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1,117
Posted By dineshkumarsrk
How to add specific bases at the beginning and ending of all the fasta sequences?
Hi,
I have to add 7 bases of specific nucleotide at the beginning and ending of all the fasta sequences of a file. For example, I have a multi fasta file namely test.fasta as given below
test.fasta...
2,085
Posted By dineshkumarsrk
Thank you Robin for your detailed explanation....
Thank you Robin for your detailed explanation. Here, I would like to repeat my question in clear manner.
I have a multiple directories, say for example org1, org2, org3 ..... org100 and each...
2,085
Posted By dineshkumarsrk
How to copy particular files from a multiple directories and paste in a new directory?
Dear all
I have a multiple directories, say for example org1, org2, org3 ..... org100 and each directory having a file namely dnaG.fasta. I need to copy all the dnaG.fasta file from each directory...
2,116
Posted By dineshkumarsrk
How to find a specific sequence pattern in a fasta file?
I have to mine the following sequence pattern from a large fasta file namely gene.fasta (contains multiple fasta sequences) along with the flanking sequences of 5 bases at starting position and...
1,461
Posted By dineshkumarsrk
@RudiC, Both serve my purpose perfectly.
@RudiC,
Both serve my purpose perfectly.
1,461
Posted By dineshkumarsrk
Dear Rudic, Below script can rename the...
Dear Rudic,
Below script can rename the characters in gene1.fasta specified in list.txt.
awk 'FNR==NR{REP[$1]=$2; next} {for (r in REP) gsub(r, REP[r])}1' FS="=" list.txt gene1.fasta
However, it...
1,461
Posted By dineshkumarsrk
Is it possible to rename fasta headers based on its position specified in another file?
I have 5 sequences in a fasta file namely gene1.fasta as follows,
gene1.fasta
>1256
ATGTAGC
>GEP
TAGAG
>GTY578
ATGCATA
>67_iga
ATGCTGA
>90_ld
ATGCTG

I need to rename the gene1.fasta...
1,937
Posted By dineshkumarsrk
How to print the "grep" result as specified keyword order?
I have a content.xls file as given below,
NC_020815.1 1891831 1894692 virb4_A0A0H2X8Z4_ 1 954 1945
NC_020815.1 1883937 1886123 vird4_A0A0P9KA26_ 1 729 1379...
2,173
Posted By dineshkumarsrk
How to replace matching words defined in one file on another file?
I have file1 and file2 as shown below,
file1:...
Forum: Open Source 06-11-2019
118,415
Posted By dineshkumarsrk
As a beginner to Linux environment, I am...
As a beginner to Linux environment, I am comfortable with ubuntu. Because it is easy to handle over other Linux distributions.
2,633
Posted By dineshkumarsrk
How to append two files?
I have two fasta files as shown below,

File:1
>Contig_1:90600-91187
AAGGCCATCAAGGACGTGGATGAGGTCGTCAAGGGCAAGGAACAGGAATTGATGACGGTC
>Contig_98:35323-35886...
1,936
Posted By dineshkumarsrk
How to extract the fasta sequences based on the partial matching strings from another files?
I have a two file as shown below,
file:1
>Contig_152_415 [51615 - 50833] (REVERSE SENSE)
>Contig_152_420 [50829 - 50215] (REVERSE SENSE)
>Contig_152_472 [46116 - 45550] (REVERSE SENSE) ...
1,080
Posted By dineshkumarsrk
I have changed my input dataset as given below, ...
I have changed my input dataset as given below,
xop_thy,80,avr_njk,50,str_nyu,60
avr_irt,70,str_nhj,60,avr_ngt,50
str_tgt,80,xop_nmg,50,xop_nth,40
cyv_gty,40,cop_thl,40,vir_tyk,80...
1,080
Posted By dineshkumarsrk
Dear Don, That is why, I changed my data set as...
Dear Don,
That is why, I changed my data set as comma separated file and modified the awk input code as awk -F","
and awk -F, respectively. But, this modification also failed to generate desired...
1,080
Posted By dineshkumarsrk
Sorry Rudic, When I tried your code, it gives...
Sorry Rudic,
When I tried your code, it gives output like this
xop_thy 80 avr_njk 50 str_nyu 60
avr_irt 70 str_nhj 60 avr_ngt 50
str_tgt ...
1,080
Posted By dineshkumarsrk
How to align/sort the column pairs of an csv file, based on keyword word specified in another file?
I have a csv file as shown below,
xop_thy 80 avr_njk 50 str_nyu 60
avr_irt 70 str_nhj 60 avr_ngt 50
str_tgt 80 xop_nmg 50 xop_nth 40
cyv_gty 40 cop_thl 40 vir_tyk 80...
766
Posted By dineshkumarsrk
This code also works perfectly with the addition...
This code also works perfectly with the addition of >=100.
Sorry Singh, I forgot to mention in my question that greater than or equal to 100 to be replace with TRUE.
766
Posted By dineshkumarsrk
It works perfectly.
It works perfectly.
766
Posted By dineshkumarsrk
How to replace the field values, which are greater than the specified value with TRUE?
I have a csv file as given below,
org1 org2 org3 org4 org5
gene1 100 80 90 80 150
gene2 30 70 50 50 115
gene3 40 120 60 40 105
gene4 20 72 40 60 20
I need to replace...
4,548
Posted By dineshkumarsrk
Dear don, Yes indeed, I could modify the last...
Dear don,
Yes indeed, I could modify the last line of the code as per my need. Your code works perfectly fine. I have realised that, I need to fix the problem by myself. Thank you for your critical...
4,548
Posted By dineshkumarsrk
I have been using your script without any issue,...
I have been using your script without any issue, until I had a data set with different row numbers (I mentioned above). So far, I had processed more than 5 groups of data sets (in each group I had...
4,548
Posted By dineshkumarsrk
Dear Don, There is a minor issue with all those...
Dear Don,
There is a minor issue with all those commands mentioned above. As I told, I have 30 excel files. among them few excel files have lesser rows than others. For example excel file 6 to 10...
4,548
Posted By dineshkumarsrk
Sorry singh, It is only printing the files as...
Sorry singh,
It is only printing the files as given below,
org1.xls
org2.xls
org3.xls
.
.
.
org30.xls
4,548
Posted By dineshkumarsrk
Its printing exactly reverse order. The last...
Its printing exactly reverse order. The last file (0rg30) columns printed first followed by org29, org28 ......org1.
4,548
Posted By dineshkumarsrk
Dear Singh, I need to add one more feature in...
Dear Singh,
I need to add one more feature in your command. I have excel file names as shown below
org1.xls org2.xls org3.xls org4.xls org5.xls ........... org30.xls
The columns 1 and 5 to be...
Showing results 1 to 25 of 47

 

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