[R] read.table mystery

[David Winsemius]

On Mar 6, 2011, at 12:47 PM, Johannes Graumann wrote:

> Thank you for pointing this out. This is really inconvenient as I do  
> not
> know a priori how many and where those darn cases containing an  
> additional
> (or more) ":" might be ...

There is a count.fields function that might assist with this task.

You seem to have a multiline (variable number of lines)  format of:

NNNN:>sp|header with "|" AND white space separators
NNNN:VARIABLE_NUMBER_OF_CAP_LETTERS_60_CHAR_WIDEEEEE
NNNN+60:VARIABLE_NUMBER_OF_CAP_LETTERS_60_CHAR_WIDEE
NNNN+120:VARIABLE_NUMBER_OF_CAP_LETTERS_60_CHAR_WIDE
NNNN+180:EXCEPT_LAST

No way that read.table can work. You might create an index with the  
location of the high-count headers and then reprocess.

log.idx <- count.fields("/tmp/testfile.txt") > 1
corpus <- readLines("/tmp/testfile.txt")

Then parse the headers and rejoin the broken multi-line content. There  
may be worked examples in the archive for variable number multi-line  
file formats.

-- 
David.


>
> The seems to work, but will fail if there's a "1:sdfjhlfkh:2:adlkjf"
> somewhere (1 & 2 both integerable).
>
> na.exclude(as.integer(scan("/tmp/ 
> testfile.txt",sep=":",what="integer")))
>
> More robust pointers anyone?
>
> Joh
>
> Sarah Goslee wrote:
>
>> Not so much a mystery. read.table() only looks at the first 5 lines  
>> when
>> decided how many columns your file has (as described in the Details
>> section of the help).
>>
>> The easiest solution is to add a col.names argument to read.table()  
>> with
>> the correct number of names.
>>
>> You may want to also include as.is=TRUE if you don't want your data  
>> to
>> be imported as factors. If you expect character but have factor you  
>> may
>> get unexpected results later.
>>
>> Sarah
>>
>> On Sun, Mar 6, 2011 at 5:04 AM, Johannes Graumann
>> <johannes_graumann at web.de> wrote:
>>> Hello,
>
>>>
>>> Please have a look at the code below, which I use to read in the  
>>> attached
>>> file. As line 18 of the file reads "1065:>sp|Q9V3T9|ADRO_DROME
>>> NADPH:adrenodoxin oxidoreductase, mitochondrial OS=Drosophila
>>> melanogaster GN=dare PE=2 SV=1", I expect the code below to  
>>> produce a 3
>>> column data frame with most of the last column empty and line 18 to
>>> produce a data.frame row like so:
>>>
>>> V1
>>>       1065
>>> V2
>>>> sp|Q9V3T9|ADRO_DROME NADPH
>>> V3
>>>       adrenodoxin oxidoreductase, mitochondrial OS=Drosophila
>>> melanogaster GN=dare PE=2 SV=1
>>>
>>> Why is that not so?
>>>
>>> Thanks for any hint.
>>>
>>> Sincerely, Joh
>>>
>>> read.table(
>>> "/tmp/testfile.txt",
>>> sep=":",
>>> header=FALSE,
>>> quote="",
>>> fill=TRUE
>>> )[19,]
>>
>> ---
>> Sarah Goslee
>> http://www.functionaldiversity.org
>
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David Winsemius, MD
Heritage Laboratories
West Hartford, CT