trim_msa

The trim_msa command will trim a MSA given a user-specified mask file, or the archaeal/bacterial mask present in the reference data.

Arguments

usage: gtdbtk trim_msa --untrimmed_msa UNTRIMMED_MSA --output OUTPUT
                       (--mask_file MASK_FILE | --reference_mask {arc,bac})
                       [--debug] [-h]

required named arguments

--untrimmed_msa

path to the untrimmed MSA file

--output

output file

mutually exclusive required arguments

--mask_file

path to a custom mask file for trimming the MSA

--reference_mask

Possible choices: arc, bac

reference mask already present in GTDB-Tk

Named Arguments

--debug

create intermediate files for debugging purposes

Example

Input

gtdbtk trim_msa --untrimmed_msa msa.faa --output msa_trim.faa --mask_file mask.txt

#### msa.faa

>genome_a
AKLAK

#### mask.txt

01011

Output

[2020-04-13 10:25:13] INFO: GTDB-Tk v1.1.0
[2020-04-13 10:25:13] INFO: gtdbtk trim_msa --untrimmed_msa msa.faa --output msa_trim.faa --mask_file mask.txt
[2020-04-13 10:25:13] INFO: Using GTDB-Tk reference data version r89: /release89
[2020-04-13 10:25:13] INFO: Done.

#### msa_trim.faa

>genome_a
KAK