))
+ coords = ((i, j) for i in inner_coords for j in inner_coords)
+ def __is_same_reversed(coord):
+ return lists[coord[0]][coord[1]] == lists[coord[1]][coord[0]]
+ if not all(map(__is_same_reversed, coords)):
+ raise MirrorError((
+ "Distance from one child to the other should be the same in both "
+ "directions."))
def __raise_valueerror_on_negative_distances(lists):
"""Check that distances between 'somethings' are all positive, otherwise,
raise an exception."""
def zero_or_positive(val):
- return val >= 0;
+ return val >= 0
# flatten lists
flattened = __flatten_list_of_lists(lists)
if not all(map(zero_or_positive, flattened)):
@@ -71,12 +77,16 @@ raise an exception."""
def __flatten_list_of_lists(parent):
return [item for child in parent for item in child]
-def nearest(lists, i, j):
+# i and j are Union[SeqOfNums, NumType], but that leads to errors where the
+# values of i or j are indexed, since the NumType type is not indexable.
+# I don't know how to type this so that it does not fail on running `mypy .`
+def nearest(lists: Sequence[SeqOfNums], i, j) -> NumType:
"""
Computes shortest distance between member(s) in `i` and member(s) in `j`.
Description:
- This is 'copied' over from genenetwork1, from https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L42-L64.
+ This is 'copied' over from genenetwork1, from
+ https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L42-L64.
This description should be updated to better describe what 'member' means in
the context where the function is used.
@@ -108,19 +118,25 @@ def nearest(lists, i, j):
__raise_mirrorerror_of_distances_one_way_are_not_same_other_way(lists)
__raise_valueerror_on_negative_distances(lists)
#### END: Guard Functions ####
- if type(i) == int and type(j) == int: # From member i to member j
+ if isinstance(i, int) and isinstance(j, int): # From member i to member j
return lists[i][j]
- elif type(i) == int and __is_list_or_tuple(j):
+
+ if isinstance(i, int) and __is_list_or_tuple(j):
return min(map(lambda j_new: nearest(lists, i, j_new), j[:-1]))
- elif type(j) == int and __is_list_or_tuple(i):
+ if isinstance(j, int) and __is_list_or_tuple(i):
return min(map(lambda i_new: nearest(lists, i_new, j), i[:-1]))
- elif __is_list_or_tuple(i) and __is_list_or_tuple(j):
+
+ if __is_list_or_tuple(i) and __is_list_or_tuple(j):
coordinate_pairs = __flatten_list_of_lists(
[[(itemi, itemj) for itemj in j[:-1]] for itemi in i[:-1]])
return min(map(lambda x: nearest(lists, x[0], x[1]), coordinate_pairs))
- else:
- raise ValueError("member values (i or j) should be lists/tuples of integers or integers")
+ raise ValueError("member values (i or j) should be lists/tuples of integers or integers")
+
+# `lists` here could be Sequence[SeqOfNums], but that leads to errors I do not
+# understand down the line
+# Might have to re-implement the function especially since the errors are thrown
+# where `listindexcopy` is involved
def slink(lists):
"""
DESCRIPTION:
@@ -144,36 +160,39 @@ def slink(lists):
"""
try:
size = len(lists)
- listindex = range(size)
listindexcopy = list(range(size))
- listscopy = [[item for item in child] for child in lists]
- initSize = size
+ listscopy = [child[:] for child in lists]
+ init_size = size
candidate = []
- while initSize >2:
+ while init_size > 2:
mindist = 1e10
- for i in range(initSize):
- for j in range(i+1,initSize):
+ for i in range(init_size):
+ for j in range(i+1, init_size):
if listscopy[i][j] < mindist:
- mindist = listscopy[i][j]
- candidate=[[i,j]]
+ mindist = listscopy[i][j]
+ candidate = [[i, j]]
elif listscopy[i][j] == mindist:
- mindist = listscopy[i][j]
- candidate.append([i,j])
+ mindist = listscopy[i][j]
+ candidate.append([i, j])
else:
pass
- newmem = (listindexcopy[candidate[0][0]],listindexcopy[candidate[0][1]],mindist)
+ newmem = (
+ listindexcopy[candidate[0][0]], listindexcopy[candidate[0][1]],
+ mindist)
listindexcopy.pop(candidate[0][1])
listindexcopy[candidate[0][0]] = newmem
- initSize -= 1
- for i in range(initSize):
- for j in range(i+1,initSize):
- listscopy[i][j] = nearest(lists,listindexcopy[i],listindexcopy[j])
+ init_size -= 1
+ for i in range(init_size):
+ for j in range(i+1, init_size):
+ listscopy[i][j] = nearest(
+ lists, listindexcopy[i], listindexcopy[j])
listscopy[j][i] = listscopy[i][j]
- listindexcopy.append(nearest(lists,listindexcopy[0],listindexcopy[1]))
+ listindexcopy.append(
+ nearest(lists, listindexcopy[0], listindexcopy[1]))
return listindexcopy
- except Exception as e:
- # TODO: Look into making the logging log output to the system's
- # configured logger(s)
- logging.warning("Exception: {}, {}".format(type(e), e))
+ except (LengthError, MirrorError, TypeError, IndexError) as exc:
+ # Look into making the logging log output to the system's
+ # configured logger(s)
+ logging.warning("Exception: %s, %s", type(exc), exc)
return []
diff --git a/gn3/db/traits.py b/gn3/db/traits.py
index a77e6a1..ae1939a 100644
--- a/gn3/db/traits.py
+++ b/gn3/db/traits.py
@@ -1,5 +1,5 @@
"""This class contains functions relating to trait data manipulation"""
-from typing import Any, Union
+from typing import Any, Dict, Union
def get_trait_csv_sample_data(conn: Any,
@@ -75,3 +75,160 @@ def update_sample_data(conn: Any,
updated_n_strains: int = cursor.rowcount
return (updated_strains, updated_published_data,
updated_se_data, updated_n_strains)
+
+
+def retrieve_trait_dataset_name(
+ trait_type: str, threshold: int, name: str, connection: Any):
+ """
+ Retrieve the name of a trait given the trait's name
+
+ This is extracted from the `webqtlDataset.retrieveName` function as is
+ implemented at
+ https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlDataset.py#L140-L169
+ """
+ columns = "Id, Name, FullName, ShortName{}".format(
+ ", DataScale" if trait_type == "ProbeSet" else "")
+ query = (
+ "SELECT {columns} "
+ "FROM {trait_type}Freeze "
+ "WHERE "
+ "public > %(threshold)s "
+ "AND "
+ "(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)").format(
+ columns=columns, trait_type=trait_type)
+ with connection.cursor() as cursor:
+ cursor.execute(query, {"threshold": threshold, "name": name})
+ return cursor.fetchone()
+
+PUBLISH_TRAIT_INFO_QUERY = (
+ "SELECT "
+ "PublishXRef.Id, Publication.PubMed_ID, "
+ "Phenotype.Pre_publication_description, "
+ "Phenotype.Post_publication_description, "
+ "Phenotype.Original_description, "
+ "Phenotype.Pre_publication_abbreviation, "
+ "Phenotype.Post_publication_abbreviation, "
+ "Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, "
+ "Phenotype.Authorized_Users, CAST(Publication.Authors AS BINARY), "
+ "Publication.Title, Publication.Abstract, Publication.Journal, "
+ "Publication.Volume, Publication.Pages, Publication.Month, "
+ "Publication.Year, PublishXRef.Sequence, Phenotype.Units, "
+ "PublishXRef.comments "
+ "FROM "
+ "PublishXRef, Publication, Phenotype, PublishFreeze "
+ "WHERE "
+ "PublishXRef.Id = %(trait_name)s AND "
+ "Phenotype.Id = PublishXRef.PhenotypeId AND "
+ "Publication.Id = PublishXRef.PublicationId AND "
+ "PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND "
+ "PublishFreeze.Id =%(trait_dataset_id)s")
+
+
+def retrieve_publish_trait_info(trait_data_source: Dict[str, Any], conn: Any):
+ """Retrieve trait information for type `Publish` traits.
+
+ https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L399-L421"""
+ with conn.cursor() as cursor:
+ cursor.execute(
+ PUBLISH_TRAIT_INFO_QUERY,
+ {
+ k:v for k, v in trait_data_source.items()
+ if k in ["trait_name", "trait_dataset_id"]
+ })
+ return cursor.fetchone()
+
+PROBESET_TRAIT_INFO_QUERY = (
+ "SELECT "
+ "ProbeSet.name, ProbeSet.symbol, ProbeSet.description, "
+ "ProbeSet.probe_target_description, ProbeSet.chr, ProbeSet.mb, "
+ "ProbeSet.alias, ProbeSet.geneid, ProbeSet.genbankid, ProbeSet.unigeneid, "
+ "ProbeSet.omim, ProbeSet.refseq_transcriptid, ProbeSet.blatseq, "
+ "ProbeSet.targetseq, ProbeSet.chipid, ProbeSet.comments, "
+ "ProbeSet.strand_probe, ProbeSet.strand_gene, "
+ "ProbeSet.probe_set_target_region, ProbeSet.proteinid, "
+ "ProbeSet.probe_set_specificity, ProbeSet.probe_set_blat_score, "
+ "ProbeSet.probe_set_blat_mb_start, ProbeSet.probe_set_blat_mb_end, "
+ "ProbeSet.probe_set_strand, ProbeSet.probe_set_note_by_rw, "
+ "ProbeSet.flag "
+ "FROM "
+ "ProbeSet, ProbeSetFreeze, ProbeSetXRef "
+ "WHERE "
+ "ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND "
+ "ProbeSetXRef.ProbeSetId = ProbeSet.Id AND "
+ "ProbeSetFreeze.Name = %(trait_dataset_name)s AND "
+ "ProbeSet.Name = %(trait_name)s")
+
+def retrieve_probeset_trait_info(trait_data_source: Dict[str, Any], conn: Any):
+ """Retrieve trait information for type `ProbeSet` traits.
+
+ https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L424-L435"""
+ with conn.cursor() as cursor:
+ cursor.execute(
+ PROBESET_TRAIT_INFO_QUERY,
+ {
+ k:v for k, v in trait_data_source.items()
+ if k in ["trait_name", "trait_dataset_name"]
+ })
+ return cursor.fetchone()
+
+GENO_TRAIT_INFO_QUERY = (
+ "SELECT "
+ "Geno.name, Geno.chr, Geno.mb, Geno.source2, Geno.sequence "
+ "FROM "
+ "Geno, GenoFreeze, GenoXRef "
+ "WHERE "
+ "GenoXRef.GenoFreezeId = GenoFreeze.Id AND GenoXRef.GenoId = Geno.Id AND "
+ "GenoFreeze.Name = %(trait_dataset_name)s AND Geno.Name = %(trait_name)s")
+
+def retrieve_geno_trait_info(trait_data_source: Dict[str, Any], conn: Any):
+ """Retrieve trait information for type `Geno` traits.
+
+ https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L438-L449"""
+ with conn.cursor() as cursor:
+ cursor.execute(
+ GENO_TRAIT_INFO_QUERY,
+ {
+ k:v for k, v in trait_data_source.items()
+ if k in ["trait_name", "trait_dataset_name"]
+ })
+ return cursor.fetchone()
+
+TEMP_TRAIT_INFO_QUERY = (
+ "SELECT name, description FROM Temp "
+ "WHERE Name = %(trait_name)s")
+
+def retrieve_temp_trait_info(trait_data_source: Dict[str, Any], conn: Any):
+ """Retrieve trait information for type `Temp` traits.
+
+ https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L450-452"""
+ with conn.cursor() as cursor:
+ cursor.execute(
+ TEMP_TRAIT_INFO_QUERY,
+ {
+ k:v for k, v in trait_data_source.items()
+ if k in ["trait_name"]
+ })
+ return cursor.fetchone()
+
+def retrieve_trait_info(
+ trait_type: str, trait_name: str, trait_dataset_id: int,
+ trait_dataset_name: str, conn: Any):
+ """Retrieves the trait information.
+
+ https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L397-L456
+
+ This function, or the dependent functions, might be incomplete as they are
+ currently."""
+ trait_info_function_table = {
+ "Publish": retrieve_publish_trait_info,
+ "ProbeSet": retrieve_probeset_trait_info,
+ "Geno": retrieve_geno_trait_info,
+ "Temp": retrieve_temp_trait_info
+ }
+ return trait_info_function_table[trait_type](
+ {
+ "trait_name": trait_name,
+ "trait_dataset_id": trait_dataset_id,
+ "trait_dataset_name":trait_dataset_name
+ },
+ conn)
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 21:41:43 +0000