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MathGroup Archive 2004

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Mathematica is destroying my sanity....

  • To: mathgroup at smc.vnet.net
  • Subject: [mg53066] Mathematica is destroying my sanity....
  • From: Todd Allen <genesplicer28 at yahoo.com>
  • Date: Wed, 22 Dec 2004 04:53:04 -0500 (EST)
  • Sender: owner-wri-mathgroup at wolfram.com

Hi everyone (and Happy Holidays!)

     I am trying to parse a 450 Mb text file for
certain important information and then would like to
save the smaller, parsed information in a suitable
file for later importation and futher analysis.  I
have made some progress, but have stumbled yet again.

Below is the situation:

In[1]:=
SetDirectory["D:\\"]
In[2]:=
blastn=OpenRead["Cpara-SelfBlast120804(2).txt"]
In[3]:=
subblastn=ReadList[blastn,Record,RecordSeparators\[Rule]{{"Value"},{">"}}];
In[7]:=
temp1=Table[StringSplit[subblastn[[i]]],{i,1,Length[subblastn]}];
In[9]:=
temp2=Table[Partition[temp1[[i]],3],{i,1,Length[temp1]}];


***The output for temp2 is a nicely organized set of
sublists:

Out[10]=
{{CEST-01-A-01,1120,0.0},{CEST-17-A-06,985,0.0},{CEST-04-E-04,52,
   
3e-07},{CEST-28-H-03,50,1e-06},{CEST-46-G-10,48,5e-06},{CEST-37-B-11,48,
   
5e-06},{CEST-21-D-05,48,5e-06},{CEST-21-A-11,48,5e-06},{CEST-21-A-10,48,
   
5e-06},{CEST-19-G-12,48,5e-06},{CEST-13-F-07,48,5e-06},{CEST-10-E-05,48,
   
5e-06},{CEST-04-E-08,48,5e-06},{CEST-60-C-12,46,2e-05},{CEST-59-D-02,46,
   
2e-05},{CEST-29-A-06,46,2e-05},{CEST-26-H-10,46,2e-05},{CEST-25-F-11,46,
   
2e-05},{CEST-20-C-11,46,2e-05},{CEST-19-F-10,46,2e-05},{CEST-11-E-06,46,
    2e-05}}

****At this point, I want to save the data and
organized structure of the data currently contained in
temp2.

I have tried numerous variations, with the following
being the best (yet still undesirable) result:

Export["subparseBlastN", temp2, "List"] (* to save
data *)

In[45]:=
tempsub=Import["subparseBlastN","Table"];

****The result of the new import in "tempsub" looks
awful and really messes up the data organization for
me:

Out[47]=
{{{"CEST-01-A-01",,"1120",,"0.0"},,{"CEST-17-A-06",,"985",,"0.0"},,{"CEST-04-\
E-04",,"52",,"3e-07"},,{"CEST-28-H-03",,"50",,"1e-06"},,{"CEST-46-G-10",,"48",\
,"5e-06"},,{"CEST-37-B-11",,"48",,"5e-06"},,{"CEST-21-D-05",,"48",,"5e-06"},,{\
"CEST-21-A-11",,"48",,"5e-06"},,{"CEST-21-A-10",,"48",,"5e-06"},,{"CEST-19-G-\
12",,"48",,"5e-06"},,{"CEST-13-F-07",,"48",,"5e-06"},,{"CEST-10-E-05",,"48",,\
"5e-06"},,{"CEST-04-E-08",,"48",,"5e-06"},,{"CEST-60-C-12",,"46",,"2e-05"},,{\
"CEST-59-D-02",,"46",,"2e-05"},,{"CEST-29-A-06",,"46",,"2e-05"},,{"CEST-26-H-\
10",,"46",,"2e-05"},,{"CEST-25-F-11",,"46",,"2e-05"},,{"CEST-20-C-11",,"46",,\
"2e-05"},,{"CEST-19-F-10",,"46",,"2e-05"},,{"CEST-11-E-06",,"46",,"2e-05"}}}

(1) Is there a way to export my original "nice"
looking list (the temp2 list), so that it will import
in exactly the same?

(2) Even though the Head of each element in both the
"temp2" and "tempsub" lists are Strings, why does
Mathematica put extra quotation marks around the newly
imported list items and not the original list items?


Whew, I am outta breath.  Any thoughts or suggestions
where I might find useful information?  As
always,thank you to the numerous people who have
helped me out in the past.  This is an excellent forum
for learning Mathematica.

Best regards,
Todd





		
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