[Baypiggies] Fwd: manipulating lists question

Thu Dec 5 11:51:54 CET 2013

My solution works for the first three elements as stated, but what you do
with the rest of the elements is tricky if they differ for a given key.

For 1302 all the fields in the slice [3:] match each other *except*
element 28:
'1302:NM_080679.2:COL11A2:TSS-UPSTREAM:UNKNOWN-INC'
'1302:NM_080680.2:COL11A2:TSS-UPSTREAM:UNKNOWN-INC'

Does this potentially happen with other elements at times? At this point
you're faced with either discarding data or mangling data together. The
"collapse" just takes the last [3:] slice encountered (for that remainder
of data). Is that acceptable?

 - Marty

On Thu, December 5, 2013 02:33, Vikram K wrote:
> In the example i have given, the second and third elements of the larger
> list (comp[7] and comp[8]) have a 1:1 mapping after the second element. So
>  i would like to keep the first element as it is and then collapse or
> merge the second and third elements (comp[7] and comp[8]) into a single
> element:
>
>
>>>> comp[6]
> ['6558', 'NM_001046.2', 'SLC12A2', '6037226', '2', 'chr5', '127502453',
> '127502454', 'het-ref', 'snp', 'A', 'T', 'A', '185', '113', '184', '112',
> 'VQHIGH', 'VQHIGH', '', '', '', '', '259974', '9', '6', '6', '15',
> '6558:NM_001046.2:SLC12A2:CDS:MISSENSE',
> '6558:NM_001046.2:SLC12A2:CDS:NO-CHANGE', 'PFAM:PF01490:Aa_trans', '', '',
>  '', '0.99', '2', '0.99', '0.998', '1.01', '1.000', '0.5', '0.46', '0.5',
>  '1', '18', '18', '19', 'ref-identical;onlyA', 'snp', '0.072', '-1',
> 'SQHIGH']
>
>
>>>> comp[7]
> ['1302', 'NM_080679.2', 'COL11A2', '6525172', '2', 'chr6', '33271374',
> '33271376', 'het-ref', 'del', 'GT', '', 'GT', '542', '542', '458', '458',
> 'VQHIGH', 'VQHIGH', '', '', '', '', '71150', '34', '106', '106', '140',
> '1302:NM_080679.2:COL11A2:TSS-UPSTREAM:UNKNOWN-INC',
> '1302:NM_080679.2:COL11A2:TSS-UPSTREAM:UNKNOWN-INC;1302:NM_080680.2:COL11A
> 2:TSS-UPSTREAM:UNKNOWN-INC;1302:NM_080681.2:COL11A2:TSS-UPSTREAM:UNKNOWN-
> INC;6257:NM_021976.3:RXRB:CDS:NO-CHANGE',
> '', '', '', '', '0.95', '2', '0.98', '0.998', '0.99', '1.000', '0.46',
> '0.42', '0.5', '0', '102', '102', '102', 'ref-identical;onlyA', 'del',
> '0.990', '6', 'SQHIGH']
>
>
>>>> comp[8]
> ['1302', 'NM_080680.2', 'COL11A2', '6525172', '2', 'chr6', '33271374',
> '33271376', 'het-ref', 'del', 'GT', '', 'GT', '542', '542', '458', '458',
> 'VQHIGH', 'VQHIGH', '', '', '', '', '71150', '34', '106', '106', '140',
> '1302:NM_080680.2:COL11A2:TSS-UPSTREAM:UNKNOWN-INC',
> '1302:NM_080679.2:COL11A2:TSS-UPSTREAM:UNKNOWN-INC;1302:NM_080680.2:COL11A
> 2:TSS-UPSTREAM:UNKNOWN-INC;1302:NM_080681.2:COL11A2:TSS-UPSTREAM:UNKNOWN-
> INC;6257:NM_021976.3:RXRB:CDS:NO-CHANGE',
> '', '', '', '', '0.95', '2', '0.98', '0.998', '0.99', '1.000', '0.46',
> '0.42', '0.5', '0', '102', '102', '102', 'ref-identical;onlyA', 'del',
> '0.990', '6', 'SQHIGH']
>
>
> After collapsing comp[7] and comp[8] i  get:
>
>
>>>> collapsed = ['1302', 'NM_080679.2,NM_080680.2', 'COL11A2',
>>>> '6525172',
>>>>
> '2', 'chr6', '33271374', '33271376', 'het-ref', 'del', 'GT', '', 'GT',
> '542', '542', '458', '458', 'VQHIGH', 'VQHIGH', '', '', '', '', '71150',
> '34', '106', '106', '140',
> '1302:NM_080680.2:COL11A2:TSS-UPSTREAM:UNKNOWN-INC',
> '1302:NM_080679.2:COL11A2:TSS-UPSTREAM:UNKNOWN-INC;1302:NM_080680.2:COL11A
> 2:TSS-UPSTREAM:UNKNOWN-INC;1302:NM_080681.2:COL11A2:TSS-UPSTREAM:UNKNOWN-
> INC;6257:NM_021976.3:RXRB:CDS:NO-CHANGE',
> '', '', '', '', '0.95', '2', '0.98', '0.998', '0.99', '1.000', '0.46',
> '0.42', '0.5', '0', '102', '102', '102', 'ref-identical;onlyA', 'del',
> '0.990', '6', 'SQHIGH']
>
>
> So in my larger list, after the modification, comp[6] is the first
> element and collapsed the second element.
>>>>
>
>
> On Thu, Dec 5, 2013 at 5:22 AM, Martin Falatic <martin at falatic.com>
> wrote:
>
>
>> Ah, genetics! Intriguing...
>>
>>
>> Do you need anything beyond the third elements of each list? Does the
>> third element always map 1:1 with the first, or could it vary? If so,
>> what then?
>>
>> To refer to the simplified example, could you have this?
>> x = [['cat', 'NM123', 12], ['cat', 'NM234', 43], ['dog', 'NM56', 65]]
>>
>> If so, what is the expected output?
>>
>>
>> - Marty
>>
>>
>>
>>
>> On Thu, December 5, 2013 02:11, Vikram K wrote:
>>
>>> i am having some difficulty in applying this to my actual problem
>>> although i love the dictionary method. Imagine the following three
>>> lists are the first, second and third elements of a larger list:
>>>
>>>>>> comp[6]
>>> ['6558', 'NM_001046.2', 'SLC12A2', '6037226', '2', 'chr5',
>>> '127502453',
>>> '127502454', 'het-ref', 'snp', 'A', 'T', 'A', '185', '113', '184',
>>> '112',
>>> 'VQHIGH', 'VQHIGH', '', '', '', '', '259974', '9', '6', '6', '15',
>>> '6558:NM_001046.2:SLC12A2:CDS:MISSENSE',
>>> '6558:NM_001046.2:SLC12A2:CDS:NO-CHANGE', 'PFAM:PF01490:Aa_trans', '',
>>>
>> '',
>>
>>> '', '0.99', '2', '0.99', '0.998', '1.01', '1.000', '0.5', '0.46',
>>> '0.5',
>>> '1', '18', '18', '19', 'ref-identical;onlyA', 'snp', '0.072', '-1',
>>> 'SQHIGH']
>>>
>>>
>>>
>>>>>> comp[7]
>>> ['1302', 'NM_080679.2', 'COL11A2', '6525172', '2', 'chr6',
>>> '33271374',
>>> '33271376', 'het-ref', 'del', 'GT', '', 'GT', '542', '542', '458',
>>> '458',
>>> 'VQHIGH', 'VQHIGH', '', '', '', '', '71150', '34', '106', '106',
>>> '140',
>>> '1302:NM_080679.2:COL11A2:TSS-UPSTREAM:UNKNOWN-INC',
>>>
>>>
>> '1302:NM_080679.2:COL11A2:TSS-UPSTREAM:UNKNOWN-INC;1302:NM_080680.2:COL
>> 11A
>>
>>> 2:TSS-UPSTREAM:UNKNOWN-INC;1302:NM_080681.2:COL11A2:TSS-UPSTREAM:UNKN
>>> OWN-
>>> INC;6257:NM_021976.3:RXRB:CDS:NO-CHANGE',
>>> '', '', '', '', '0.95', '2', '0.98', '0.998', '0.99', '1.000', '0.46',
>>>  '0.42', '0.5', '0', '102', '102', '102', 'ref-identical;onlyA',
>>> 'del',
>>> '0.990', '6', 'SQHIGH']
>>>
>>>
>>>
>>>>>> comp[8]
>>> ['1302', 'NM_080680.2', 'COL11A2', '6525172', '2', 'chr6',
>>> '33271374',
>>> '33271376', 'het-ref', 'del', 'GT', '', 'GT', '542', '542', '458',
>>> '458',
>>> 'VQHIGH', 'VQHIGH', '', '', '', '', '71150', '34', '106', '106',
>>> '140',
>>> '1302:NM_080680.2:COL11A2:TSS-UPSTREAM:UNKNOWN-INC',
>>>
>>>
>> '1302:NM_080679.2:COL11A2:TSS-UPSTREAM:UNKNOWN-INC;1302:NM_080680.2:COL
>> 11A
>>
>>> 2:TSS-UPSTREAM:UNKNOWN-INC;1302:NM_080681.2:COL11A2:TSS-UPSTREAM:UNKN
>>> OWN-
>>> INC;6257:NM_021976.3:RXRB:CDS:NO-CHANGE',
>>> '', '', '', '', '0.95', '2', '0.98', '0.998', '0.99', '1.000', '0.46',
>>>  '0.42', '0.5', '0', '102', '102', '102', 'ref-identical;onlyA',
>>> 'del',
>>> '0.990', '6', 'SQHIGH']
>>>
>>>
>>>>>>
>>>
>>> ------
>>> Can we apply the dictionary method to the problem where the key of the
>>>  dictionary is the first element of the three smaller lists
>> ('6558','1302',
>>
>>> '1302'). The second and third elements of the larger list (starting
>>> with '1302') need to be collapsed into a single element, based on
>>> their second element ( 'NM_080679.2') and ('NM_080680.2') in a way
>>> similar to how we had tackled the toy problem:
>>>
>>> x = [['cat', 'NM123', 12], ['cat', 'NM234', 12], ['dog', 'NM56', 65]]
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Thu, Dec 5, 2013 at 4:18 AM, Michiel Overtoom <motoom at xs4all.nl>
>>> wrote:
>>>
>>>
>>>
>>>>
>>>> On Dec 5, 2013, at 10:09, Vikram K wrote:
>>>>
>>>>
>>>>
>>>>> another option could have been to obtain a dictionary like so:
>>>>> {'dog':
>>>>> ['NM56', 65], 'cat': ['NM123,NM234', 12]}
>>>>>
>>>>>
>>>>
>>>> Oh, in that case the code can become somewhat simpler:
>>>>
>>>>
>>>>
>>>> x = [['cat', 'NM123', 12], ['cat', 'NM234', 12], ['dog', 'NM56',
>>>> 65]]
>>>>
>>>>
>>>> d = {} for key, label, quant in x: if key in d: d[key][0] += ", " +
>>>>
>> label
>>>> else:
>>>> d[key] = [label, quant]
>>>>
>>>> print d
>>>>
>>>>
>>>> I agree with Michael that the problem is somewhat underspecified,
>>>> but it's a starting point.
>>>>
>>>> Greetings,
>>>>
>>>>
>>>>
>>>> --
>>>> "If you don't know, the thing to do is not to get scared, but to
>>>> learn." -
>>>> Ayn Rand
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
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>>
>>
>>
>