Pattern match

On Apr 21, 2011, at 5:27 AM, neetika nath wrote:

 Thank you Dennis,

yes the problem is the input file. i have .rdf file and the format is in
same way i have posted earlier. if i open that file in notepad++ the lines
are divided or broken  with CR+LF character. so any suggestion to retrieve
SpeciesScientific information without changing the input file?

You might consider attaching the original file named with an extension of
`.txt`, since your verbal description does not match your included example.
What I see after the various servers have passed this around and inserted
line-ends is the string `SpeciesScientific` in the first line, rather than
in the third.

--
David

--

Thank you

On Wed, Apr 20, 2011 at 9:49 PM, Dennis Murphy <djmuser at gmail.com> wrote:

 Hi:

This is a bit of a roundabout approach; I'm sure that folks with regex
expertise will trump this in a heartbeat. I modified the last piece of
the string a bit to accommodate the approach below. Depending on where
the strings have line breaks, you may have some odd '\n' characters
inserted.

# Step 1: read the input as a single character string
u <- "SpeciesCommon=(Human);SpeciesScientific=(Homo


sapiens);ReactiveCentres=(N,C,C,C,+H,O,C,C,C,C,O,H);BondInvolved=(C-H);EzCatDBID=(S00343);BondFormed=(O-H,O-H);Bond=(255B);Cofactors=(Cu(II),CU,501,A,Cu(II),CU,502,A);CatalyticSwissProt=(P25006);SpeciesScientific=(Achromobacter
cycloclastes);SpeciesCommon=(Bacteria);Reactive=(Ce+)"

# Step 2: Split input lines by the ';' delimiter and then use lapply()
to split variable names from values.
# This results in a nested list for ulist2.
ulist <- strsplit(u, ';')
ulist2 <- lapply(ulist, function(s) strsplit(s, '='))

# Step 3: Break out the results into a matrix whose first column is
the variable name
# and whose second column is the value (with parens included)
# This avoids dealing with nested lists
v <- matrix(unlist(ulist2), ncol = 2, byrow = TRUE)

# Step 4: Strip off the parens
w <- apply(v, 2, function(s) gsub('([\\(\\)])', '', s))
colnames(w) <- c('Name', 'Value')
w
   Name                 Value
[1,] "SpeciesCommon"      "Human"
[2,] "SpeciesScientific"  "Homo sapiens"
[3,] "ReactiveCentres"    "N,C,C,C,+H,O,C,C,C,C,O,H"
[4,] "BondInvolved"       "C-H"
[5,] "EzCatDBID"          "S00343"
[6,] "BondFormed"         "O-H,O-H"
[7,] "Bond"               "255B"
[8,] "Cofactors"          "CuII,CU,501,A,CuII,CU,502,A"
[9,] "CatalyticSwissProt" "P25006"
[10,] "SpeciesScientific"  "Achromobacter\ncycloclastes"
[11,] "SpeciesCommon"      "Bacteria"
[12,] "Reactive"           "Ce+"

# Step 5: Subset out the values of the SpeciesScientific variables
subset(as.data.frame(w), Name == 'SpeciesScientific', select = 'Value')
                      Value
2                 Homo sapiens
10 Achromobacter\ncycloclastes


One possible 'advantage' of this approach is that if you have a number
of string records of this type, you can create nested lists for each
string and then manipulate the lists to get what you need. Hopefully
you can use some of these ideas for other purposes as well.

Dennis



On Wed, Apr 20, 2011 at 10:17 AM, Neeti <nikkihathi at gmail.com> wrote:

Hi ALL,

I have very simple question regarding pattern matching. Could anyone
tell

me

how to I can use R to retrieve string pattern from text file.  for

example

my file contain following information

SpeciesCommon=(Human);SpeciesScientific=(Homo
sapiens);ReactiveCentres=(N,C,C,C,+

H,O,C,C,C,C,O,H);BondInvolved=(C-H);EzCatDBID=(S00343);BondFormed=(O-H,O-H);Bond+

255B);Cofactors=(Cu(II),CU,501,A,Cu(II),CU,502,A);CatalyticSwissProt=(P25006);Sp+

eciesScientific=(Achromobacter
cycloclastes);SpeciesCommon=(Bacteria);ReactiveCe+

and I want to extract ?SpeciesScientific = (?)? information from this

file.

Problem is in 3rd line where SpeciesScientific word is divided with +.

Could anyone help me please?
Thank you


--
View this message in context:

http://r.789695.n4.nabble.com/Pattern-match-tp3463625p3463625.html

Sent from the R help mailing list archive at Nabble.com.

       [[alternative HTML version deleted]]

David Winsemius, MD
West Hartford, CT