User: Badh2

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Badh20
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Posts by Badh2

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Comment: C: Deleting an illegal character (') in taxon names from many nexus alignments usin
... It worked with a little modification Genomax. Thanks! I used following with a just an extra < for filename in *.nex; do cat ${filename} | tr -d "'" < ${filename} > N_${filename}; done ...
written 12 months ago by Badh20
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Deleting an illegal character (') in taxon names from many nexus alignments using tr -d
... Hello, I want to remove the chacater ' (apostrophe) from a taxon name in all my nexus alignments (~600). I got it worked for a single file but I need help to put this into a loop. Any help on this is appreciated. Following worked for a single file. `tr -d "'" < test.nex > testX.nex` Follo ...
tr -d deleting character written 12 months ago by Badh20
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Comment: C: Removing the last part of fasta header in many alignmnet files
... Thank you very much for all the solutions JC and Dave. I tried the first one and it worked perfectly!! ...
written 13 months ago by Badh20
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Removing the last part of fasta header in many alignmnet files
... Hello, I'm trying to remove the - symbol and anything after that in the following fasta sequence headers in the gene 1 alignment. I have ~500 genes like this to do the same thing. I could get this done only for one gene alignment but I need some help to reiterate this to ~500 alignments. I prefer .F ...
fasta loop sed bash written 13 months ago by Badh20 • updated 13 months ago by JC12k
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Comment: C: How to concatenate .fa files from different directory
... Thanks!! I will try this out. ...
written 15 months ago by Badh20
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Comment: C: How to concatenate .fa files from different directory
... I replaced my directory names and file names :) I just used file1 etc. for easiness now. I want to send a snapshot of what I ran, but this doesn't let me attach an image. But, I'm not sure what you meant by "files" and with what I have to replace it. to do a test run, I made 3 directories, test 1 ...
written 16 months ago by Badh20
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Comment: C: How to concatenate .fa files from different directory
... Hi Genomax, I tried your code exactly as it is. But it gave me "no such file or directory" error. I can't copy paste my code so I just typed the code exactly how I had it. $ ls -R .: files test1 test2 test3 ./test1: file1.FNA file2.FNA file3.FNA ./test2: file1.FNA file2.FNA file3.FNA ./test3: ...
written 16 months ago by Badh20
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Comment: C: How to concatenate .fa files from different directory
... Hello, I wanted to do a similar task and tried the following code, it worked. I wanted to concatenate 3 files with the same name but were in 3 different sub-directories.I have to repeat this for 600+ files so can you help me to put this into a loop. I'm running these in cluster environment. c ...
written 16 months ago by Badh20 • updated 16 months ago by genomax92k
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Comment: C: How to remove Bad Nucleotides represented by "N" from FASTA file by using UNIX?
... WOW!! it worked! Thanks! ...
written 20 months ago by Badh20
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Comment: C: How to remove Bad Nucleotides represented by "N" from FASTA file by using UNIX?
... Hi Genomax, I used sed 's/N//g' your_fasta > new.fa to remove all 'N' from a fasta sequence. It worked but now it has white space in the places of N's. Can you tell me how to get rid of these spaces as well? Following is how it looks like now. Thank you. >DAT1-COMP102480-C1-SEQ1-1788-1 ...
written 20 months ago by Badh20 • updated 20 months ago by genomax92k

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