Merge fasta and group files

Commands in mothur
1

Hi

I am trying to merge a fasta and group files that look like this:

  1. fasta file:

HCZRAFT02HJAN7
A-G-A-T----AAC------AG-C-C-C-AC-C-A-----A-GG-C-G–A-T–G-A—T–AC-A–T–A–G—C-T-G-G-TCT–G-AG—A–G-G-AT–G-AA-C-A-G-CCA-C-…
HCZRAFT02HUO5K
A-G-G-T----AAC------GG-C-T-C-AC-C-A-C…

  1. and a group file specifying which sequence is found in which sample:

HCZRAFT02JI33I C_129
HCZRAFT02IMY3H C_129
…


I'd like to end up with a file that looks like this:

C_129_HCZRAFT02JI33I
A-G-A-T----AAC------AG-C-C-C-AC-C-A-----A-GG-C-G–A-T–G-A—T–AC-A–T–A–G—C-T-G-G-TCT–G-AG—A–G-G-AT–G-AA-C-A-G-CCA-C-…
C_129_HCZRAFT02IMY3H
-G-G-T----AAC------GG-C-T-C-AC-C-A-C…

Could the merge.files command in mothur would work for this?

Any help would be greatly appreciated

Andres

2

Yep, have you tried running merge.files yet?

3

Yes, It basically gave me All the sequences first and then all the info in the group files, so not quite what we wanted, I want my sequence file to have my sample name first, like:

C_129_HCZRAFT02HXC4S

from these 2 files:

Group
HCZRAFT02HXC4S C_129

Seq

HCZRAFT02J3HFZ
GGAACTGAGACGACCGGTCCAGACCTCCGTACGGGGAGGCAGCAGGTGGGGAATCTTC

4

Sorry, I don’t understand what you’re trying to do. Can you also provide the actual command you called?

5

Thanks Pat.

I have come up with a perl script that took me a long time to write and that worked well for what I wanted, but it’d be great mothur would allow to do this:

I have a fasta file and a group file, my fasta file does not have any information on sample affiliation, just a code that looks like this:

HCZRAFT02IZ45I
AAGGCAACGATCAGTAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGTCCAAACTCCTACGGGAGGCAGCAGTGAGGAATATTGGTCAATGGGCGAGAGCCTGAACCAGCCAAGTAGCGTGCAGGACGACGGCCCTATGGGTTGTAAACTGCTTTTATAGGGGAATAAAGTGAGCCACGTGTGGCTTTTTGCATGTACCCTATGAATAAGGACCGGCTAATTCCG
HCZRAFT02JHPKN
ATTACCGCGCTGCTGGCACGTAGTAAGCCGATGCTTCCTCAGTAGGTACCGTCCATTCTCGTCCCCACCTGACAAAGGTTTAACAATCCGAAGACC…


my group file has info o which sequence belongs to which sample. HCZRAFT02IZ45I C_129 HCZRAFT02JHPKN C_128
I want to merge the 2 files in one so that my fasta file incorporates the sample id before sequence ID, like this:

C_128_HCZRAFT02IZ45I
AAGGCAACGATCAGTAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGTCCAAACTCCTACGGGAGGCAGCAGTGAGGAATATTGGTCAATGGGCGAGAGCCTGAACCAGCCAAGTAGCGTGCAGGACGACGGCCCTATGGGTTGTAAACTGCTTTTATAGGGGAATAAAGTGAGCCACGTGTGGCTTTTTGCATGTACCCTATGAATAAGGACCGGCTAATTCCG
C_129_HCZRAFT02JHPKN
ATTACCGCGCTGCTGGCACGTAGTAAGCCGATGCTTCCTCAGTAGGTACCGTCCATTCTCGTCCCCACCTGACAAAGGTTTAACAATCCGAAGACC…

The whole idea is to be able to use a curated fasta file to get qiime to give me a .biome OTU table to use in PICRUSt later. It’d be great if mothur had that option. I always use mothur to curate my sequences, because I believe I get way better quality data but qiime and galaxy have other very interesting analysis tools.

Thanks

Andres

6

So I used :
merge.files (input=All_Howler.fasta-All_Howler.groups, output=Merged.fasta)

7

We had a similar request, Manipulate Sequence Identifiers The rename.seqs command will be part of 1.32.0. The command appends the group name to the original sequence name.

HCZRAFT02JI33I C_129 would become HCZRAFT02JI33I_C_129.