How do I separate the pattern counts with R?

0
votes

via a program I have received the following pattern count.

Counter({'CCCC': 22115, 'TTTT': 22043, 'AAAA': 22037, 'GGGG': 21930, 'AAAC': 154, 'TTAT': 152, 'CCCA': 152, 'CCTC': 152, 'GGGC': 151, 'TTTG': 150, 'GTGG': 149, 'GCCC': 148, 'CCGC': 145, 'CGGG': 145, 'TGGG': 144, 'AGAA': 144, 'TTGT': 144, 'GAAA': 142, 'CCCG': 142, 'CCCT': 142, 'TCCC': 141, 'CAAA': 139, 'ATTT': 137, 'CGCC': 134, 'GGTG': 133, 'GAGG': 133, 'TTTA': 132, 'CTTT': 131, 'TCTT': 131, 'ACCC': 130, 'AGGG': 130, 'GGAG': 129, 'AACA': 129, 'TAAA': 129, 'TATT': 128, 'TTTC': 128, 'AAGA': 127, 'GGGA': 126, 'ACAA': 126, 'TTCT': 125, 'CTCC': 124, 'GCGG': 124, 'ATAA': 123, 'GGCG': 120, 'CACC': 119, 'AAAT': 118, 'AATA': 117, 'AAAG': 114, 'GTTT': 114, 'TGTT': 112, 'GGGT': 112, 'CCAC': 110, 'CGCG': 45, 'AACC': 43, 'TTAA': 41, 'CTCT': 41, 'GGCC': 41, 'ACTC': 40, 'CTTC': 40, 'GCCG': 39, 'ATTA': 39, 'ACCT': 39, 'TGCG': 39, 'ATAT': 39, 'TCTC': 38, 'ACGG': 38, 'TATA': 37, 'ATCA': 37, 'CGGC': 37, 'CGAG': 36, 'AGAG': 36, 'GACA': 35, 'GTTG': 35, 'TGAG': 35, 'TGGT': 35, 'CCAA': 35, 'TTGG': 34, 'GTGT': 34, 'GCGC': 34, 'CACA': 34, 'GTAA': 34, 'GTAG': 34, 'TCCA': 34, 'TCCT': 34, 'AAGG': 34, 'GAGA': 34, 'GCTT': 34, 'GTGC': 33, 'CTAT': 33, 'TTGC': 33, 'CGGA': 33, 'AGGA': 32, 'GACG': 32, 'AATT': 32, 'CAAC': 32, 'CTGC': 32, 'CTAC': 32, 'ACGA': 32, 'CGAC': 32, 'CCGG': 32, 'TCTG': 32, 'GGAA': 32, 'GGAT': 32, 'TGCT': 32, 'TTAG': 32, 'GCTG': 32, 'GAGT': 31, 'AGGC': 31, 'TTCC': 31, 'ATGA': 31, 'TTCA': 31, 'CCAT': 31, 'AAGT': 31, 'GAGC': 31, 'GTAT': 31, 'CGAA': 31, 'TCAT': 31, 'ATTC': 31, 'TGTG': 30, 'AGTT': 30, 'ATCC': 30, 'AGCA': 30, 'GTCT': 30, 'TGTC': 30, 'TCAC': 30, 'CACT': 30, 'ACTA': 30, 'TAAT': 30, 'CCGT': 30, 'CCTA': 29, 'TCGG': 29, 'GGTA': 29, 'TATG': 29, 'AACG': 29, 'CACG': 29, 'GATT': 29, 'ATCT': 29, 'TGGC': 29, 'AGCC': 29, 'TATC': 29, 'GCTC': 29, 'GGCT': 29, 'TCTA': 29, 'AACT': 28, 'CCTT': 28, 'CTTA': 28, 'TGTA': 28, 'TAGT': 28, 'AGTG': 28, 'CCGA': 27, 'AATG': 27, 'CCTG': 27, 'CTGT': 27, 'AGTC': 27, 'GTCC': 27, 'GGTT': 27, 'ACAC': 26, 'TACC': 26, 'CATC': 26, 'CATA': 26, 'GTGA': 26, 'TGAA': 26, 'GGTC': 26, 'CTTG': 26, 'GCAC': 26, 'GGCA': 26, 'CGTC': 26, 'CTGG': 26, 'TAAG': 26, 'TCGT': 26, 'TGAT': 25, 'CAGA': 25, 'GAAC': 25, 'ACCA': 25, 'TTAC': 25, 'CATT': 25, 'AGAT': 25, 'CGGT': 25, 'ATTG': 25, 'TTGA': 25, 'GATA': 24, 'GGAC': 24, 'AAGC': 24, 'GTCA': 24, 'CAAT': 24, 'GCAG': 24, 'ACAT': 24, 'TGCC': 24, 'ATAG': 24, 'CGTG': 24, 'CGCA': 24, 'TAGG': 23, 'ACCG': 23, 'TTCG': 23, 'AGCG': 23, 'GTTC': 23, 'ACTT': 23, 'CGTT': 23, 'AGAC': 23, 'GCAT': 22, 'TCCG': 22, 'TAAC': 22, 'ACGC': 22, 'CAGC': 22, 'GACC': 22, 'CATG': 22, 'TCGA': 22, 'TAGA': 22, 'GCAA': 22, 'CTCG': 22, 'TACT': 22, 'AATC': 21, 'CGCT': 21, 'GAAT': 21, 'GCGT': 21, 'AGTA': 21, 'GCCA': 21, 'ATGG': 21, 'TCAA': 21, 'CTCA': 21, 'TGGA': 20, 'GAAG': 20, 'GATC': 20, 'TGCA': 20, 'GCCT': 19, 'GTCG': 19, 'CAAG': 19, 'TCGC': 19, 'CTGA': 19, 'GATG': 19, 'CTAA': 19, 'GCGA': 19, 'ATAC': 18, 'GTTA': 18, 'GCTA': 18, 'AGGT': 18, 'CCAG': 18, 'ACAG': 18, 'CTAG': 17, 'CGTA': 17, 'ACGT': 17, 'TACA': 17, 'AGCT': 16, 'CAGG': 16, 'ATGT': 16, 'ATCG': 16, 'ATGC': 15, 'TGAC': 14, 'TAGC': 14, 'ACTG': 14, 'TCAG': 14, 'CGAT': 14, 'TACG': 13, 'CAGT': 11, 'GTAC': 10, 'GACT': 9})

I want to convert it now as a list, so that in the first column "AAAA" there are all corresponding values and so also for all combinations. Does anyone have an idea how to program this well?

This is how I read the data into R:

daten <- read.table("/PATTERN.txt", header = FALSE, sep = "\t");

So far I've tried direct reading, but somehow it doesn't really work. It should look like this:

AAAA CCCC

1 22128 22127

Thank you very much!

2
rsortinggenericspattern-matching
The pattern is a python collections.Counter() object, you can covert that to a table/csv file before writing it and then feed that that to your Rscript – Chris_Rands
What did you try so far? How should the result look like? – Selaron
Can you do that directly in R? – drenz
Is the question about Python or R? Do you need alphabetic sorting or what? – hyperTrashPanda
No, no sorting, but to bring this read string into a list form. – drenz

2 Answers

1
votes

If Lines shown reproducibly in the Note at the end contains the data then in it replace Counter( with [, ) with ] and ' with " and read that in using fromJSON:

library(jsonlite)

fromJSON(gsub("'", '"', 
           sub("\\)", "]", 
             sub("Counter.","[", Lines))))

giving:

   CCCC  TTTT  AAAA  GGGG AAAC TTAT CCCA CCTC GGGC TTTG GTGG GCCC CCGC CGGG
1 22115 22043 22037 21930  154  152  152  152  151  150  149  148  145  145
  TGGG AGAA TTGT GAAA CCCG CCCT TCCC CAAA ATTT CGCC GGTG GAGG TTTA CTTT TCTT
1  144  144  144  142  142  142  141  139  137  134  133  133  132  131  131
  ACCC AGGG GGAG AACA TAAA TATT TTTC AAGA GGGA ACAA TTCT CTCC GCGG ATAA GGCG
1  130  130  129  129  129  128  128  127  126  126  125  124  124  123  120
  CACC AAAT AATA AAAG GTTT TGTT GGGT CCAC CGCG AACC TTAA CTCT GGCC ACTC CTTC
1  119  118  117  114  114  112  112  110   45   43   41   41   41   40   40
  GCCG ATTA ACCT TGCG ATAT TCTC ACGG TATA ATCA CGGC CGAG AGAG GACA GTTG TGAG
1   39   39   39   39   39   38   38   37   37   37   36   36   35   35   35
  TGGT CCAA TTGG GTGT GCGC CACA GTAA GTAG TCCA TCCT AAGG GAGA GCTT GTGC CTAT
1   35   35   34   34   34   34   34   34   34   34   34   34   34   33   33
  TTGC CGGA AGGA GACG AATT CAAC CTGC CTAC ACGA CGAC CCGG TCTG GGAA GGAT TGCT
1   33   33   32   32   32   32   32   32   32   32   32   32   32   32   32
  TTAG GCTG GAGT AGGC TTCC ATGA TTCA CCAT AAGT GAGC GTAT CGAA TCAT ATTC TGTG
1   32   32   31   31   31   31   31   31   31   31   31   31   31   31   30
  AGTT ATCC AGCA GTCT TGTC TCAC CACT ACTA TAAT CCGT CCTA TCGG GGTA TATG AACG
1   30   30   30   30   30   30   30   30   30   30   29   29   29   29   29
  CACG GATT ATCT TGGC AGCC TATC GCTC GGCT TCTA AACT CCTT CTTA TGTA TAGT AGTG
1   29   29   29   29   29   29   29   29   29   28   28   28   28   28   28
  CCGA AATG CCTG CTGT AGTC GTCC GGTT ACAC TACC CATC CATA GTGA TGAA GGTC CTTG
1   27   27   27   27   27   27   27   26   26   26   26   26   26   26   26
  GCAC GGCA CGTC CTGG TAAG TCGT TGAT CAGA GAAC ACCA TTAC CATT AGAT CGGT ATTG
1   26   26   26   26   26   26   25   25   25   25   25   25   25   25   25
  TTGA GATA GGAC AAGC GTCA CAAT GCAG ACAT TGCC ATAG CGTG CGCA TAGG ACCG TTCG
1   25   24   24   24   24   24   24   24   24   24   24   24   23   23   23
  AGCG GTTC ACTT CGTT AGAC GCAT TCCG TAAC ACGC CAGC GACC CATG TCGA TAGA GCAA
1   23   23   23   23   23   22   22   22   22   22   22   22   22   22   22
  CTCG TACT AATC CGCT GAAT GCGT AGTA GCCA ATGG TCAA CTCA TGGA GAAG GATC TGCA
1   22   22   21   21   21   21   21   21   21   21   21   20   20   20   20
  GCCT GTCG CAAG TCGC CTGA GATG CTAA GCGA ATAC GTTA GCTA AGGT CCAG ACAG CTAG
1   19   19   19   19   19   19   19   19   18   18   18   18   18   18   17
  CGTA ACGT TACA AGCT CAGG ATGT ATCG ATGC TGAC TAGC ACTG TCAG CGAT TACG CAGT
1   17   17   17   16   16   16   16   15   14   14   14   14   14   13   11
  GTAC GACT
1   10    9

Note

Lines <- "
Counter({'CCCC': 22115, 'TTTT': 22043, 'AAAA': 22037, 'GGGG':21930, 'AAAC': 154, 'TTAT': 152, 'CCCA': 152, 'CCTC': 152, 'GGGC': 151, 'TTTG': 150, 'GTGG': 149, 'GCCC': 148, 'CCGC': 145, 'CGGG': 145, 'TGGG': 144, 'AGAA': 144, 'TTGT': 144, 'GAAA': 142, 'CCCG': 142, 'CCCT': 142, 'TCCC': 141, 'CAAA': 139, 'ATTT': 137, 'CGCC': 134, 'GGTG': 133, 'GAGG': 133, 'TTTA': 132, 'CTTT': 131, 'TCTT': 131, 'ACCC': 130, 'AGGG': 130, 'GGAG': 129, 'AACA': 129, 'TAAA': 129, 'TATT': 128, 'TTTC': 128, 'AAGA': 127, 'GGGA': 126, 'ACAA': 126, 'TTCT': 125, 'CTCC': 124, 'GCGG': 124, 'ATAA': 123, 'GGCG': 120, 'CACC': 119, 'AAAT': 118, 'AATA': 117, 'AAAG': 114, 'GTTT': 114, 'TGTT': 112, 'GGGT': 112, 'CCAC': 110, 'CGCG': 45, 'AACC': 43, 'TTAA': 41, 'CTCT': 41, 'GGCC': 41, 'ACTC': 40, 'CTTC': 40, 'GCCG': 39, 'ATTA': 39, 'ACCT': 39, 'TGCG': 39, 'ATAT': 39, 'TCTC': 38, 'ACGG': 38, 'TATA': 37, 'ATCA': 37, 'CGGC': 37, 'CGAG': 36, 'AGAG': 36, 'GACA': 35, 'GTTG': 35, 'TGAG': 35, 'TGGT': 35, 'CCAA': 35, 'TTGG': 34, 'GTGT': 34, 'GCGC': 34, 'CACA': 34, 'GTAA': 34, 'GTAG': 34, 'TCCA': 34, 'TCCT': 34, 'AAGG': 34, 'GAGA': 34, 'GCTT': 34, 'GTGC': 33, 'CTAT': 33, 'TTGC': 33, 'CGGA': 33, 'AGGA': 32, 'GACG': 32, 'AATT': 32, 'CAAC': 32, 'CTGC': 32, 'CTAC': 32, 'ACGA': 32, 'CGAC': 32, 'CCGG': 32, 'TCTG': 32, 'GGAA': 32, 'GGAT': 32, 'TGCT': 32, 'TTAG': 32, 'GCTG': 32, 'GAGT': 31, 'AGGC': 31, 'TTCC': 31, 'ATGA': 31, 'TTCA': 31, 'CCAT': 31, 'AAGT': 31, 'GAGC': 31, 'GTAT': 31, 'CGAA': 31, 'TCAT': 31, 'ATTC': 31, 'TGTG': 30, 'AGTT': 30, 'ATCC': 30, 'AGCA': 30, 'GTCT': 30, 'TGTC': 30, 'TCAC': 30, 'CACT': 30, 'ACTA': 30, 'TAAT': 30, 'CCGT': 30, 'CCTA': 29, 'TCGG': 29, 'GGTA': 29, 'TATG': 29, 'AACG': 29, 'CACG': 29, 'GATT': 29, 'ATCT': 29, 'TGGC': 29, 'AGCC': 29, 'TATC': 29, 'GCTC': 29, 'GGCT': 29, 'TCTA': 29, 'AACT': 28, 'CCTT': 28, 'CTTA': 28, 'TGTA': 28, 'TAGT': 28, 'AGTG': 28, 'CCGA': 27, 'AATG': 27, 'CCTG': 27, 'CTGT': 27, 'AGTC': 27, 'GTCC': 27, 'GGTT': 27, 'ACAC': 26, 'TACC': 26, 'CATC': 26, 'CATA': 26, 'GTGA': 26, 'TGAA': 26, 'GGTC': 26, 'CTTG': 26, 'GCAC': 26, 'GGCA': 26, 'CGTC': 26, 'CTGG': 26, 'TAAG': 26, 'TCGT': 26, 'TGAT': 25, 'CAGA': 25, 'GAAC': 25, 'ACCA': 25, 'TTAC': 25, 'CATT': 25, 'AGAT': 25, 'CGGT': 25, 'ATTG': 25, 'TTGA': 25, 'GATA': 24, 'GGAC': 24, 'AAGC': 24, 'GTCA': 24, 'CAAT': 24, 'GCAG': 24, 'ACAT': 24, 'TGCC': 24, 'ATAG': 24, 'CGTG': 24, 'CGCA': 24, 'TAGG': 23, 'ACCG': 23, 'TTCG': 23, 'AGCG': 23, 'GTTC': 23, 'ACTT': 23, 'CGTT': 23, 'AGAC': 23, 'GCAT': 22, 'TCCG': 22, 'TAAC': 22, 'ACGC': 22, 'CAGC': 22, 'GACC': 22, 'CATG': 22, 'TCGA': 22, 'TAGA': 22, 'GCAA': 22, 'CTCG': 22, 'TACT': 22, 'AATC': 21, 'CGCT': 21, 'GAAT': 21, 'GCGT': 21, 'AGTA': 21, 'GCCA': 21, 'ATGG': 21, 'TCAA': 21, 'CTCA': 21, 'TGGA': 20, 'GAAG': 20, 'GATC': 20, 'TGCA': 20, 'GCCT': 19, 'GTCG': 19, 'CAAG': 19, 'TCGC': 19, 'CTGA': 19, 'GATG': 19, 'CTAA': 19, 'GCGA': 19, 'ATAC': 18, 'GTTA': 18, 'GCTA': 18, 'AGGT': 18, 'CCAG': 18, 'ACAG': 18, 'CTAG': 17, 'CGTA': 17, 'ACGT': 17, 'TACA': 17, 'AGCT': 16, 'CAGG': 16, 'ATGT': 16, 'ATCG': 16, 'ATGC': 15, 'TGAC': 14, 'TAGC': 14, 'ACTG': 14, 'TCAG': 14, 'CGAT': 14, 'TACG': 13, 'CAGT': 11, 'GTAC': 10, 'GACT': 9})"
0
votes

This answer may help you in this particular case, but you should insist that whoever produced that result to export in such a way that can be easily imported with every programming language. Here you have a string representation of a python object which is definitely not a good way for exchanging data.

However, you can try this:

#place here the correct path to the file
fn <- "pattern.txt"
#here we read the content of the file as is
filecontent <- readChar(fn,file.info(fn)$size)
#we manipulate the string a bit to have an R list
res <- eval(parse(text = gsub("[\\{\\}\n]", "", 
         gsub(":", "=", sub("Counter", "list", filecontent)))))