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write_tab
Outputting the data stream as a table can be done with [write_tab] which will write generate one row per record with the values as columns.
... | write_tab [options]
[-? | --help] # Print full usage description.
[-x | --no_stream] # Do not emit records.
[-o <file> | --data_out=<file>] # Write result to file.
[-c | --comment] # Print comment line - Default=no
[-p | --pretty] # Pretty print table.
[-C | --commify] # Commify numbers when pretty printing.
[-d <string> | --delimit=<string>] # Changes delimiter - Default='\t'
[-k <string> | --keys=<string>] # Comma separated list of keys to print in that order.
[-K <string> | --no_keys=<string>] # Comma separated list of keys to ignore.
[-I <file!> | --stream_in=<file!>] # Read input from stream file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output to stream file - Default=STDOUT
[-Z <string> | --compress=<string>] # Compress output using <gzip|bzip2>.
[-v | --verbose] # Verbose output.
Consider the following records in the stream:
Organism: Human
Count: 23524
Sequence: ATACGTCAG
---
Organism: Dog
Count: 2442
Sequence: AGCATGAC
---
Organism: Mouse
Count: 234
Sequence: GACTG
---
Organism: Cat
Count: 2342
Sequence: AAATGCA
---
To write all records from the stream as a table, do:
... | write_tab -x
Human 23524 ATACGTCAG
Dog 2442 AGCATGAC
Mouse 234 GACTG
Cat 2342 AAATGCA
If you supply the optional -c switch, when the first row in the table will be a 'comment' line prefixed with a '#':
... | write_tab -c -x
#Organism Count Sequence
Human 23524 ATACGTCAG
Dog 2442 AGCATGAC
Mouse 234 GACTG
Cat 2342 AAATGCA
You can also change the delimiter from the default (tab) to e.g. ',':
... | write_tab -d ',' -x
Human,23524,ATACGTCAG
Dog,2442,AGCATGAC
Mouse,234,GACTG
Cat,2342,AAATGCA
If you want the values output in a specific order you have to supply a comma
separated list using the -k switch that will print only those keys in that order:
... | write_tab -k Sequence,Count -x
ATACGTCAG 23524
AGCATGAC 2442
GACTG 234
AAATGCA 2342
Keys from e.g. [read_tab] V0, V1, V2 ... Vn, is automagically sorted numerically.
Alternatively, if you have some keys that you don't want in the tabular output,
use the -K switch. So to print all keys except SEQ and SEQ_TYPE do:
... | write_tab -K Sequence -x
Human 23524
Dog 2442
Mouse 234
Cat 2342
And if you want a pretty printed table use the -p switch and throw in the -C switch
if you want commified numbers.
... | write_tab -cpC -x
+----------+--------+-----------+
| Organism | Count | Sequence |
+----------+--------+-----------+
| Human | 23,524 | ATACGTCAG |
| Dog | 2,442 | AGCATGAC |
| Mouse | 234 | GACTG |
| Cat | 2,342 | AAATGCA |
+----------+--------+-----------+
[read_tab]
[grab]
Martin Asser Hansen - Copyright (C) - All rights reserved.
August 2007
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
[write_tab] is part of the Biopieces framework.