Problem with FASTA filtering

Question

[Janey]

Hi

I already used the following command to extract sequence from fasta file by IDs list.

cut -c 2- ID.text | xargs -n 1 samtools faidx in.fasta > out.fasta

but now i get this error:

xargs: samtools: No such file or directory

I tried to use the seqkit, but seqkit is not worked in my unix system.

I used following commands:

perl -e 'open(F,"File1.txt");while(<F>){/(\S+)/; $k{$1}++}; while(<>){if(/>\s*(\S+?)(\.| )/){if($k{$1}){$k=1}else{$k=0}; } print if $k==1;}' File2.fa
awk -F'[ .]' 'NR==FNR{a[$0]; next}/^>/{p=$2 in a}p' file1 file2
grep -x -F -A 1 -f 'File 2' 'File 1'
cat IDs.txt | awk '{gsub("_","\\_",$0);$0="(?s)^>"$0".*?(?=\\n(\\z|>))"}1' | pcregrep -oM -f - f1.fasta
alias FASTAgrep="awk '{gsub(\"_\",\"\\\_\",\$0);\$0=\"(?s)^>\"\$0\".*?(?=\\\n(\\\z|>))\"}1' | pcregrep -oM -f -"
cat IDs.txt | FASTAgrep f1.fasta

and ........

But in all of these cases, the output file was either empty or contains a full input file. So confused please help me.

[Pierre Lindenbaum]

samtools: No such file or directory

install samtools and/or set your PATH https://stackoverflow.com/questions/14637979/

[Janey]

Do you suggest to download and install the samtools again?

[Pierre Lindenbaum]

if samtools is installed so

samtools: No such file or directory

means that it's not in your PATH. you'll need to update your $PATH variable

[Janey]

samtools was installed Successfully. and this command "cut -c 2- ID.text | xargs -n 1 samtools faidx in.fasta > out.fasta" was worked. my unis system was changed.

[WouterDeCoster]

my unis system was changed.

Assuming you mean here "the computer system of my university was changed" then indeed it looks like you need to reinstall samtools. We don't know what has changed on your system though since you don't provide a lot of information.

[Pierre Lindenbaum]

I used following commands:

what is this supposed to do ?

[Janey]

I wanted to use other methods (commands) to extract sequences from fasta file by IDs list. In addition, I must say that I am a biologist and so I'm not familiar with the programming language. Thanks for helping me with more details about commands.

[Pierre Lindenbaum]

to extract sequences from fasta file by IDs list.

How To Extract A Sequence From A Big (6Gb) Multifasta File ?

Extract sequence with header from a fasta file with specific ID given in another file

extract sequences from multi fasta using partial ID

Extract A Group Of Fasta Sequences From A File

Extract Sequence From Fasta File Using Ids From A Separate File

....

[cpad0112]

@OP: I think you tried too many. please post few entries from list and matching records from fasta. There are easy and established codes (methods) to do whatever you are trying. It is as simple as seqtk subseq <input.fa> <ids.list>.

output:

$ seqtk subseq test.fa ids.txt 
>a
atgc
>c
agtc

input:

$ cat test.fa 
>a
atgc
>b
cggat
>c
agtc

$ cat ids.txt 
a
c