I`m trying to do functional categorization of a species and I need to join 3 files for that. I want to look up the code for each record in file 3 in file 1 ,
code indicated within brackets[] for example OR is the code forAt1g31340, J is the code for At1g53930.
Then I would like to find the description of the code from file 2.
The R in any code can be ignored unless it is [R] itself.
For example [OR], [JR] should be treated as [O] and [J] but [R] is treated as [R].
This doesn't produce any output, even with the sample data.
Not sure why! This is what I get.
Sample input datas:
Code:
$ cat file1.txt
[OR] KOG0001 Ubiquitin and ubiquitin-like proteins
ath: At1g31340
ath: At1g53930
ath: At1g53950
[J] KOG0002 60s ribosomal protein L39
ath: At2g36170
ath: At3g02190
$ cat file2.txt
INFORMATION STORAGE AND PROCESSING
[J] Translation, ribosomal structure and biogenesis
[A] RNA processing and modification
[K] Transcription
[L] Replication, recombination and repair
[B] Chromatin structure and dynamics
CELLULAR PROCESSES AND SIGNALING
[D] Cell cycle control, cell division, chromosome partitioning
[Y] Nuclear structure
[V] Defense mechanisms
[T] Signal transduction mechanisms
[M] Cell wall/membrane/envelope biogenesis
[N] Cell motility
[Z] Cytoskeleton
[W] Extracellular structures
[U] Intracellular trafficking, secretion, and vesicular transport
[O] Posttranslational modification, protein turnover, chaperones
METABOLISM
[C] Energy production and conversion
[G] Carbohydrate transport and metabolism
[E] Amino acid transport and metabolism
[F] Nucleotide transport and metabolism
[H] Coenzyme transport and metabolism
[I] Lipid transport and metabolism
[P] Inorganic ion transport and metabolism
[Q] Secondary metabolites biosynthesis, transport and catabolism
POORLY CHARACTERIZED
[R] General function prediction only
[S] Function unknown
$ cat file3.txt
At1g53930
At2g36170
Output:
Code:
$ ./prog.awk
At1g53930|O|Posttranslational modification, protein turnover, chaperones |CELLULAR PROCESSES AND SIGNALING
At2g36170|J|Translation, ribosomal structure and biogenesis |INFORMATION STORAGE AND PROCESSING
# cat file1.txt
[OR] KOG0001 Ubiquitin and ubiquitin-like proteins
ath: At1g31340
ath: At1g53930
ath: At1g53950
[J] KOG0002 60s ribosomal protein L39
ath: At2g36170
ath: At3g02190
# cat file2.txt
INFORMATION STORAGE AND PROCESSING
[J] Translation, ribosomal structure and biogenesis
[A] RNA processing and modification
[K] Transcription
[L] Replication, recombination and repair
[B] Chromatin structure and dynamics
CELLULAR PROCESSES AND SIGNALING
[D] Cell cycle control, cell division, chromosome partitioning
[Y] Nuclear structure
[V] Defense mechanisms
[T] Signal transduction mechanisms
[M] Cell wall/membrane/envelope biogenesis
[N] Cell motility
[Z] Cytoskeleton
[W] Extracellular structures
[U] Intracellular trafficking, secretion, and vesicular transport
[O] Posttranslational modification, protein turnover, chaperones
METABOLISM
[C] Energy production and conversion
[G] Carbohydrate transport and metabolism
[E] Amino acid transport and metabolism
[F] Nucleotide transport and metabolism
[H] Coenzyme transport and metabolism
[I] Lipid transport and metabolism
[P] Inorganic ion transport and metabolism
[Q] Secondary metabolites biosynthesis, transport and catabolism
POORLY CHARACTERIZED
[R] General function prediction only
[S] Function unknown [root@scalemp fescue_genome]# more file2.txt
INFORMATION STORAGE AND PROCESSING
[J] Translation, ribosomal structure and biogenesis
[A] RNA processing and modification
[K] Transcription
[L] Replication, recombination and repair
[B] Chromatin structure and dynamics
CELLULAR PROCESSES AND SIGNALING
[D] Cell cycle control, cell division, chromosome partitioning
[Y] Nuclear structure
[V] Defense mechanisms
[T] Signal transduction mechanisms
[M] Cell wall/membrane/envelope biogenesis
[N] Cell motility
[Z] Cytoskeleton
[W] Extracellular structures
[U] Intracellular trafficking, secretion, and vesicular transport
[O] Posttranslational modification, protein turnover, chaperones
METABOLISM
[C] Energy production and conversion
[G] Carbohydrate transport and metabolism
[E] Amino acid transport and metabolism
[F] Nucleotide transport and metabolism
[H] Coenzyme transport and metabolism
[I] Lipid transport and metabolism
[P] Inorganic ion transport and metabolism
[Q] Secondary metabolites biosynthesis, transport and catabolism
POORLY CHARACTERIZED
[R] General function prediction only
[S] Function unknown
# cat file3.txt
At1g53930
At2g36170
# ./prog.awk
#
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