Dear All!
I have this elements
In [445]: pt = line.split("\t")[9]
In [446]: pt
Out[446]: 'gene_id "ENSG00000223972"; gene_version "5"; transcript_id
"ENST00000456328"; transcript_version "2"; exon_number "1"; gene_name
"DDX11L1"; gene_source "havana"; gene_biotype
"transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-002";
transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id
"ENSE00002234944"; exon_version "1"; tag "basic"; transcript_support_level
"1";\n'
and I want to create a dictionary like this
gene_id = "ENSG00000223972"; ...
I found on stack over flow this way to create a dictionary of dictionary
(http://stackoverflow.com/questions/8550912/python-dictionary-of-dictionaries)
# This is our sample data
data = [("Milter", "Miller", 4), ("Milter", "Miler", 4), ("Milter", "Malter",
2)]
# dictionary we want for the result
dictionary = {}
# loop that makes it work
for realName, falseName, position in data:
dictionary.setdefault(realName, {})[falseName] = position
I want to create a dictionary using setdefault but I have difficult to
trasform pt as list of tuple.
data = pt.split(";")
<ipython-input-456-300c276109c6> in <module>()
1 for i in data:
2 l = i.split()
----> 3 print l[0]
4
IndexError: list index out of range
In [457]: for i in data:
l = i.split()
print l
.....:
['gene_id', '"ENSG00000223972"']
['gene_version', '"5"']
['transcript_id', '"ENST00000456328"']
['transcript_version', '"2"']
['exon_number', '"1"']
['gene_name', '"DDX11L1"']
['gene_source', '"havana"']
['gene_biotype', '"transcribed_unprocessed_pseudogene"']
['transcript_name', '"DDX11L1-002"']
['transcript_source', '"havana"']
['transcript_biotype', '"processed_transcript"']
['exon_id', '"ENSE00002234944"']
['exon_version', '"1"']
['tag', '"basic"']
['transcript_support_level', '"1"']
[]
So how can do that more elegant way?
thanks so much!!
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