Shell Programming and Scripting

outstanding !! thank you

Hi All,

Thanks for all the help. I am faced with a little complication now with respect to the last problem.The substring to be extracted must take care of the padded S values(column 6 in file2).
This column has values like 36M, 5S31M , 32M4S etc. The number associated with the leading S must be added to the starting position of the substring in the original string.So for 5S31M, 5 must be added to ($8-$2) of the print statement in the code. 32M4S should be ignored and treated as before, since it does not have a leading S. By leading S, I meant the character 'S' must be present at the beginning of the value of column 6, if the value is 2S30M4S, only the value 2 (associated with the leading S) and not 4 is to be considered for calculations. I hope I`m clear.

Thanks again,
Alpesh

---------- Post updated at 12:03 PM ---------- Previous update was at 09:52 AM ----------
This is what I came up with. Doesn't work, please help debug/change.

Code:

awk 'NR == FNR {
   f2[$1] = $10;
   f2[$2]=$6;next
   }
 $4 in f2 {
awk '{x=f2[$6];gsub(/[0-9]+[^0-9S]/,z);p=$1+0};
   print $0 "\t" substr(f2[$4], $8 - $2 +1 + $p, $9 - $8)
   }'  file2_truncated.txt file1_truncated.txt  | head

Hi radoulov and vgersh99,

Can you help me out please?

Thanks,
Alpesh

not tested

Code:

awk 'NR == FNR {   
    f2[$1] = $10
    f2pad[$1]=(match("^[0-9]+S", $6))?(substr($6,1,RLENGTH-1)):0
    next   
  } 
  $4 in f2 {
      print $0, substr(f2[$4], $8 - $2 + f2pad[$4], $9 - $8)    
}' file2_truncated.txt file1_truncated.txt |      head

Just to add that if you post an example of the expected output, based on the provided input, you'll probably receive a quicker answer.

Hi radoulov,

I will try to explain my question with two examples. Sorry if its a lengthy read, I`m sure the answer will take you much less time than reading the question. This is a continuation of the substring code that you helped me with earlier. I have attached file1 and file 2 samples for testing.

File2$6 can have 'M' and 'S' along with other alphebets and numbers.There can be no S, or max 2 S. There has to be at least 1 'M' and at most two 'M's. As a rule , we ignore the S and take the M.
S will only be present at the beginning and/or ending of $6 and not the middle.
example 23S4M9S, 1S34M1S, 34M2S are valid but 23M1S12M is invalid.

Lets take an example of file1$4=SNPSTER1_0001:7:60:876:131#0/1

So if file2$6 is 20M769N15M1S for $10 string ATAGCCAATATCCCCAACAGGTTGAGGGAACTGTTT
,we divide it into 4 segments.

s1=0=first 0 characters to ignore since there is no leading S
s2=1=last 1 character to ignore = T
m1=20=first 20 characters after s1,ATAGCCAATATCCCCAACAG
m2=15=last 15 characters before s2, GTTGAGGGAACTGTT





So we have 2 strings(m1 and m2), and substring is to be extracted from one of them based on the following condition.

if (file2$4+s1+m1) > file1$9
choose string m1 for substring operation
else
choose string m2 for substring opeartion



Substring operation

when file2$1=file1$4,

print file1$0 , the substring of m1 or m2 with parameters file1$8 - file1$2 + 1, file1$9 - file1$8



In this case file1$2=15735490
file1$8=15735496
file1$9=15735497

file2$4=15734702



(file2$4+s1+m1)=15734722 is less than file1$9=15735497

so we choose m2=GTTGAGGGAACTGTT for substring operation.

answer = substring (GTTGAGGGAACTGTT,7,1) = G

##########################################################

Another example

file1$4=file2$1=SNPSTER1_0001:7:115:1082:672#0/1
file2$10 = ATCTTGGGCCGCGAGCATCTTCAACCGCAAAATTTG

file 2$6=1S24M186N11M


s1=1 ignore first character 'A'
s2=0
m1=24 , TCTTGGGCCGCGAGCATCTTCAAC
m2=11, CGCAAAATTTG

In this case file1$2=4044310
file1$8=4044316
file1$9=4044317


file2$4=4044311

Here (file2$4+s1+m1)=4044336 > file1$9=4044317

So we choose m1=TCTTGGGCCGCGAGCATCTTCAA for subtring operation


answer = substring (TCTTGGGCCGCGAGCATCTTCAA ,7,1) = G


############################################################


Thanks,
Alpesh

Try this:

Code:

awk 'NR == FNR {
  while (match($6, /[0-9]*[SM]/)) {
    p1 = substr($6, RSTART + RLENGTH - 1, 1)
    f2[$1, p1, ++t[$1, p1]] = substr($6, RSTART, RLENGTH - 1) 
    $6 = substr($6, RSTART + RLENGTH)
    }
  f2s1[$1] = ($1, "S", 1) in f2 ? f2[$1, "S", 1] : 0 
  f2s2[$1] = ($1, "S", 2) in f2 ? f2[$1, "S", 2] : 0
  f2m1[$1] = ($1, "M", 1) in f2 ? f2[$1, "M", 1] : 0
  f2m2[$1] = ($1, "M", 2) in f2 ? f2[$1, "M", 2] : 0 
  f2m1s[$1] = substr($10, f2s1[$1], f2m1[$1])
  f2m2s[$1] = substr($10, length($10) - f2m2[$1] - f2s2[$1], f2m2[$1])
  f2_4[$1] = $4
  next    
  }
$4 in f2s1 {
  _sub = (f2_4[$4] + f2s1[$4] + f2m1[$4]) > $9 ? f2m1s[$4] : f2m2s[$4]
  print $0, substr(_sub, $8 - $2 + 1, $9 - $8)
  }' file2_sample.txt file1_sample.txt