03-02-2009
Delete parts of a string of character in one given column of a tab delimited file
I would like to remove characters from column 7 so that from an input file looking like this:
>HWI-EAS422_12:4:1:69:89 GGTTTAAATATTGCACAAAAGGTATAGAGCGT U0 1 0 0 ref_chr8.fa 6527777 F DD
I get something like that in an output file:
>HWI-EAS422_12:4:1:69:89 GGTTTAAATATTGCACAAAAGGTATAGAGCGT U0 1 0 0 chr8 6527777 F DD
where in column 7, "ref_chr8.fa" becomes "chr8" only.
Note: some lines of the file may present a letter instead of a number after chr, and two numbers before the dot and after chr: e.g. "ref_chrY.fa" should become "chrY", or "ref_chr10.fa" should become "chr10"
Thanks in advance for your help!!!!
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LEARN ABOUT FREEBSD
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