Oh ok. I think what I need the difference between two columns. To provide some context the A's and G's are biological genetic mutation data. One column is the reference, and the other is a tumor sample. I am trying to extract all entries where there is an insertion OR deletion of at least 3base pairs (A's G's C's or T's).
The best way to do this is to look at the reference and tumor column and ask if there is at least a difference of 3 letters.
I have a text file like:
"10","server","","11111",JLB,
I need a way to say if the 3rd field has data in it, move the contents of the entire line to a new file.
Any ideas?
Thanks, (5 Replies)
Hi, all
I need to get fields in a line that are separated by commas, some of the fields are enclosed with double quotes, and they are supposed to be treated as a single field even if there are commas inside the quotes.
sample input:
for this line, 5 fields are supposed to be extracted, they... (8 Replies)
First, thanks for the help in previous posts... couldn't have gotten where I am now without it!
So here is what I have, I use AWK to match $1 and $2 as 1 string in file1 to $1 and $2 as 1 string in file2. Now I'm wondering if I can extend this AWK command to incorporate the following:
If $1... (4 Replies)
Hello experts
I have a file with paragraphs begining with a keeping date and ending with "END":
20120301 num num
John num num A keepnum1 num num
kathrin num num A keepnum1 num num
kathrin num num B keepnum2 num num
Pete num num A keepnum1 num num
Jacob num... (2 Replies)
I am trying to parse the input in awk to include the |gc= in $4 but am not able to. The below is close:
awk so far:
awk '{sub(/\|]+]++/, ""); print }' input.txt Input
chr1 955543 955763 AGRN-6|pr=2|gc=75 0 +
chr1 957571 957852 AGRN-7|pr=3|gc=61.2 0 +
chr1 970621 ... (7 Replies)
We have a csv file as mentioned below and the requirement is to change the date format in file as mentioned below.
Current file (file.csv)
----------------------
empname,date_of_join,dept,date_of_resignation
ram,08/09/2015,sales,21/06/2016
"akash,sahu",08/10/2015,IT,21/07/2016
... (6 Replies)
I am trying to output a tab-delimited result that uses the data from a tab-delimited file to combine and subtract specific lines.
If $4 matches in each line then the first matching sequential $6 value is added to $2, unless the value is 1, then the original $2 is used (like in the case of line... (3 Replies)
In the awk below I am trying to set/update the value of $14 in file2 in
bold, using the matching NM_ in $12 or $9 in file2
with the NM_ in $2 of file1.
The lengths of $9 and $12 can be variable but what is consistent is the start pattern
will always be NM_ and the end pattern is always ;... (2 Replies)
The awk below produces the current output, which will add +1 to $3. However, I am trying to add the length of the matching characters between $5 and $6 to $3. I have tried using sub as a variable to store the length but am not able to do so correctly. I added comments to each line and the... (4 Replies)
Hi,
So awk is driving me crazy on this one. I have searched everywhere and read man, docs and every related post Google can find and still no luck. The actual files I need to run this on are sensitive in nature, but it is the same thing as if I needed to calculate weighted grades for multiple... (15 Replies)
Discussion started by: cotilloe
15 Replies
LEARN ABOUT DEBIAN
psc
PSC(1) General Commands Manual PSC(1)NAME
psc - prepare sc files
SYNOPSIS
psc [-fLkrSPv] [-s cell] [-R n] [-C n] [-n n] [-d c]
DESCRIPTION
Psc is used to prepare data for input to the spreadsheet calculator sc(1). It accepts normal ascii data on standard input. Standard out-
put is a sc file. With no options, psc starts the spreadsheet in cell A0. Strings are right justified. All data on a line is entered on
the same row; new input lines cause the output row number to increment by one. The default delimiters are tab and space. The column for-
mats are set to one larger than the number of columns required to hold the largest value in the column.
OPTIONS -f Omit column width calculations. This option is for preparing data to be merged with an existing spreadsheet. If the option is not
specified, the column widths calculated for the data read by psc will override those already set in the existing spreadsheet.
-L Left justify strings.
-k Keep all delimiters. This option causes the output cell to change on each new delimiter encountered in the input stream. The
default action is to condense multiple delimiters to one, so that the cell only changes once per input data item.
-r Output the data by row first then column. For input consisting of a single column, this option will result in output of one row
with multiple columns instead of a single column spreadsheet.
-s cell
Start the top left corner of the spreadsheet in cell. For example, -s B33 will arrange the output data so that the spreadsheet
starts in column B, row 33.
-R n Increment by n on each new output row.
-C n Increment by n on each new output column.
-n n Output n rows before advancing to the next column. This option is used when the input is arranged in a single column and the
spreadsheet is to have multiple columns, each of which is to be length n.
-d c Use the single character c as the delimiter between input fields.
-P Plain numbers only. A field is a number only when there is no imbedded [-+eE].
-S All numbers are strings.
-v Print the version of psc
SEE ALSO sc(1)AUTHOR
Robert Bond
PSC 7.16 19 September 2002 PSC(1)