tabmergep - Online in the Cloud

PROGRAM:

NAME

tabmerge - unify delimited files on common fields

SYNOPSIS

tabmerge [action] [options] file1 file2 [...]

Actions:

--min Take only fields present in all files [DEFAULT]
--max Take all fields present
-f|--fields=f1[,f2] Take only the fields mentioned in the
comma-separated list

Options:

-l|--list List available fields
--fs=x Use "x" as the field separator
(default is tab "\t")
--rs=x Use "x" as the record separator
(default is newline "\n")
-s|--sort=f1[,f2] Sort data ASCII-betically on field(s)
--stdout Print data in original delimited format
(i.e., not in a table format)

--help Show brief help and quit
--man Show full documentation

DESCRIPTION

This program merges the fields -- not the rows -- of delimited text files. That is, if
several files are almost but not quite entirely unlike each other in their structure (in
their field names, numbers or orders), this script allows you to easily unify the files
into one file with all the same fields. The output can be based on fields as determined
by the three "action" flags.

For the following examples, consider three files that contain the following fields:

+------------+---------------------------------+
| File | Fields |
+------------+---------------------------------+
| merge1.tab | name, type, position |
| merge2.tab | name, type, position, lod_score |
| merge3.tab | name, position |
+------------+---------------------------------+

To list all available fields in the files and the number of times they are present:

$ tabmerge --list merge*
+-----------+-------------------+
| Field | No. Times Present |
+-----------+-------------------+
| lod_score | 1 |
| name | 3 |
| position | 3 |
| type | 2 |
+-----------+-------------------+

To merge the files on the minimum overlapping fields:

$ tabmerge merge*
+----------+----------+
| name | position |
+----------+----------+
| RM104 | 2.30 |
| RM105 | 4.5 |
| TX5509 | 10.4 |
| UU189 | 19.0 |
| Xpsm122 | 3.3 |
| Xpsr9556 | 4.5 |
| DRTL | 2.30 |
| ALTX | 4.5 |
| DWRF | 10.4 |
+----------+----------+

To merge the files and include all the fields:

$ tabmerge --max merge*
+-----------+----------+----------+--------+
| lod_score | name | position | type |
+-----------+----------+----------+--------+
| | RM104 | 2.30 | RFLP |
| | RM105 | 4.5 | RFLP |
| | TX5509 | 10.4 | AFLP |
| 2.4 | UU189 | 19.0 | SSR |
| 1.2 | Xpsm122 | 3.3 | Marker |
| 1.2 | Xpsr9556 | 4.5 | Marker |
| | DRTL | 2.30 | |
| | ALTX | 4.5 | |
| | DWRF | 10.4 | |
+-----------+----------+----------+--------+

To merge and extract just the "name" and "type" fields:

$ tabmerge -f name,type merge*
+----------+--------+
| name | type |
+----------+--------+
| RM104 | RFLP |
| RM105 | RFLP |
| TX5509 | AFLP |
| UU189 | SSR |
| Xpsm122 | Marker |
| Xpsr9556 | Marker |
| DRTL | |
| ALTX | |
| DWRF | |
+----------+--------+

To merge the files on just the "name" and "lod_score" fields and sort on the name:

$ tabmerge -f name,lod_score -s name merge*
+----------+-----------+
| name | lod_score |
+----------+-----------+
| ALTX | |
| DRTL | |
| DWRF | |
| RM104 | |
| RM105 | |
| TX5509 | |
| UU189 | 2.4 |
| Xpsm122 | 1.2 |
| Xpsr9556 | 1.2 |
+----------+-----------+

To do the same but mimic the original tab-delimited input:

$ tabmerge -f name,lod_score -s name --stdout merge*
name lod_score
ALTX
DRTL
DWRF
RM104
RM105
TX5509
UU189 2.4
Xpsm122 1.2
Xpsr9556 1.2

Why would you want to do this? Suppose you have several delimited text files with nearly
the same structure and want to create just one file from them, but the fields may be in a
different order in each file and/or some files may contain more or fewer fields than
others. (As far-fetched as it may seem, it happens to the author more than he'd like.)

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