concatenating fasta files with TAB seperating loci

[schwentner]

Hi,

I have a problem concatenating files so that I can load them into Arlequin. I have a few thousand fasta (or nexus) files each representing a single gene. However, not all individuals are present in all files. I want to concatenate these in such a way, that missing genes are filled with Ns or ? or - and that genes are seperated by TAB. I have found many tools, but none allowed TAB seperation of loci. I would be happy for any ideas.

Examples:

Input 1
Neo001_0 CGTAAAAATTTGTTCCGAAACATA
Neo001_1 CGTAAAAATTTGTTCCGAAACATA
Neo003_0 CGTAAAAATTTGTTCCGAAACATA
Neo003_1 CGTAAAAATTTGTTCCGAAACATA
Neo004_0 CGTAAAAATTTGTTCCGAAACATA
Neo004_1 CGTAAAAATTTGTTCCGAAACATA


Input2
Neo001_0 CGATGTATTTGGTATCCTAC
Neo001_1 CGATGTATTTGGTATCCTAC
Neo002_0 CGATGTATTTGGTATCCTAC
Neo002_1 CGATGTATTTGGTATCCTAC
Neo003_0 CGATGTATTTGGTATCCTAC
Neo003_1 CGATGTATTTGGTATCCTAC
Neo004_0 CGATGTATTTGGTATCCTAC
Neo004_1 CGATGTATTTGGTATCCTAC




Expected output:
Expected output:
Neo001_0 CGTAAAAATTTGTTCCGAAACATA CGATGTATTTGGTATCCTAC
Neo001_1 CGTAAAAATTTGTTCCGAAACATA CGATGTATTTGGTATCCTAC
Neo002_0 NNNNNNNNNNNNNNNNNNNNNNNN CGATGTATTTGGTATCCTAC
Neo002_1 NNNNNNNNNNNNNNNNNNNNNNNN CGATGTATTTGGTATCCTAC
Neo003_0 CGTAAAAATTTGTTCCGAAACATA CGATGTATTTGGTATCCTAC
Neo003_1 CGTAAAAATTTGTTCCGAAACATA CGATGTATTTGGTATCCTAC
Neo004_0 CGTAAAAATTTGTTCCGAAACATA CGATGTATTTGGTATCCTAC
Neo004_1 CGTAAAAATTTGTTCCGAAACATA CGATGTATTTGGTATCCTAC


Many thanks,
Martin

[ATϟGC]

The concatenate function of Seqkit [https://bioinf.shenwei.me/seqkit/usage/#concat] will concatenate sequences with matching ID's from two fasta files.

I converted your inputs into fasta format and the following command concatenated matching ID's together.

$seqkit concat input1.txt input2.txt >output.txt

But it did not add the N's and there is no space delimiting the two sequences. Maybe you can get it to add a delimiter.

[kmcarr]

Sometimes the old solutions are the best solutions, the good ol' Unix join command:

join -e 'NNNNNNNNNNNNNNNNNNNNNNNN' -1 1 -2 1 -a 1 -a 2 -o '0,1.2,2.2' Input1.txt Input2.txt

Assumptions

• Your input files as shown are named Input1.txt and Input2.txt
• The input files have both been sorted prior to running the join command

Read the man page for join to learn what all the various command line parameters are doing.