def process_overhangs(repo, project, overhangs_file, instanceid, authorid,
date):
with open(overhangs_file) as file:
inputlines = file.readlines()
validate_input_file(inputlines[0], overhangs_file)
if len(inputlines) <= 1:
return
collections = {}
collections['authorid'] = authorid
collections['datecreated'] = date
collections['description'] = 'Overhangs described in ' + instanceid
collections['name'] = 'overhang-' + instanceid
collectionid = uuid.uuid4()
collections['idcollection'] = collectionid
repo['collections'].append(collections)
repository.add_object_to_collection(repo, collectionid,
project['idcollection'], 'COLLECTION',
authorid, date)
for line in inputlines:
if ',' not in line:
continue
tokens = line.split(',')
featurename = 'overhang-' + tokens[0]
featuresequence = tokens[1].lower()
featureid = repository.create_feature(repo, featurename,
featuresequence, 'overhang',
date)
repository.add_object_to_collection(repo, collectionid, featureid,
'FEATURE', authorid, date)
def add_new_family_to_all_collections(repo, partfamily, allcollections, project, instanceid, authorid, date):
family = {}
family['name'] = partfamily
family['idfamily'] = partfamily
repo['families'].append(family)
collection = {}
collection['authorid'] = authorid
collection['datecreated'] = date
collection['description'] = 'Parts of ' + partfamily+ ' family described in ' + instanceid
collection['name'] = partfamily + '-part-' + instanceid
collectionid = uuid.uuid4()
collection['idcollection'] = collectionid
repo['collections'].append(collection)
allcollections[partfamily] = collection
repository.add_object_to_collection(repo, project['idcollection'], collection['idcollection'], 'COLLECTION', authorid, date)
def create_collections_by_family(repo, project, instanceid, authorid, date):
allcollections = {}
families = repo['families']
for fam in families:
famname = fam['name']
collection = {}
collection['authorid'] = authorid
collection['datecreated'] = date
collection['description'] = 'Parts of ' + famname + ' family described in ' + instanceid
collection['name'] = famname + '-part-' + instanceid
collectionid = uuid.uuid4()
collection['idcollection'] = collectionid
repo['collections'].append(collection)
allcollections[famname] = collection
repository.add_object_to_collection(repo, project['idcollection'], collection['idcollection'], 'COLLECTION', authorid, date)
return allcollections
def process_plasmids(repo, project, plasmidsfiles, directories, instanceid,
authorid, date):
for plasmidsfile in plasmidsfiles:
with open(plasmidsfile) as file:
lines = file.readlines()
validate_input_file(lines[0], plasmidsfile)
if len(lines) <= 1:
continue
plasmids = {}
plasmids['authorid'] = authorid
plasmids['datecreated'] = date
plasmids['description'] = 'Parts described in ' + instanceid
plasmids['name'] = 'part-' + instanceid
collectionid = uuid.uuid4()
plasmids['idcollection'] = collectionid
repo['collections'].append(plasmids)
# Create dict of 'family name : collection dict'
allcollections = create_collections_by_family(repo, project,
instanceid, authorid,
date)
lineno = 1
for line in lines[1:]:
tokens = line.split(',')
tokens = [t.strip() for t in tokens if len(t.strip()) > 0]
if len(tokens) < 4:
raise ValueError(
'The plasmids.csv file does not comply with the format.'
'Line ', lineno, ' has ', len(tokens),
' tokens, but should have at least 4.')
plasmidfilename = tokens[0]
partfamily = tokens[1].lower()
partname = 'Part-' + tokens[2]
vectorname = 'Vector-' + tokens[3]
if len(tokens) > 4:
description = tokens[4]
else:
description = 'From ' + plasmidfilename + ' part ' + partname + ' vector ' \
+ vectorname + ' of type ' + partfamily + '.'
directories = [d for d in directories if os.path.isdir(d)]
for directory in directories:
files = os.listdir(directory)
if plasmidfilename in files:
plasmidsequence = read_genbank_file(directory + '/' +
plasmidfilename)
break
if not plasmidsequence:
raise ValueError('Could not retrieve plasmid sequence.')
partsequence = get_part_sequence(repo, plasmidsequence, vectorname)
part = repository.persist_part(repo, partname, partsequence,
description, True, authorid, date)
persist_part_overhang_annotations(repo, vectorname, part, authorid,
date)
persist_part_feature(repo, vectorname, part, partfamily, authorid,
date)
repository.add_object_to_collection(repo, collectionid,
part['idpart'], 'PART',
authorid, date)
# TODO - I add new families, instead of raising an error. See Java line 702+
if partfamily.lower() not in allcollections:
add_new_family_to_all_collections(repo, partfamily,
allcollections, project,
instanceid, authorid, date)
repository.add_object_to_collection(
repo, allcollections[partfamily]['idcollection'],
part['idpart'], 'PART', authorid, date)
vector = [
v for v in repo['vectors']
if v['name'].lower() == vectorname.lower()
][0]
repository.persist_plasmid(repo, 'PLASMID-' + tokens[2], part,
vector, authorid, date)
lineno += 1
def process_vectors(repo, project, vectorsfiles, directories, instanceid,
authorid, date):
for vectorsfile in vectorsfiles:
with open(vectorsfile) as file:
lines = file.readlines()
validate_input_file(lines[0], vectorsfile)
if len(lines) <= 1:
continue
vectors = {}
vectors['authorid'] = authorid
vectors['datecreated'] = date
vectors['description'] = 'Vectors described in ' + instanceid
collectionid = uuid.uuid4()
vectors['idcollection'] = collectionid
repo['collections'].append(vectors)
repository.add_object_to_collection(repo, project['idcollection'],
vectors['idcollection'],
'COLLECTION', authorid, date)
lineno = 0
for line in lines[1:]:
tokens = line.split(',')
tokens = [t.strip() for t in tokens if len(t.strip()) > 0]
if len(tokens) < 5:
raise ValueError(
'The Values.csv file does not have the required number of tokens on line '
+ lineno)
vectorfilename = tokens[0]
vectorname = 'Vector-' + tokens[1]
resistancename = 'Resistance-' + tokens[2]
fiveprimeoverhangname = 'Overhang-' + tokens[3]
threeprimeoverhangname = 'Overhang-' + tokens[4]
if len(tokens) > 5:
description = tokens[5]
else:
description = 'From ' + vectorfilename + ': ' + \
fiveprimeoverhangname + ', ' + \
threeprimeoverhangname + ', ' + resistancename
directories = [d for d in directories if os.path.isdir(d)]
for directory in directories:
files = os.listdir(directory)
if vectorfilename in files:
vectorsequence = read_genbank_file(directory + '/' +
vectorfilename)
break
vector = {}
vector['authorid'] = authorid
vector['datecreated'] = date
vector['description'] = description
vector['name'] = vectorname
vectorid = uuid.uuid4()
vector['idvector'] = vectorid
nucseq = {}
nucseq['datecreated'] = date
nucseq['idnucseq'] = vectorid
nucseq['sequence'] = vectorsequence
vector['nucseq'] = nucseq
vector['iscircular'] = True
repo['nucseq'].append(nucseq)
repo['vectors'].append(vector)
ft2 = {}
foundfeature1 = False
foundfeature2 = False
overhangfeatures = repository.get_features_by_family_name(
repo, 'overhang')
for feature in overhangfeatures:
if not foundfeature1 and feature['name'].upper(
) == fiveprimeoverhangname.upper():
position = repository.get_overhang_position_in_vector(
vectorsequence, feature['nucseq']['sequence'])
repository.add_feature_to_nucseq(repo, vectorname, nucseq,
feature, position,
authorid, date)
foundfeature1 = True
if not foundfeature2 and feature['name'].upper(
) == threeprimeoverhangname.upper():
position = repository.get_overhang_position_in_vector(
vectorsequence, feature['nucseq']['sequence'])
repository.add_feature_to_nucseq(repo, vectorname, nucseq,
feature, position,
authorid, date)
ft2 = feature
foundfeature2 = True
if not foundfeature1 or not foundfeature2:
raise ValueError(
'The overhangs caused by vector ' + vectorname +
' were not defined in the overhangs manifest.')
foundfeature = False
for feature in repository.get_features_by_family_name(
repo, 'resistance'):
if feature['name'].upper() == resistancename.upper():
position = nucseq['sequence'].find(
feature['nucseq']['sequence'])
repository.add_feature_to_nucseq(repo, vectorname, nucseq,
feature, position,
authorid, date)
foundfeature = True
if not foundfeature:
overhangpos = repository.get_overhang_position_in_vector(
vectorsequence, ft2['nucseq']['sequence'])
if overhangpos < 0:
raise ValueError('The overhang ' + ft2['name'] +
' could not be found in the vector ' +
vectorname)
startpos = overhangpos + len(ft2['nucseq']['sequence']) + 1
resistancesequence = nucseq['sequence'][
startpos:len(nucseq['sequence'])]
f = repository.create_feature(repo, resistancename,
resistancesequence, 'resistance',
date)
position = nucseq['sequence'].find(f['nucseq']['sequence'])
repository.add_feature_to_nucseq(repo, vectorname, nucseq, f,
position, authorid, date)
repository.add_object_to_collection(repo, collectionid,
f['idfeature'], 'FEATURE',
authorid, date)
repository.add_object_to_collection(repo, collectionid, vectorid,
'VECTOR', authorid, date)
lineno += 1