I have a task to do. I am doing multiple sequence analysis for some genes. I have several files with sequences in order. I would like to extract first sequence of each file into new file and like till the last sequence. I know only how to do with first or any specific line with awk. awk 'FNR == 2 {print; nextfile}' *.txt > newfile
Now I learned for two files with this
paste File1 File2 | awk '{ p=$2;$2="" }NR%2{ k=p; print }!(NR%2){ v=p; print $1 RS k RS v }'
Here I have input like this
File 1
Saureus081.1
ATCGGCCCTTAA
Saureus081.2
ATGCCTTAAGCTATA
Saureus081.3
ATCCTAAAGGTAAGG
File 2
SaureusRF1.1
ATCGGCCCTTAC
SauruesRF1.2
ATGCCTTAAGCTAGG
SaureusRF1.3
ATCCTAAAGGTAAGC
File 3
SaureusN305.1
ATCGGCCCTTACT
SauruesN305.2
ATGCCTTAAGCTAGA
SaureusN305.3
ATCCTAAAGGTAATG
And similar files 12 are there File 3 File 4 . . . .File 12 Required
Output
Saureus081.1
ATCGGCCCTTAA
SaureusRF1.1
ATCGGCCCTTAC
SaureusN305.1
ATCGGCCCTTACT
Saureus081.2
ATGCCTTAAGCTATA
SaureusRF1.2
ATGCCTTAAGCTAGG
SauruesN305.2
ATGCCTTAAGCTAGA
Saureus081.3
ATCCTAAAGGTAAGG
SaureusRF1.3
ATCCTAAAGGTAAGC
SaureusN305.3
ATCCTAAAGGTAATG
Thank you
2 answers
Just a paste and awk based approach based on the assumption that a) the sequence is in one line and not wrapped b) no tabs spaces in parent fasta. The getline function in awk gets the next line and it is then skipped by awk.
paste -d "\t" *.fa |awk '{getline y;split(y,z,"\t");for (i=1;i<=NF;i++){print $i "\n" z[i]} }'
using sqlite3: just put your sequence in a database and pull them out.
v=1 && \
rm -f db.sqlite3 && \
sqlite3 db.sqlite3 'create table S(name,sequence,num,file);' && \
for F in input1.txt input2.txt input3.txt
do
awk -v fidx=$v '{if(NR%2==1) {printf("insert into S(name,sequence,num,file) values(\"%s\",\"",$0);} else {num++;printf("%s\",%d,%d);\n",$0,num,fidx);}}' $F |\
sqlite3 db.sqlite3;
((v++))
done && \
v=$(sqlite3 db.sqlite3 'select max(num) from S;') && \
while [ $v -gt 0 ]
do
sqlite3 db.sqlite3 "select (name||x'0A'||sequence) from S where num=$v order by file;" > out${v}.txt ;((v--));
done
Hi Thanks for script but when I am running this script I am getting these errors
Error: near line 1: near "v": syntax error
Error: near line 5: near "do": syntax error
Error: incomplete SQL: ((v++))
done && \
v=$(sqlite3 db.sqlite3 'select max(num) from S;') && \
while [ $v -gt 0 ]
do
sqlite3 db.sqlite3 "select (name||x'0A'||sequence) from S where num=$v order by file;" > out${v}.txt ;((v--));
done
I don't know the reason because I never used sqlite earlier. Thank you
Ah yes, I've reformatted it on the fly. I've just removed a semicolon, can you please try again please.
I tried but again same errors I want to edit my question once. Please take a look and thank you for your help
Error: near line 1: near "v": syntax error
Error: incomplete SQL: ((v++))
done && \
v=$(sqlite3 db.sqlite3 'select max(num) from S;') && \
while [ $v -gt 0 ]
do
sqlite3 db.sqlite3 "select (name||x'0A'||sequence) from S where num=$v order by file;" > out${v}.txt ;((v--));
done
okay here is the gist that worked on my machine:
Sorry again Only syntax errors are coming
Error: near line 1: near "v": syntax error
Error: near line 5: near "do": syntax error
Error: near line 8: near "(": syntax error
Error: near line 9: near "done": syntax error
Error: incomplete SQL: do
sqlite3 db.sqlite3 "select (name||x'0A'||sequence) from S where num=$v order by file;" > out${v}.txt ;((v--));
done
Maybe fault with my data?
Shell is bin/zsh
Sorry I can't add more replies since I am a new user. So I am editing my previous commnet. Thank you
what is your shell ?
Log in to answer this question.
Why the output has
Can you precisely tell what is the output ? Do you want to create a separate file for each sequence and write the sequence from all the files ? Write seq1 from all files to a single file, and seq2 from all files to another file ... and so on ?
I typed those just for example Sorry for the laziness. Its nothing but Seq of next file with sequence.
works with bash shell. Install seqkit from here. Keep your fasta files in a separate folder. Output will be out.fasta and extension can be customized.
Code that works (on ubuntu/mint with bash shell):
input files (input files are copy/pasted from above):
input:
Post ouptut:
output (from the above command): .