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Subtracting values from 2 columns in a file
Post 302567475 by wolf_blue on Monday 24th of October 2011 09:49:38 AM
10-24-2011
Subtracting values from 2 columns in a file
Hello,
I have a file with 5 columns that looks like this:
A1BG chr19 + 58863335 58866549
A1BG chr19 - 58858171 58864865
A2LD1 chr13 - 101182417 101186056
A2LD1 chr13 - 101182417 101241046
A2M chr12 - 9220303 9268558
A2ML1 chr12 + 8975149 9029377
I want to subtract the value in column 5 from column 4 and send the results to a 6th column and the file to look like this (6th col = values in 5th- values in 4th
A1BG chr19 + 58863335 58866549 3214
A1BG chr19 - 58858171 58864865 6694
A2LD1 chr13 - 101182417 101186056 3639
A2LD1 chr13 - 101182417 101241046 58629
A2M chr12 - 9220303 9268558 48255
A2ML1 chr12 + 8975149 9029377 54228
Then I want the file to get rid of the duplicates (I already used the sort and uniq commands and I still have some left e.g A1BG, A2LD1)
I want my final file to look like this, with only the genes with greatest length recorded (as below: only the largest values for genes A1BG and ALD1 were recorded:
A1BG chr19 - 58858171 58864865 6694
A2LD1 chr13 - 101182417 101241046 58629
A2M chr12 - 9220303 9268558 48255
A2ML1 chr12 + 8975149 9029377 54228
Please help!
Thanks so much!
I have a file with 5 columns that looks like this:
A1BG chr19 + 58863335 58866549
A1BG chr19 - 58858171 58864865
A2LD1 chr13 - 101182417 101186056
A2LD1 chr13 - 101182417 101241046
A2M chr12 - 9220303 9268558
A2ML1 chr12 + 8975149 9029377
I want to subtract the value in column 5 from column 4 and send the results to a 6th column and the file to look like this (6th col = values in 5th- values in 4th
A1BG chr19 + 58863335 58866549 3214
A1BG chr19 - 58858171 58864865 6694
A2LD1 chr13 - 101182417 101186056 3639
A2LD1 chr13 - 101182417 101241046 58629
A2M chr12 - 9220303 9268558 48255
A2ML1 chr12 + 8975149 9029377 54228
Then I want the file to get rid of the duplicates (I already used the sort and uniq commands and I still have some left e.g A1BG, A2LD1)
I want my final file to look like this, with only the genes with greatest length recorded (as below: only the largest values for genes A1BG and ALD1 were recorded:
A1BG chr19 - 58858171 58864865 6694
A2LD1 chr13 - 101182417 101241046 58629
A2M chr12 - 9220303 9268558 48255
A2ML1 chr12 + 8975149 9029377 54228
Please help!
Thanks so much!
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LEARN ABOUT LINUX
colrm
COLRM(1) BSD General Commands Manual COLRM(1) NAME
colrm -- remove columns from a file SYNOPSIS
colrm [start [stop]] DESCRIPTION
The colrm utility removes selected columns from the lines of a file. A column is defined as a single character in a line. Input is read from the standard input. Output is written to the standard output. If only the start column is specified, columns numbered less than the start column will be written. If both start and stop columns are spec- ified, columns numbered less than the start column or greater than the stop column will be written. Column numbering starts with one, not zero. Tab characters increment the column count to the next multiple of eight. Backspace characters decrement the column count by one. ENVIRONMENT
The LANG, LC_ALL and LC_CTYPE environment variables affect the execution of colrm as described in environ(7). EXIT STATUS
The colrm utility exits 0 on success, and >0 if an error occurs. SEE ALSO
awk(1), column(1), cut(1), paste(1) HISTORY
The colrm command appeared in 3.0BSD. BSD
August 4, 2004 BSD