diff options
| -rw-r--r-- | wqflask/base/trait_collection.py | 39 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/data/load_genotypes_lei.py | 181 |
2 files changed, 220 insertions, 0 deletions
diff --git a/wqflask/base/trait_collection.py b/wqflask/base/trait_collection.py index 797a4d63..49b0eaea 100644 --- a/wqflask/base/trait_collection.py +++ b/wqflask/base/trait_collection.py @@ -22,6 +22,45 @@ from sqlalchemy import (Column, Integer, String, Table, ForeignKey, Unicode, Boo Text, Index) from sqlalchemy.orm import relationship, backref +#from redis import StrictRedis +import redis +Redis = redis.StrictRedis() + from wqflask.database import Base, init_db class TraitCollection(object): + + +class AnonCollection(TraitCollection): + + def __init__(self, anon_id) + self.anon_id = anon_id + self.collection_members = Redis.smembers(self.anon_id) + print("self.collection_members is:", self.collection_members) + self.num_members = len(self.collection_members) + + + @app.route("/collections/remove", methods=('POST',)) + def remove_traits(traits_to_remove): + print("traits_to_remove:", traits_to_remove) + for trait in traits_to_remove: + Redis.srem(self.anon_id, trait) + members_now = self.collection_members - traits_to_remove + print("members_now:", members_now) + print("Went from {} to {} members in set.".format(len(self.collection_members), len(members_now))) + + # We need to return something so we'll return this...maybe in the future + # we can use it to check the results + return str(len(members_now)) + + @property + def num_members(self): + print("members are:", json.loads(self.members)) + return len(json.loads(self.members)) + + #@property + #def display_num_members(self): + # return display_collapsible(self.num_members) + + def members_as_set(self): + return set(json.loads(self.members)) \ No newline at end of file diff --git a/wqflask/wqflask/my_pylmm/data/load_genotypes_lei.py b/wqflask/wqflask/my_pylmm/data/load_genotypes_lei.py new file mode 100644 index 00000000..e3144733 --- /dev/null +++ b/wqflask/wqflask/my_pylmm/data/load_genotypes_lei.py @@ -0,0 +1,181 @@ +""" +Do whatever else is needed with the Marker object +Probably create Genofile object as well +Make sure rest of code works with params object (though +everything in the params object should probably just be the parameters of +the Genofile object) + +Continue to rename variables in ways that make sense and to add underscores between words + +Look at genofile_parser.py that I (Zach) wrote a while back and how much of it can just be reused + +Get rid of/improve uninformative comments + +""" + + +from __future__ import absolute_import, print_function, division + +import sys +import re +import argparse + +import utilities +import datastructure + +def main(): + parser = argparse.ArgumentParser(description='Load Genotypes') + parser.add_argument('-c', '--config') + opts = parser.parse_args() + config = opts.config + # config + config = utilities.get_config(config) + print("config:") + for item in config.items('config'): + print("\t", str(item)) + parse_genofile(fetch_parameters(config)) + +def fetch_parameters(config): + # variables + params = {} + params['inbredsetid'] = config.get('config', 'inbredsetid') + species = datastructure.get_species(params['inbredsetid']) + params["speciesid"] = species[0] + genofreeze = datastructure.get_genofreeze_byinbredsetid(params['inbredsetid']) + params['genofreezeid'] = genofreeze[0] + params['dataid'] = datastructure.get_nextdataid_genotype() + params['genofile'] = config.get('config', 'genofile') + + return params + +def parse_genofile(params): + # genofile + with open(params['genofile']) as genofile: + meta_data = {} + print() + # parse genofile + for line in genofile: + line = line.strip() + if not line: + pass + elif line.startswith('#'): + pass + elif line.startswith('@'): + line = line.strip('@') + for item in line.split(';'): + kv = re.split(':|=', item) + meta_data[kv[0].strip()] = kv[1].strip() + + elif line.lower().startswith("chr"): + print("geno file meta:") + for key, value in meta_data.iteritems(): + print("\t{}: {}".format(key, value)) + print("geno file head:\n\t{}\n".format(line)) + strain_names = line.split()[4:] + strains = datastructure.get_strains_bynames(inbredsetid=inbredsetid, + strain_names=strain_names, + updatestrainxref="yes") + + else: + # geno file line + marker = Marker(line) + # + geno_id = check_or_insert_geno(params, marker) + + if check_genoxref(params): #Check if this can go earlier + continue + + insert_genodata(params) + insert_genoxref(params) + data_id += 1 + + +class Marker(object): + def __init__(self, line): + self.cells = line.split() + self.chromosome = cells[0] + self.locus = cells[1] + self.cm = cells[2] + self.mb = cells[3] + self.values = cells[4:] + +def check_or_insert_geno(params, marker): + cursor, con = utilities.get_cursor() + sql = """ + SELECT Geno.`Id` + FROM Geno + WHERE Geno.`SpeciesId`=%s + AND Geno.`Name` like %s + """ + cursor.execute(sql, (speciesid, locus)) #This is correct + result = cursor.fetchone() + if result: + geno_id = result[0] + print("get geno record: ", geno_id) + else: + sql = """ + INSERT INTO Geno + SET + Geno.`SpeciesId`=%s, + Geno.`Name`=%s, + Geno.`Marker_Name`=%s, + Geno.`Chr`=%s, + Geno.`Mb`=%s + """ + cursor.execute(sql, (species_id, locus, locus, chr, mb)) + row_count = cursor.rowcount + geno_id = con.insert_id() + print("INSERT INTO Geno: %d record: %d" % (row_count, geno_id)) + return geno_id + +def check_GenoXRef(): + sql = """ + select GenoXRef.* + from GenoXRef + where GenoXRef.`GenoFreezeId`=%s + AND GenoXRef.`GenoId`=%s + """ + cursor.execute(sql, (geno_freeze_id, geno_id)) + row_count = cursor.rowcount + return row_count + +def insert_genodata(): + for index, strain in enumerate(strains): + strain_id = strain[0] + value = utilities.to_db_string(values[index], None) + if not value: + continue + value = config.get('config', "genovalue_" + value) + try: + number = int(value) + except ValueError: + continue + if number not in [-1, 0, 1]: + continue + sql = """ + INSERT INTO GenoData + SET + GenoData.`Id`=%s, + GenoData.`StrainId`=%s, + GenoData.`value`=%s + """ + cursor.execute(sql, (dataid, strainid, number)) + +def insert_genoxref(): + sql = """ + INSERT INTO GenoXRef + SET + GenoXRef.`GenoFreezeId`=%s, + GenoXRef.`GenoId`=%s, + GenoXRef.`DataId`=%s, + GenoXRef.`cM`=%s, + GenoXRef.`Used_for_mapping`=%s + """ + cursor.execute(sql, (genofreezeid, genoid, dataid, cm, 'N')) + rowcount = cursor.rowcount + print("INSERT INTO GenoXRef: %d record" % (rowcount)) + +if __name__ == "__main__": + print("command line arguments:\n\t%s" % sys.argv) + main() + print("exit successfully") |