Search Results

Search: Posts Made By: the_simpsons
1,350
Posted By the_simpsons
hi, this is not a homework. This is related to my...
hi, this is not a homework. This is related to my bioinformatics research. I do not know how to programming.

The key in B file appear twice in file A.
1,350
Posted By the_simpsons
How to extract specific information?
hi, i have a file A like this:


******************* No 2823 ********************
contig15205-
G383C4U02H4G80+ is in contig15205-
G383C4U02HGLXM- is in...
797
Posted By the_simpsons
Thanks, that works perfectly.
Thanks, that works perfectly.
797
Posted By the_simpsons
Delete some words
hi, i have a fasta file like this:

>contig00003 length=363 numreads=45 gene=isogroup00001 status=it_thresh
GATTTTTTACCCTGGGAGTGAGGAGGACGAGGTTGAGGATGAAGAAAAGAGAAAGATGAAGAGGTTGAGGATGTT...
1,631
Posted By the_simpsons
0000000 J A T _ 1 5 6 6 2 \n ...
0000000 J A T _ 1 5 6 6 2 \n J A T _ 2 1
0000020 1 0 5 \n J A T _ 2 3 7 6 8 \n J A
0000040 T _ 1 1 6 8 3 \n J A ...
1,631
Posted By the_simpsons
I already tried, but the file is empty.
I already tried, but the file is empty.
1,631
Posted By the_simpsons
I'm using a mac. It probably is not the awk...
I'm using a mac. It probably is not the awk problem.
1,631
Posted By the_simpsons
Hi, protocomm, Thanks, however, I didn't get...
Hi, protocomm,

Thanks, however, I didn't get anything using your code.
1,631
Posted By the_simpsons
Hi, jim. Thanks for your response. However,...
Hi, jim.
Thanks for your response. However, when i tried your code, the resultfile is exactly same as the bigfile.

There are about 4500 keys in the key file.
I haven't tried other methods...
1,631
Posted By the_simpsons
How to extract information a file according key id in another file?
hi, i have a large file containing the detailed information of a bunch of keys like this:


JAT_0001 contig102_342_3_n2 contig102_342 atgcacgacta 30 50 20...
898
Posted By the_simpsons
How to delete strings in a file?
hi, i have a big file like this:

>s31 length=12 numreads=6 gene=isotig454 status=igo
ldfddfdfdfdkkkkkkfdfdkkkksdfdkkkkkkkkkksdfd
dfdfdfldfdkdffdlfddflfdjkkkkkkfdgkkgfhghfgkkk...
2,295
Posted By the_simpsons
Thanks!! It works perfect
Thanks!! It works perfect
2,295
Posted By the_simpsons
Thanks a lot, i will try it
Thanks a lot, i will try it
2,295
Posted By the_simpsons
Sorry, i think i didn't say it clearly. I...
Sorry, i think i didn't say it clearly.

I have a xml file A like this:

<Iteration>
<Iteration_iter-num>3</Iteration_iter-num>
<Iteration_query-ID>lcl|3_0</Iteration_query-ID>
...
2,295
Posted By the_simpsons
Actually both files are very large, and the...
Actually both files are very large, and the inquires in file B are not continuous.
2,295
Posted By the_simpsons
How to extract information from a file?
Hi, i have a file like this:

<Iteration>
<Iteration_iter-num>3</Iteration_iter-num>
<Iteration_query-ID>lcl|3_0</Iteration_query-ID>
<Iteration_query-def>G383C4U01EQA0A...
936
Posted By the_simpsons
hi, itkamaraj, Thanks for your response, but it...
hi, itkamaraj,
Thanks for your response, but it did not work. It seems only the length=100, 100x, 100xx were deleted.
936
Posted By the_simpsons
How to delete lines like this??
hi, i have a very large file like this:


<Iteration>
<Iteration_iter-num>1073</Iteration_iter-num>
<Iteration_query-ID>lcl|1073_0</Iteration_query-ID>
...
774
Posted By the_simpsons
Add column to file A according to file B
Hi, i have a file A like this:

JAT1
JAT2
JAT3
JAT4
JAT5
JAT6
...



and file B:

JAT2 1.2
JAT4 2.3
JAT6 1.5
...
994
Posted By the_simpsons
Rudic, Thanks!!! If i want to replace...
Rudic, Thanks!!!

If i want to replace contig00002 length=24 ... to contig00002_newbler, contig00004 length=30 ... to contig00004_newbler, and so on.

What should i do??
994
Posted By the_simpsons
Replace names in a file
Hi, I have a file like this:

>Contig1
TTTTCATCAGCAATAGGTGCCTTCAACAAGTTTGAGAATTTTTTACACATGACTACAGGG
CACGTGCACAATGTTTTGAGCACTGCCAATGTCGTCTTTTCTTCCCTGCTGATTCTATTT...
1,230
Posted By the_simpsons
Delete lines according to a key words in that line
HI, I have a file A like this:

c 1
length 14432
width 3434
temp 34
c 2
length 3343
width 0923
height 9383
hm 902
temp34
c 3
length 938
height 982
hm 9292
temp 23
...
3,568
Posted By the_simpsons
Thanks, but it seems not work.
Thanks, but it seems not work.
3,568
Posted By the_simpsons
How to grep paragraph?
Hi, I have A file like this:

>Contig1
AAAAAAATTTTTTCCCAATATATGAT
ATATATAEATATATAT
>Contig2
AAAAAAATTTTTTCCCAATATATGAT
ATATATAEAATTTTTAATTTTTTCCCA
ATCCCAAATATATAT
>Contig3...
1,022
Posted By the_simpsons
Calculation
Hi, i have a large file like this:
Contig1 1 5
Contig1 2 4
Contig1 3 3
Contig1 4 5
Contig1 5 3
Contig1 6 4
Contig2 1 3
Contig2 2 7
Contig2 3 2
Contig2 4 9
Contig2 5 10
Contig2 6 3...
Showing results 1 to 25 of 35

 
All times are GMT -4. The time now is 11:04 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy