def dGenomeExport(project):
# Is there something to be exported?
organism = Organism(project)
if organism.howMany() == 0:
logger.info('No genomic data can be exported at this time')
return False
else:
logger.info('Exporting protein data')
genome = Genome(project)
for org in organism.getAll():
nprots = SeqIO.write([x for x in genome.getRecords(org.org_id)],
open('%s.faa'%org.org_id,'w'), 'fasta')
logger.info('Saved %d proteins from %s (%s)'%(nprots,
org.org_id,
'%s.faa'%org.org_id))
logger.info('Exporting Kegg data')
logger.info('Exporting KO map data')
kegg = Kegg(project)
for org in organism.getAll():
fname = 'ko_%s.tsv'%org.org_id
fout = open(fname,'w')
i = 0
for prot_id, ko_id in kegg.getAllKO(org.org_id):
fout.write('%s\t%s\n'%(prot_id, ko_id.lstrip('ko:')))
i += 1
fout.close()
if i == 0:
os.remove(fname)
logger.warning('No KO links available for %s'%org.org_id)
else:
logger.info('Saved %d KO links for %s (%s)'%(i, org.org_id,
fname))
logger.info('Exporting Kegg reactions data')
for org in organism.getAll():
fname = 'reactions_%s.tsv'%org.org_id
fout = open(fname,'w')
i = 0
for prot_id, re_id in kegg.getAllReactions(org.org_id):
fout.write('%s\t%s\n'%(prot_id, re_id.lstrip('rn:')))
i += 1
fout.close()
if i == 0:
os.remove(fname)
logger.warning('No Kegg reactions available for %s'%org.org_id)
else:
logger.info('Saved %d Kegg reactions links for %s (%s)'%
(i, org.org_id, fname))
proj = Project(project)
if proj.isPanGenome():
logger.info('Exporting pangenome data')
dG = genome.getPanGenome()
if len(dG) == 0:
logger.warning('No pangenome available')
else:
fname = 'pangenome.tsv'
fout = open(fname,'w')
for group, prots in dG.iteritems():
for prot in prots:
fout.write('%s\t%s\n'%(group,prot))
fout.close()
logger.info('Exported %d orthologs (%s)'%(len(dG),fname))
fname = 'pangenome_category.tsv'
fout = open(fname,'w')
dG = genome.getPanGenomeOrgs()
for group in genome.getCore():
fout.write('%s\t%s\t%s\n'%(group.group_id,
'core',
'-'.join(dG[group.group_id])))
for group in genome.getAcc():
fout.write('%s\t%s\t%s\n'%(group.group_id,
'accessory',
'-'.join(dG[group.group_id])))
for group in genome.getUni():
fout.write('%s\t%s\t%s\n'%(group.group_id,
'unique',
'-'.join(dG[group.group_id])))
fout.close()
logger.info('Exported orthologs informations (%s)'%fname)
return True
