Hello,

I am trying to write a perl one liner that I can input a txt file into, and output the contents of that text file in fasta format.

Text file attributes: -100,000 rows (100,000 sequences) in text file -Headings of my txt file are: Sequence, Name, Count, Countb

I want the output to look like:
>Sequence1_Name_Count_Countb

Sequence1

>Sequence2_Name_Count_Countb

Sequence2

...

>Sequence100000_Name_Count_Countb

Sequence100000

The Perl one liner I have so far is:

cat file.txt | perl -ne 'chomp;@a=split(/\t/);$a[0]=~s/\s+//g;$a[1]=~s/\s+//g;$a[2]=~s/\s+//g;$a[3]=~s/\s+//g; print ">$a[0]_$a[2]_$a[1]_$a[3]\n$a[0]\n";' > fastafile.fa

THe only thing that ends up printing at all, is the first sequence in fasta format. Nothing else prints at all. Can someone help me modify my one liner so that it prints every row of the txt file in the correct format rather than just the first? Am I missing a loop??

Thank you in advance.

In reply to Printing all lines of a file using a perl one liner by la

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