Skip to content

PTV-1860: Update Assembly ID to display refs. #13

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
dakotablair wants to merge 3 commits into
base: master
Choose a base branch
from
+41 −41
Open

PTV-1860: Update Assembly ID to display refs. #13

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
66c90b1
Updated report to include assembly ref.
dakotablair Apr 8, 2025
8b8367a
Fixed whitespace, enabled assembly_set test.
dakotablair Apr 10, 2025
bf98d13
Fix columns.
dakotablair Apr 10, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions kbase.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,8 +8,8 @@ service-language:
python

module-version:
1.2.2
1.2.3

owners:
[landml]
[dakota, landml]

60 changes: 30 additions & 30 deletions lib/kb_ObjectInfo/CreateAssemblyReport.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,11 +10,11 @@ def __init__(self, config):
self.callback_url = os.environ['SDK_CALLBACK_URL']
self.dfu = DataFileUtil(self.callback_url)


def assembly_overview(self,obj_list):
header = "OVERVIEW"
this_list = [["Assembly Name","Type","Assembly Type"]]

for assembly in obj_list['data']:
name = "Assembly Data Object"
type_assem = ''
Expand All @@ -26,25 +26,26 @@ def assembly_overview(self,obj_list):
type_assem = assembly['data']['type']

this_list.extend([[name,object_type,type_assem]])

return (header,this_list)

def assembly_metadata(self,obj_list):
header = "METADATA"
this_list = [['Assembly Name','Assembly ID', 'DNA size', 'GC content', 'Number contigs',
'FastA handle reference', 'MD5', 'Type', 'Taxon reference','Original filename']]
list = ['assembly_id', 'dna_size', 'gc_content', 'num_contigs',

items = ['dna_size', 'gc_content', 'num_contigs',
'fasta_handle_ref', 'md5', 'type', 'taxon_ref']


# DataFileUtil guarantees that 'info' contains object_info:
# https://github.com/kbaseapps/DataFileUtil/blob/master/DataFileUtil.spec#L499-L506
for assembly in obj_list['data']:
name = "Assembly Data Object"
if 'info' in assembly:
name = assembly['info'][1]
name = assembly['info'][1]
ref = f"{assembly['info'][6]}/{assembly['info'][0]}/{assembly['info'][4]}"

# Create the row for the one assembly
assem_list = [name]
for item in list:
assem_list = [name, ref]
for item in items:
if item in assembly['data']:
assem_list.append(str(assembly['data'][item]))
else:
Expand All @@ -54,18 +55,18 @@ def assembly_metadata(self,obj_list):
assem_list.append(assembly['data']['fasta_handle_info']['node_file_name'])
else:
assem_list.append(" ")

# Add the row to the list that will be returned
this_list.extend([assem_list])

return (header,this_list)

def assembly_dnabases(self,obj_list):
header = "DNA Composition"
this_list = [["Assembly Name","Total DNA Bases",
"A Count","A Percent","C Count","C Percent",
"G Count","G Percent","T Count","T Percent"]]

for assembly in obj_list['data']:
name = "Assembly Data Object"
if 'info' in assembly:
Expand All @@ -74,49 +75,49 @@ def assembly_dnabases(self,obj_list):
pct = 1.00
if 'dna_size' in assembly['data']:
dna_size = assembly['data']['dna_size']

assem_list = [name,str(dna_size)]
for base in ["A","C","G","T"]:
pct = round(100 * assembly['data']['base_counts'][base] / dna_size,2)
assem_list.append(str(assembly['data']['base_counts'][base]))
assem_list.append(str(pct))

this_list.extend([assem_list])

return(header,this_list)

def assembly_contigs(self,obj_list):
header = "Contigs in the Assembly"
this_list= [["Assembly Name","Contig Name","Length","GC content","Number of Ns","Contig ID","Description"]]

for assembly in obj_list['data']:
name = "Assembly Data Object"
if 'info' in assembly:
name = assembly['info'][1]

if 'contigs' in assembly['data']:
myContig = assembly['data']['contigs']
for ctg in myContig:
list = ['length', 'gc_content', 'Ncount', 'contig_id', 'description']
ctg_list = [name,ctg]

for item in list:
if item in myContig[ctg]:
ctg_list.append(format(myContig[ctg][item]))
else:
ctg_list.append("")

this_list.append(ctg_list)

return(header,this_list)


def assembly_dna(self,obj_list,scratch):
header = "Contig FastA files found in the download files."
fasta_list = []
dna_string = ""
cf = CreateFasta(self.config)

for assembly in obj_list['data']:
name = "Assembly Data Object"
input_ref = ''
Expand All @@ -126,14 +127,13 @@ def assembly_dna(self,obj_list,scratch):

fasta_list = cf.get_assembly_sequence(input_ref)
report_path = os.path.join(scratch, name + '.fna')

# Write the DNA string out to a Fasta file
report_txt = open(report_path, "w")
for dna_seq in fasta_list:
dna = "\n".join(dna_seq)+"\n"
report_txt.write(dna)
dna_string += dna
report_txt.close()

return(header)

18 changes: 9 additions & 9 deletions test/kb_ObjectInfo_test.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -82,7 +82,7 @@ def setUpClass(cls):
"generate_ids_if_needed": 1,
"generate_missing_genes": 1
})['genome_ref']

# Prepare the Genome from gbff File
cls.genbank_file_name = 'Carsonella_ruddii_HT_isolate_Thao2000.gbff'
# Set the path to file in scratch
Expand Down Expand Up @@ -251,9 +251,9 @@ def mytest_assembly_metadata(self):
self.assertIn('report_name', ret[0])
self.assertIn('report_ref', ret[0])
pass
def mytest_assembly_set(self):
assemblyset_ref = '69870/28/2'

def test_assembly_set(self):
assemblyset_ref = '72131/16/1'
ret = self.getImpl().assemblyset_report(self.getContext(),
{'workspace_name': self.ws_info[1],
'input_ref': assemblyset_ref,
Expand All @@ -264,7 +264,7 @@ def mytest_assembly_set(self):
self.assertIn('report_name', ret[0])
self.assertIn('report_ref', ret[0])
pass

def mytest_genome_protein_list(self):
genome_ref = self.genome_ref
genome_ref = '40843/4/1'
Expand All @@ -281,7 +281,7 @@ def mytest_genome_protein_list(self):
self.assertIn('report_name', ret[0])
self.assertIn('report_ref', ret[0])
pass

def mytest_genome_protein_fasta(self):
ret = self.getImpl().genome_report(self.getContext(),
{'workspace_name': self.ws_info[1],
Expand Down Expand Up @@ -394,7 +394,7 @@ def mytest_featureSet_unordered(self):
self.assertIn('report_name', ret[0])
self.assertIn('report_ref', ret[0])
pass

def mytest_sequenceSet(self):
featset_ref = '27092/23/1'
ret = self.getImpl().featseq_report(self.getContext(),
Expand All @@ -405,7 +405,7 @@ def mytest_sequenceSet(self):
self.assertIn('report_name', ret[0])
self.assertIn('report_ref', ret[0])
pass

def mytest_ProtComp(self):
protcomp_ref = '29939/15/1'
ret = self.getImpl().protcomp_report(self.getContext(),
Expand All @@ -428,7 +428,7 @@ def mytest_genomeComp(self):
self.assertIn('report_name', ret[0])
self.assertIn('report_ref', ret[0])
pass

def mytest_MSA(self):
msa_ref = '70362/27/1'
ret = self.getImpl().msa_report(self.getContext(),
Expand Down