[Tutor] Mapping elements in various lists - walking over lists and their elements

[Srinivas Iyyer]

Dear Tutors,
I have a huge string and 2 lists.  List A consists of
tabed elements, where first tab represents entry
somewhere in string(ndat).
ndat has 'Contig27915_RC' and List A [nbat]has
'Contig27915_RC\tXM_945977'.  List B [nmlist]has
elements, for instance ['XM_945977\tNM_152513'].  Now
my task, is to take each element in nbat(listA) search
in string ndat and nmlist, if found in nmlist, replace
with its tabed counterpart in ndat string.

How did I choose to solve:
1. I could not think in the most smartest way as said
easily above. Say take element from nbat, see if
modified version of it
 available in nmlist, if found replace that modifed
element in string.

So I chose to take element from listA (nbat), search
in string ndat. If found replace with it tabed
element(Contig27915_RC\tXM_945977 => XM_945977) and
store that in a new list.  Now loop over this new list
for each element check if a new version available in
nmlist. If so replace and print.

One of the proble is that, Contig27915_RC is seen
associated with many XM entries in nbat.  However,
with the above script I could replace only once in
xta. I could not print Contig27915_RC with many XM_
guys in nbat. How can this be done.

Finally, this whole process seems to be more
cumbersome to me. Could any one tip me with a new way
of dealing this 3 way mapping.

Thanks

Script:

xt = ''
for m in nbat:
        cols = m.split('\t')
        old = cols[0]
        new = cols[1]
        if ndat.find(old):
                xt = ndat.replace(old,new)

xta = xt.split('\n')
>>> for x in xta:
...         for m in nmlist:
...                 cols = m.split('\t')
...                 colold = cols[0]
...                 colnew = cols[1]
...                 if x == colold:
...                         print x+'\t'+colnew
...
XM_945977       NM_152513


-XTA result --- snip---
Contig25622_RC
Contig13475_RC
Contig40179_RC
XM_945977  <- <- <- ['Contig27915_RC\tXM_945977']
Contig44682_RC
Contig35934_RC
--------------






ndat =
"""Pro25G\nvariant_gridline\nG3PDH_570\nPro25G_onG3PDH570_20bp\nPro25G_onG3PDH570_10Ts\nr60_1\nr60_3\nr60_n9\nr60_a22\nr60_a104\nr60_a107\nr60_a135\nr60_a97\nr60_a20\nr60_n11\nContig45645_RC\nContig44916_RC\nD25272\nJ00129\nContig29982_RC\nContig26811\nD25274\nContig36292\nContig42854\nContig34839\nContig8376_RC\nContig42014_RC\nD49958\nContig25622_RC\nContig13475_RC\nContig40179_RC\nContig27915_RC\nContig44682_RC\nContig35934_RC\nContig29373_RC\nAF155648\nContig46975_RCx"""


nbat = ['Contig45645_RC\tNM_022469',
'Contig44916_RC\tNM_080764', 'J00129\tNM_005141',
'Contig29982_RC\tNM_173833', 'D25274\tNM_006908',
'D25274\tNM_018890', 'D25274\tNM_198829',
'D49958\tNM_201591', 'D49958\tNM_005277',
'D49958\tNM_201592', 'Contig13475_RC\tNM_212555',
'Contig40179_RC\tNM_138570',
'Contig27915_RC\tXM_934912',
'Contig27915_RC\tXM_934911',
'Contig27915_RC\tXM_934908',
'Contig27915_RC\tXM_934906',
'Contig27915_RC\tXM_934902',
'Contig27915_RC\tXM_934901',
'Contig27915_RC\tXM_934899',
'Contig27915_RC\tXM_934897',
'Contig27915_RC\tXM_934896',
'Contig27915_RC\tXM_945989',
'Contig27915_RC\tXM_945987',
'Contig27915_RC\tXM_945986',
'Contig27915_RC\tXM_945985',
'Contig27915_RC\tXM_945983',
'Contig27915_RC\tXM_945982',
'Contig27915_RC\tXM_945980',
'Contig27915_RC\tXM_945978',
'Contig27915_RC\tXM_945977']

nmlist = ['XM_929405\tNM_001039615',
'XM_934896\tNM_152513', 'XM_934897\tNM_152513',
'XM_934899\tNM_152513', 'XM_934901\tNM_152513',
'XM_934902\tNM_152513', 'XM_934904\tNM_152513',
'XM_934906\tNM_152513', 'XM_934908\tNM_152513',
'XM_934911\tNM_152513', 'XM_934912\tNM_152513',
'XM_945977\tNM_152513', 'XM_945978\tNM_152513',
'XM_945980\tNM_152513', 'XM_945982\tNM_152513',
'XM_945983\tNM_152513', 'XM_945984\tNM_152513',
'XM_945985\tNM_152513', 'XM_945986\tNM_152513',
'XM_945987\tNM_152513', 'XM_945989\tNM_152513',
'XM_085261\tNM_001039958', 'XM_938609\tNM_001039958',
'XM_373868\tNM_001009931', 'NM_001012239\tNM_173683',
'XM_929314\tNM_001609', 'XM_940521\tNM_001609',
'XM_932741\tNM_001262', 'XM_945305\tNM_001262',
'XM_928890\tNM_152830']



__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com