10 More Discussions You Might Find Interesting
1. Shell Programming and Scripting
Input File:
>Seq1
ASDADAFASFASFADGSDGFSDFSDFSDFSDFSDFSDFSDFSDFSDFSDFSD
>Seq2
SDASDAQEQWEQeqAdfaasd
>Seq3
ASDSALGHIUDFJANCAGPATHLACJHPAUTYNJKG
......
Desired Output File
>Seq1
ASDADAFASF
ASFADGSDGF
SDFSDFSDFS
DFSDFSDFSD
FSDFSDFSDF
SD
>Seq2 (4 Replies)
Discussion started by: patrick87
4 Replies
2. UNIX for Dummies Questions & Answers
I have the following script:
awk 'FNR==NR{s+=$3;next;} { print $1 , $2, 100*$3/s }'
and the following file:
>P39PT-1224 Freq 900
cccctacgacggcattggtaatggctcagctgctccggatcccgcaagccatcttggatatgagggttcgtcggcctcttcagccaagg-cccccagcagaacatccagctgatcg
>P39PT-784 Freq 2... (2 Replies)
Discussion started by: Xterra
2 Replies
3. Shell Programming and Scripting
Hello, here I am posting my query again with modified data input files.
see my query is :
i have two input files file1 and file2.
file1 is smalldata.fasta
>gi|546671471|gb|AWWX01449637.1| Bubalus bubalis breed Mediterranean WGS:AWWX01:contig449636, whole genome shotgun sequence... (20 Replies)
Discussion started by: harpreetmanku04
20 Replies
4. Shell Programming and Scripting
I would like to take a fasta file formated like
>0001
agttcgaggtcagaatt
>0002
agttcgag
>0003
ggtaacctga
and use command line perl to move the all sample gt 8 in length to a new file. the result would be
>0001
agttcgaggtcagaatt
>0003
ggtaacctga
cat ${sample}.fasta | perl -lane... (2 Replies)
Discussion started by: jdilts
2 Replies
5. Shell Programming and Scripting
Hi,
I want to match the sequence id (sub-string of line starting with '>' and extract the information upto next '>' line ). Please help .
input
> fefrwefrwef X900
AGAGGGAATTGG
AGGGGCCTGGAG
GGTTCTCTTC
> fefrwefrwef X932
AGAGGGAATTGG
AGGAGGTGGAG
GGTTCTCTTC
> fefrwefrwef X937... (2 Replies)
Discussion started by: ritakadm
2 Replies
6. UNIX for Dummies Questions & Answers
Hi, I have a file1 of many long sequences, each preceded by a unique header line. file2 is 3-columns list: headers name, start position, end position. I'd like to extract the sequence region of file1 specified in file2.
Based on a post elsewhere, I found the code:
awk... (2 Replies)
Discussion started by: pathunkathunk
2 Replies
7. UNIX for Dummies Questions & Answers
Hi
I have an alignment file (.fasta) with ~80 sequences. They look like this-
>JV101.contig00066(+):25302-42404|sequence_index=0|block_index=4|species=JV101|JV101_4_0
GAGGTTAATTATCGATAACGTTTAATTAAAGTGTTTAGGTGTCATAATTT
TAAATGACGATTTCTCATTACCATACACCTAAATTATCATCAATCTGAAT... (2 Replies)
Discussion started by: baika
2 Replies
8. Shell Programming and Scripting
Hello guys,
I guess you are fed up with sed command and parse questions, but after a while researching the forum, I could not get an answer to my doubt. I know it must be easy done with sed command, but unfortunately, I never get right syntax of this command
OK, this is what I have in my... (3 Replies)
Discussion started by: manolain
3 Replies
9. Shell Programming and Scripting
Hi,
I have 3 kind of files that contains date data needed to be masked. The file is like this:
File 1 (all contents in 1 line):
input:DTM+7:201103281411:203'LOC+175+SGSIN:139:6+TERMINATOR......'DTM+132:201103281413:203'LOC....
output:... (4 Replies)
Discussion started by: Alvin123
4 Replies
10. Shell Programming and Scripting
Hi.. I have a seperate chromosome sequences and i wanted to parse some regions of chromosome based on start site and end site.. how can i achieve this?
For Example Chr 1 is in following format
I need regions from 2 - 10 should give me AATTCCAAA
and in a similar way 15- 25 should give... (8 Replies)
Discussion started by: empyrean
8 Replies