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#!/usr/bin/python3
'''
:py:mod:`obitab`: converts a sequence file to a tabular file
============================================================
.. codeauthor:: Eric Coissac <eric.coissac@metabarcoding.org>
:py:mod:`obitab` command converts sequence file to a tabular file that
can be open by a spreadsheet program or R.
'''
from obitools.options import getOptionManager
from obitools.format.options import addInOutputOption
def addTableOptions(optionManager):
optionManager.add_option('-n','--na-string',
action="store", dest="NA",
metavar="<NOT AVAILABLE STRING>",
type="string",
default="NA",
help="String write in the table for not available value"
)
optionManager.add_option('','--output-field-separator',
action="store", dest="ofs",
metavar="STRING",
type="string",
default="\t",
help="Field separator for CSV file"
)
optionManager.add_option('-o','--output-seq',
action="store_true", dest="sequence",
default=False,
help="Add an extra column for sequence"
)
optionManager.add_option('-d','--no-definition',
action="store_false", dest="definition",
default=True,
help="Remove column for sequence definition"
)
optionManager.add_option('-a','--omit-attribute',
action="append", dest="omit",
metavar="<KEY>",
default=[],
help="Add attribute name to omit in the output tab"
)
def headerCmp(h1,h2):
if type(h1) is str and type(h2) is str:
return cmp(h1, h2)
if type(h1) is str and type(h2) is tuple:
return cmp(h1, h2[0])
if type(h1) is tuple and type(h2) is str:
return cmp(h1[0], h2)
if type(h1) is tuple and type(h2) is tuple:
c = cmp(h1[0],h2[0])
if c==0:
c = cmp(h1[1],h2[1])
return c
raise AssertionError
if __name__=='__main__':
optionParser = getOptionManager([addTableOptions,addInOutputOption])
(options, entries) = optionParser()
column = {}
subcol = {}
db = []
for seq in entries:
db.append(seq)
keys = list(seq.keys())
for k in keys:
t=type(seq[k])
if k in column:
column[k].add(t)
else:
column[k]=set([t])
if t is dict:
if k not in subcol:
subcol[k]=set()
subcol[k]|=set(seq[k].keys())
headers = set()
for c in column:
if len(column[c])==1:
column[c]=column[c].pop()
else:
column[c]=str
if column[c] not in (str,int,float,dict,bool):
column[c]=str
if column[c] is not dict:
headers.add(c)
else:
for sc in subcol[c]:
headers.add((c,sc))
omit = set(options.omit)
headers=list(headers)
headers.sort(headerCmp)
OFS = options.ofs
s = "id"
if options.definition:
s = '%s%sdefinition'%(s,OFS)
for k in headers:
if type(k) is str:
if k not in omit:
s = '%s%s%s'%(s,OFS,k)
else:
if k[0] not in omit:
if type(k[1]) is tuple:
sk = ":".join([str(x) for x in k[1]])
else:
sk = str(k[1])
if k[0][0:7]=='merged_':
s = '%s%s%s:%s' % (s,OFS,k[0][7:],sk)
else:
s = '%s%s%s:%s' % (s,OFS,k[0],sk)
if options.sequence:
s = "%s%ssequence"%(s,OFS)
print(s)
for seq in db:
s = seq.id
if options.definition:
s = '%s%s%s'%(s,OFS,seq.definition)
for k in headers:
if type(k) is str:
if k not in omit:
if k in seq:
v = seq[k]
if v is None:
v=options.NA
s = '%s%s%s'%(s,OFS,v)
else:
s = '%s%s%s'%(s,OFS,options.NA)
else:
if k[0] not in omit:
if k[0] in seq:
sk = seq[k[0]]
else:
sk={}
if k[1] in sk:
v = sk[k[1]]
if v is None:
v=options.NA
s = '%s%s%s'%(s,OFS,v)
else:
if k[0][0:7]=='merged_':
s = '%s%s0'%(s,OFS)
else:
s = '%s%s%s'%(s,OFS,options.NA)
if options.sequence:
s = '%s%s%s'%(s,OFS,str(seq))
print(s)
|
