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Data parsing

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# 1  
Old 09-29-2011
Data parsing
Hi,
I do have a data file which is divided into compartments by ---------. I would like to extract (parse) some of the data and numbers either using awk or sed
The file has the format:
Code:
[CGT]CATGC[AT]

Best GO enrichment: 

Genes/ORF that have the motifs (genes are sorted by max(pa+pd+po)):

A1_1100
  Expression: 103

  Position	 pa	 pd	 po
      -313	5.3	0.0	0.0	tgctttggctGCATGCAttttttatat
      -286	5.3	0.0	0.0	atgcaaaattGCATGCAacgcatgcag
      -277	5.3	0.0	0.0	tgcatgcaacGCATGCAgattttacat
      -314	5.3	0.0	0.0	ttgctttggcTGCATGCattttttata
      -287	5.3	0.0	0.0	tatgcaaaatTGCATGCaacgcatgca

A1_3110
  Expression: 103

  Position	 pa	 pd	 po
      -382	5.3	0.0	0.0	aataataattGCATGCAtgcaattttt
      -104	5.3	0.0	0.0	taccgtcactGCATGCAttacgtgttt
      -383	5.3	0.0	0.0	gaataataatTGCATGCatgcaatttt
      -105	5.3	0.0	0.0	ataccgtcacTGCATGCattacgtgtt

A1_1690
  Expression: 44

  Position	 pa	 pd	 po
      -274	4.8	0.0	0.0	ttaactagttGCATGCAtgaaagaaag
      -275	4.8	0.0	0.0	tttaactagtTGCATGCatgaaagaaa
      -239	4.8	0.0	0.0	aataaatgatTGCATGCgactagaata
---------------------------------------------------------------------------

CC[CT]CAC.

Best GO enrichment: 

Genes/ORF that have the motifs (genes are sorted by max(pa+pd+po)):

A1_2970
  Expression: 38

  Position	 pa	 pd	 po
      -315	2.7	0.0	1.1	ttttggacgcAGTGAGGattaaaatat

A1_3030
  Expression: 38

  Position	 pa	 pd	 po
       -57	2.7	0.0	1.1	aaacgggaaaAGTGAGGaataaatgag
---------------------------------------------------------------------------
.TTCCA.

Best GO enrichment: 

Genes/ORF that have the motifs (genes are sorted by max(pa+pd+po)):

A3_3490
  Expression: 104

  Position	 pa	 pd	 po
      -210	2.7	0.0	0.0	tttaactgaaTTTCCAAttttagttac

A3_880
  Expression: 104

  Position	 pa	 pd	 po
      -245	2.7	0.0	0.0	aaccctattaTTTCCAAatataaaatc
      -317	2.7	0.0	0.0	aaagttgaagCTGGAACactcaaatat
---------------------------------------------------------------------------

What I need to be parsed out is a file with the following format.

Code:
[CGT]CATGC[AT]
A1_1100 103
A1_3110 103
A1_1690 44

CC[CT]CAC.
A1_2970 38
A1_3030 38

.TTCCA.

A3_3490 104
A3_880 104

Please let me know.
# 2  
Old 09-29-2011
Code:
 awk '{printf NF==1?RS $0:FS $0}' infile |awk '/Best GO/{print $1}/Expression/{print $1,$3}/----/{printf RS}'

# 3  
Old 09-29-2011
I got the following syntax error:
Code:
awk: syntax error at source line 1
 context is
	{printf >>>  NF== <<< 
awk: illegal statement at source line 1
awk: illegal statement at source line 1

Would you please look into it
# 4  
Old 09-29-2011
use nawk or /usr/xpg4/bin/awk in Solaris
# 5  
Old 09-29-2011
sorry I am on a mac
# 6  
Old 09-29-2011
Can you show us the awk version?

Code:
awk -V

# 7  
Old 09-29-2011
In my machine awk -V seems not the right command to know the version.
Code:
awk: unknown option -V ignored

awk: no program given

---------- Post updated at 10:17 PM ---------- Previous update was at 10:08 PM ----------

I got it

awk version 20070501
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