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Full Discussion: Merge rows in bid data file
Top Forums UNIX for Dummies Questions & Answers Merge rows in bid data file Post 302605940 by Ygor on Friday 9th of March 2012 06:38:57 AM
Old 03-09-2012
If your file is tab-delimited, as described, and records are grouped together in fours, then try...
Code:
$ cat file1
A_AA960715      leucine-rich repeat-containing protein  GO:0006952      defense response        P
A_AA960715      leucine-rich repeat-containing protein  GO:0008152      metabolic process       P
A_AA960715      leucine-rich repeat-containing protein  GO:0016491      oxidoreductase activity F
A_AA960715      leucine-rich repeat-containing protein  GO:0007165      signal transduction     P
A_AA960716      protein GO:0007075      defense response        P
A_AA960716      protein GO:0008082      metabolic process       P
A_AA960716      protein GO:0016583      oxidoreductase activity F
A_AA960716      protein GO:0009295      signal transduction     P

$ paste - - - - < file1 | awk -F \\t '{printf "%s | %-40s | %s %s %s %s | %s, %s, %s, %s | %s, %s, %s, %s \n", $1, $2, $3, $8, $13, $18, $4, $9, $14, $19, $5, $10, $15, $20}'
A_AA960715 | leucine-rich repeat-containing protein   | GO:0006952 GO:0008152 GO:0016491 GO:0007165 | defense response, metabolic process, oxidoreductase activity, signal transduction | P, P, F, P
A_AA960716 | protein                                  | GO:0007075 GO:0008082 GO:0016583 GO:0009295 | defense response, metabolic process, oxidoreductase activity, signal transduction | P, P, F, P
$

 

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LEARN ABOUT DEBIAN

probalign

PROBALIGN(1)							   User Commands						      PROBALIGN(1)

NAME

       probalign - Align sequences in MFAFILE(s) and print result to standard output

DESCRIPTION

       PROBALIGN  Version  1.4	(Nov 2010) aligns multiple protein sequences and prints to the standard output. Written by Satish Chikkagoudar and
       Usman Roshan using code from PROBCONS version 1.1 (written by Chuong Do) and based upon probA (written by Ulrike Muckstein).

       PROBALIGN 1.4 comes with ABSOLUTELY NO WARRANTY.  This is free software, and you are welcome to redistribute it under  certain  conditions.
       See the README file for details.

   Usage:
	      probalign [OPTION]... [MFAFILE]...

   Description:
	      Align sequences in MFAFILE(s) and print result to standard output

       -clustalw

	      use CLUSTALW output format instead of MFA

       -v, --verbose

	      report progress while aligning (default: off)

       -a, --alignment-order

	      print sequences in alignment order rather than input order (default: off)

       -T, -temperature

	      Sets the thermodynamic temperature parameter

	      (default: 5 (for protein data mode), 1 ( for nucleotide data mode)).

       -score_matrix, --score_matrix

	      Sets  the  type of scoring matrix used to calculate the posterior probabilities (default: gonnet_160, representing gonnet 160, refer
	      README for details)

       -go, --gap-open

	      This option can be used to specify the gap open parameter. The default for Gonnet 160 (protein) is 22 and nucleotide (simple matrix)
	      is 4.

       -ge, --gap-extension

	      This  option  can  be  used to specify the gap extension parameter. The default for Gonnet 160 (protein) is 1 and nucleotide (simple
	      matrix) is 0.25.

       -nuc

	      Specify this option to indicate that inputted sequences are nucleotide sequences

       -prot

	      Specify this option to indicate that inputted sequences are protein sequences [DEFAULT]

       -showPP

	      Outputs the posterior probabilities of alignment columns as a new sequence named Posterior Probabilities (The probability values are
	      scaled to be between integers between 0 and 9).

probalign 1.4							     May 2011							      PROBALIGN(1)
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