GenomeComb

Genomecomb moved to github on https://github.com/derijkp/genomecomb with documentation on https://derijkp.github.io/genomecomb. For up to date versions, go there. These pages only remain here for the data on the older scientific application (or if someone really needs a long obsolete version of the software)

cat

Format

cg cat ?options? file ?file? ...

Summary

Concatenate tab separated files and print on the standard output (stripping headers of files other than the first).

Description

Concatenate tab separated files and print on the standard output. Headers of tab files others than the first one will be stripped. If one of the tab file does not have the same fields as the first, an error is given, unless the merge or force options are used.

Arguments

file ...
files to be concatenated

Options

-m 0/1 (--merge)
if the merge option is given, tab files with different fields will be merged: The resulting tab file has each field that occurs in at least one of the source files. If a given field is not present in one of the source files, it will be empty for each line coming from this file.
-f 0/1 (--force)
if the force option is given, tab files with different fields will still be concatenated without error.
-s 0/1 (--sort)
if the sort option is given, the files will be sorted (natural sort order) before being concatenated. This is usefull for e.g. concatenating files split over chromosomes in the correct order.
-c 0/1/f/n (--comments)
Determines what will be in the comments of the result file. if -c is 1 (default), the names of the files that are concatenated are added in the comment in addition to the comments of all source files. if 0 the comments of all source files are there, but no extra comments (file names) are added. You can use the value f to only display the comment of the first file, or n to leave out comments completely.
-n fieldname (--fieldname)
if -n is not empty, a column with the name fieldname will be added, that contains the filename where the line came from
-fields fields (--fields)
only return the given fields in the concatenated output

Category

tsv