Re: Mathematica is destroying my sanity....
- To: mathgroup at smc.vnet.net
- Subject: [mg53083] Re: Mathematica is destroying my sanity....
- From: David Bailey <dave at Remove_Thisdbailey.co.uk>
- Date: Thu, 23 Dec 2004 07:58:12 -0500 (EST)
- References: <cqbhb8$4kv$1@smc.vnet.net>
- Sender: owner-wri-mathgroup at wolfram.com
Todd Allen wrote:
> 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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Hi,
If you REALLY want to control the contents of the file you create, why
not write yourself a function that uses OpenWrite to get a stream and
then use functions like Write/WriteString/ToString to lay it all out
exactly as you desire?
I suggest you 'practice' on a mini-file, but as you work, be careful to
time your code, because different methods might run at significantly
different speeds, and you don't want a surprise when you scale it back
up to the real problem.
David Bailey
dbaileyconsultancy.co.uk