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Thanks Ravinder!

Hi,
I have an input file that looks like this (columns are tab delimited:

Data000005-RA GO:0003735 GO:0005840 GO:0006412
Data000005-RA GO:0003735 ...

Hi bakunin
thanks for taking the time to go through it and providing the example.
you are right:
DD!! # after second passis exactly what I need.
This is irrespective of the codon, reading...

Hi Unix Gurus,

I have a file with data like:

>header_1
TCCCCGA
>header_2
CCAATTGGGTA
The data to work with starts from the next line after '>header_xx'.
(1)
I want to search the three...

Both working fine! Thanks a lot!

Hi Unix gurus,

I've a dna sequence in a file format known as fasta format (sequence header starts with > and ignored), an example shown below:

>sequence_1
CGTATTCTCCGAATACC
ATACG
>sequence_2...

awk - because in some previous example I found it simple, easy to use and re usability in other similar problems.
what I naively tried e.g. 'list.data.txt' seems working ok.
paste <(awk '/^>/ {...

Hi,
I've two list files and two corresponding data files which looks like:

list1.txt
list1.data.txt
Similarly:
list2.txt
list2.data.txt
What I need is merging two list files into one list...

Hi,

I am looking for bash or awk script to solve the following.
Input File 1:

>Min_0-t10270-RA|>Min_0-t10270-RA protein AED:0.41 eAED:0.46 QI:0|0|0|0.25|1|1|4|0|190...

save the text in a file e.g. 'file.txt':
input: file.txt
T111||T222||T444||T222||T555
command:
cat file.txt |tr -s '||' '\n'|sort|uniq -u|tr -s '\n' ' '
output:
T111 T444 T555

Dear Yoda,

Thanks for your reply. Your code is working, it adds the 'NNNN's after each subject line, it would be great if code is modified to add 'NNNN's at the end of the Sbjct of a whole block...

I need some help to construct a long 'Sbjct' string from the following input using incremental order of 'Sbjct' starting number (e.g. 26325115,33716368,33769033,34869860 etc.)
Different 'Sbject'...

Hi Everyone,

I need some help to construct a long 'Sbjct' string from the following input using incremental order of 'Sbjct' starting number (e.g. 26325115,33716368,33769033,34869860 etc.)...

Thanks. I don't have 'nawk' in my MAC-OSX. So replacing 'nawk' with 'awk' and with your code and the data files above I get the following output, which appears incorrect:
TTGAGATCCG
G
TTCCTGTTCA

Hi everyone,

I have a large text file containing DNA sequences in fasta format as follows:
>someseq
GAACTTGAGATCCGGGGAGCAGTGGATCTC
CACCAGCGGCCAGAACTGGTGCACCTCCAG
GCCAGCCTCGTCCTGCGTGTC...

Thanks for your reply mirni. Just two issues:
1) If I am not mistaken your code seems producing the output exactly as the input
2) On top of the criteria I described at the beginning of the post....

Working Fine. Thanks a lot!

Thanks for your reply. However, it seems I don't have 'nawk' in my MacOSX 10.6.8. Any idea how to run it or any 'awk' equivalent? Thanks.

Hi,

I have a file with the lines as below:
C_10_A05_T7
C_10_A06_SP6
C_10_B05_SP6
C_10_B05_T7
C_10_B01_SP6
C_10_B01_T7
C_12_G07_SP6
C_12_G11_SP6
C_12_G11_T7
C_2_H18_T7
C_2_I02_SP6...

Gr8.Working Fine.Thanks.

Thanks for your reply.
Both the files are ordered. Thats right.
However, there are more numbers than records in the datafile.
For example, there are three L1_T1 headers, however, for this the...

I am trying to search and replace using two different files with strict search rules.
One file contain some data and the other file contain some numbers as shown below.
DataFile.txt

>L1_T1
text...

Hi I've two text files FILE_1 and FILE_2 as shown below:

FILE_1.txt


CO Contig1 342 12 11 U
GGGCTGACGTGGCCGCTAATACGACTCACTATAGGG*AGAGAAGTCATTTTCTTGTTTAG

BQ
35 35 35 50 50 50 50 50 50 50...

Hi,
Thanks for your reply.
I've tried your code:
awk 'NR==FNR{A[RS$1]=$0;next}A[$1]{print ">"A[$1];next}1' RS=\> MainFile.txt RS="\n" OtherFile*.txt

However, it's just giving me he '>Header',...

Hi,

I have several text files. One main file contains the detail data, other have some information to extract data from the main file, and some are empty files. Examples are shown below:
The main...