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Tools to post-process sequence files (and some other related stuff)

Renaming of sequences within NEXUS files

The tool can be given a nexus file and a file that gives a mapping from sequence names (as found in the input file) to the names that should be used in the generated NEXUS files. The first word (without spaces) in each line is interpreted as the input name and the rest as the output name.

For instance, the following command

nexus --rename input.nex names.nds

will generate a file called input.renamed.nex which is the input nexus files with the specified renaming applied

The .nds file is of the form

 Name0 new name 0
 Name1 new name 1

Renaming of sequences within FASTA files

The tool can be given a fasta file and a file that gives a mapping from sequence names (as found in the input file) to the names that should be used in the generated FASTA files. The first word (without spaces) in each line is interpreted as the input name and the rest as the output name.

For instance, the following command

fasta --rename input.fas names.nds

will generate a file called input.renamed.fas which is the input fasta file with the specified renaming applied.

The .nds file is of the form

 Name0 new name 0
 Name1 new name 1

Addition of traits into NEXUS files

The tool can generate a bunch of NEXUS files post processed with the addition of trait and/or geotag blocks. It must be given a nexus file and a configuration file. Additionally, two other files must be provided:

  • a CSV file containing some trait information. One column in this file contains the sequence names as found in the input NEXUS file. The first line of the CSV file must contain the column names.
  • a file that gives a mapping from sequence names (as found in the input file) to the names that should be used in the generated NEXUS files. The first word (without spaces) in each line is interpreted as the input name and the rest as the output name.

The configuration file points to these two as well as to other information. Example:

traits_file: path_to_csv_file.csv
name_mappings_file: path_to_name_mapping_file.nds

# Name of the column containing the sequence names in the input NEXUS file
key: arb name
# Column containing the decimal latitude (optional)
lat: lat decimal
# Column containing the decimal longitude (optional)
lon: lon decimal
# If lat/lon is provided, the number of clusters that popart should use to classify the sequences geographically
ncluters: 5
# The trait columns
traits:
 - habitat

The tool is then called with this configuration file and the NEXUS file

nexus input.nex postprocess.config

it will create a directory called like the input file, but without the extension (here input). In this directory will be created one nexus file and one CSV file per trait. The csv file contains the trait matrix (as stored in the nexus file). If geotags are provided, one nexus file with a geotags block and one CSV file are generated as well.

input/geotags.nex
input/geotags.csv
input/habitat.nex
input/habitat.csv

If a trait is unknown for a sequence, set the corresponding cell to ? in the CSV file