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Allow gene sequence retrieval from previous step
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@pablocarb
pablocarb committed Jan 21, 2020
1 parent cfbbc15 commit 02dd54d
Showing 1 changed file with 59 additions and 35 deletions.
94 changes: 59 additions & 35 deletions synbioParts.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,10 +49,17 @@ def doeGetSBOL(pfile='RefParts.csv', gfile='GeneParts.csv', libsize=32,
Perform the DoE and generate the SBOL file from the
parts and genes files
- RefParts.csv: Name, Type, Part
- GeneParts.csv: Name, Type, Part, Step
Type: origin, resistance, promoter, gene
Name: part name
Type: origin, resistance, promoter, gene
Part: SynBioHub URI
- GeneParts.csv: Name, Type, Part, Step, Sequence
Name: gene name
Type: gene
Step: Enzyme step in the pathway (eventually could be implemented
for the other genetic parts)
for the other genetic parts)
Part: identifier (UniProt, etc) or SynBioHub URI
Sequence: gene sequence (optional: if not given they are retrieved
from UniProt or SynBioHub)
"""
parts = pd.read_csv(pfile)
genes = pd.read_csv(gfile)
Expand Down Expand Up @@ -85,7 +92,8 @@ def _defineParts(doc,parts,getSequences=True,backtranslate=True,codontable='Eeco
""" Parts is a dataframe containing columns: Name, Type, Part is read
and each part in added to the SBOL doc.
Part type should is overriden by the ontology definition in the registry.
If sequences should be provided, select if backtranslate and provide codon table:
If sequences should be provided in the SBOL doc, check if they are on the parts table
or select if backtranslate from UniProt and provide codon table:
(Eecoli.cut, Eyeast.cut, etc) See https://www.ebi.ac.uk/Tools/st/emboss_backtranseq/ """

sboldef = {'promoter': sbol.SO_PROMOTER, 'gene': sbol.SO_CDS,
Expand Down Expand Up @@ -141,41 +149,49 @@ def _defineParts(doc,parts,getSequences=True,backtranslate=True,codontable='Eeco
doc.addComponentDefinition(origin)
elif ptype == 'gene' or ptype == 'resistance':
if getSequences:
# try to get the part from the repository by its URI, if given
try:
repo.pull(part,doc)
origin = doc.getComponentDefinition(part)
except:
# if failed, retrieve the amino acid sequence from Uniprot and backtranslate using EMBOSS web service
# Get from the Sequence column if given (assume naseq)
if 'Sequence' in parts and not pd.isnan( parts.loc[i,'Sequence'] ):
seq = parts.loc[i,'Sequence']
seqdef = sbol.Sequence( name, seq, 'https://www.qmul.ac.uk/sbcs/iubmb/misc/naseq.html' )
origin = sbol.ComponentDefinition(name)
origin.sequence = seqdef
else:
# try to get the part from the repository by its URI, if given
try:
query = 'https://www.uniprot.org/uniprot/' + name + '.fasta'
response = requests.get(query)
if backtranslate:
resp = requests.post( 'https://www.ebi.ac.uk/Tools/services/rest/emboss_backtranseq/run',
{'email': '@'.join(['pablo.carbonell','manchester.ac.uk']), 'title':'OpBioDes SBOL',
'codontable': codontable, 'sequence': response.text} )
jobid = resp.text
status = 'RUNNING'
while status == 'RUNNING':
resp1 = requests.get('https://www.ebi.ac.uk/Tools/services/rest/emboss_backtranseq/status/'+jobid)
status = resp1.text
time.sleep(0.1)
if status == 'FINISHED':
resp2 = requests.get('https://www.ebi.ac.uk/Tools/services/rest/emboss_backtranseq/result/'+jobid+'/out')
seq = ''.join( resp2.text.split('\n')[1:] )
seqdef = sbol.Sequence( name, seq, 'https://www.qmul.ac.uk/sbcs/iubmb/misc/naseq.html' )
repo.pull(part,doc)
origin = doc.getComponentDefinition(part)
except:
# if failed, retrieve the amino acid sequence from Uniprot and backtranslate using EMBOSS web service
try:
query = 'https://www.uniprot.org/uniprot/' + name + '.fasta'
response = requests.get(query)
if backtranslate:
resp = requests.post( 'https://www.ebi.ac.uk/Tools/services/rest/emboss_backtranseq/run',
{'email': '@'.join(['pablo.carbonell','manchester.ac.uk']), 'title':'OptBioDes SBOL',
'codontable': codontable, 'sequence': response.text} )
jobid = resp.text
status = 'RUNNING'
while status == 'RUNNING':
resp1 = requests.get('https://www.ebi.ac.uk/Tools/services/rest/emboss_backtranseq/status/'+jobid)
status = resp1.text
time.sleep(0.1)
if status == 'FINISHED':
resp2 = requests.get('https://www.ebi.ac.uk/Tools/services/rest/emboss_backtranseq/result/'+jobid+'/out')
seq = ''.join( resp2.text.split('\n')[1:] )
seqdef = sbol.Sequence( name, seq, 'https://www.qmul.ac.uk/sbcs/iubmb/misc/naseq.html' )
else:
seq = ''.join( response.text.split('\n')[1:] )
seqdef = sbol.Sequence( name, seq, 'https://www.qmul.ac.uk/sbcs/iupac/AminoAcid/' )
else:
seq = ''.join( response.text.split('\n')[1:] )
seq = ''.join( response.text.split('\n')[1:] )
seqdef = sbol.Sequence( name, seq, 'https://www.qmul.ac.uk/sbcs/iupac/AminoAcid/' )
else:
seq = ''.join( response.text.split('\n')[1:] )
seqdef = sbol.Sequence( name, seq, 'https://www.qmul.ac.uk/sbcs/iupac/AminoAcid/' )
origin = sbol.ComponentDefinition(name)
origin.sequence = seqdef
except:
origin = sbol.ComponentDefinition(name)
origin = sbol.ComponentDefinition(name)
origin.sequence = seqdef
# If UniProt/EMBOSS was not succesful, leave the sequence empty
except:
origin = sbol.ComponentDefinition(name)
else:
origin = sbol.ComponentDefinition(name)
origin = sbol.ComponentDefinition(name)
origin.roles = sboldef[ptype]
origin.setPropertyValue('http://purl.org/dc/terms/description',part)
origin.name = name
Expand Down Expand Up @@ -252,6 +268,14 @@ def getTheDoe(parts, genes,size=32):


def getSBOL(parts,genes,cons,getSequences=True,backtranslate=True,codontable='Eecoli.cut'):
"""
parts: df with parts (see doeGetSBOL)
genes: df with genes (see doeGetSBOL)
cons: library of constructs generated by the DoE
getSequences: retrieve sequences if not available in the gene list
backtranslate: back translate protein sequences if not given
codontable: only required for back translation
"""
dic = {}
for p in parts.index:
dic[parts.loc[p,'Name']] = parts.loc[p,'Part']
Expand Down

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