10 More Discussions You Might Find Interesting
1. UNIX for Beginners Questions & Answers
I could calculate the length of entire fasta sequences by following command,
awk '/^>/{if (l!="") print l; print; l=0; next}{l+=length($0)}END{print l}' unique.fasta
But, I need to calculate the length of a particular fasta sequence specified/listed in another txt file. The results to to be... (14 Replies)
Discussion started by: dineshkumarsrk
14 Replies
2. Shell Programming and Scripting
I have this file:
>ID1
AA
>ID2
TTTTTT
>ID-3
AAAAAAAAA
>ID4
TTTTTTGGAGATCAGTAGCAGATGACAG-GGGGG-TGCACCCC
Add I am trying to use this script to output sequences longer than 15 characters:
sed -r '/^>/N;{/^.{,15}$/d}'
The desire output would be this:
>ID4... (8 Replies)
Discussion started by: Xterra
8 Replies
3. Shell Programming and Scripting
Hi All,
hope you all are doing well!
I kindly ask you for shell scripting help, here is the description:
I have huge number of files shown below on date wise, which contains different strings(numbers you can say) including 505001 and 602001.
... (14 Replies)
Discussion started by: VasuKukkapalli
14 Replies
4. Shell Programming and Scripting
I have two files. File1 is shown below.
>153L:B|PDBID|CHAIN|SEQUENCE
RTDCYGNVNRIDTTGASCKTAKPEGLSYCGVSASKKIAERDLQAMDRYKTIIKKVGEKLCVEPAVIAGIISRESHAGKVL
KNGWGDRGNGFGLMQVDKRSHKPQGTWNGEVHITQGTTILINFIKTIQKKFPSWTKDQQLKGGISAYNAGAGNVRSYARM
DIGTTHDDYANDVVARAQYYKQHGY
>16VP:A|PDBID|CHAIN|SEQUENCE... (7 Replies)
Discussion started by: nelsonfrans
7 Replies
5. Shell Programming and Scripting
I have a text file, input.fasta contains some protein sequences. input.fasta is shown below.
>P02649
MKVLWAALLVTFLAGCQAKVEQAVETEPEPELRQQTEWQSGQRWELALGRFWDYLRWVQT
LSEQVQEELLSSQVTQELRALMDETMKELKAYKSELEEQLTPVAEETRARLSKELQAAQA
RLGADMEDVCGRLVQYRGEVQAMLGQSTEELRVRLASHLRKLRKRLLRDADDLQKRLAVY... (8 Replies)
Discussion started by: rahim42
8 Replies
6. Shell Programming and Scripting
Hello to all,
I would like to search sequences of bytes inside big binary file.
The bin file contains blocks of information, each block begins is estructured as follow:
1- Each block begins with the hex 32 (1 byte) and ends with FF. After the FF of the last block, it follows 33.
2- Next... (59 Replies)
Discussion started by: Ophiuchus
59 Replies
7. Shell Programming and Scripting
Hi gurus,
I am trying to figure out how to extract substring from file line (all lines in file), as specified position and specified legth.
Example input (file lines)
dhaskjdsa dsadhkjsa dhsakjdsad hsadkjh
dsahjdksahdsad sahkjd sahdkjsahd sajkdh adhjsak
I want to extract substring on... (5 Replies)
Discussion started by: ProsteJa
5 Replies
8. Shell Programming and Scripting
Hi,
I have a file with more than 28000 records and it looks like below..
>mm10_refflat_ABCD range=chr1:1234567-2345678
tgtgcacactacacatgactagtacatgactagac....so on
>mm10_refflat_BCD range=chr1:3234567-4545678...
tgtgcacactacacatgactagtatgtgcacactacacatgactagta
.
.
.
.
.
so on
... (2 Replies)
Discussion started by: Diya123
2 Replies
9. UNIX for Dummies Questions & Answers
Hi, all.
I need to convert a file tab delimited/variable length file in AIX to a fixed lenght file delimited by spaces. This is the input file:
10200002<tab>US$ COM<tab>16/12/2008<tab>2,3775<tab>2,3783
19300978<tab>EURO<tab>16/12/2008<tab>3,28523<tab>3,28657
And this is the expected... (2 Replies)
Discussion started by: Everton_Silveir
2 Replies
10. Shell Programming and Scripting
I want a shell script which extract data from a log file which contains date and time-wise data and i need the data for a perticular interval of time...what can i do??? (3 Replies)
Discussion started by: abhishek27
3 Replies