Sorry for the very long email. and I my brain is dead
to create some related generic snippet. Thus, I shrunk
the string and lists into as short as I could.
apologies again.
srini
--- Srinivas Iyyer <[EMAIL PROTECTED]> wrote:
> 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']
>
>
>
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