Insert a list from a dataset into the a section of a config.yml file!

[ccbaumler]

Please consider the documentation at dib-lab/genome-grist#284 to rapidly include lists into a config file.

This is able to take the tsv sample below and import the list of Assembly Accession identifiers directly into the config file for the spacegraphcats workflow:

The config:

# This is the file path to the metadata file.
# In this case, the file is the full metadata
# output of the SRA Run Selector.

metadata_file_path: metadata/SraRunTable.txt

# Directories
workdir: ~/dissertation-project/seqs

outdir: dissertation-project/seqs

prevent_sra_download: False

# The kmer size within the database (`sourmash sig fileinfo`)
k_size:
  - 21
  - 31
#  - 51 is too large for khmer abundtrimming

# Query genomes for spacegraphcats
query_genomes:
 - GCA_000349525.1

query_radius:
  - 1
  - 5
  - 10

# The amount to scale representative kmer set
scale:
  - 1000

The tsv:

Assembly Accession	Assembly Name	Organism Name	Annotation Name	Assembly Stats Total Sequence Length	Assembly Level	Assembly Release Date	WGS project accession
GCA_000143535.4	ASM14353v4	Botrytis cinerea B05.10	Annotation submitted by Syngenta Biotechnology, Inc.	42630066	Complete Genome	2015-02-05	
GCF_000143535.2	ASM14353v4	Botrytis cinerea B05.10	Annotation submitted by Syngenta Biotechnology, Inc.	42630066	Complete Genome	2015-02-05	
GCA_019186565.1	ASM1918656v1	Botrytis cinerea		42721243	Contig	2021-07-09	JAHHFM01
GCA_019186575.1	ASM1918657v1	Botrytis cinerea		42739314	Contig	2021-07-09	JAHHFN01
GCA_031205075.1	Bcin_M3a_1.1	Botrytis cinerea		43592014	Contig	2023-09-07	JARWBL01
GCA_015148055.1	ASM1514805v1	Botrytis cinerea		41439596	Contig	2020-10-30	JACVFN01

The code:

awk -F'\t' 'NR>1 && NF {print " - " $1}' assembly-test.tsv | sed "/query_genomes:/r /dev/stdin" -i sgc-prep-config.yml

The updated config:

# This is the file path to the metadata file.
# In this case, the file is the full metadata
# output of the SRA Run Selector.

metadata_file_path: metadata/SraRunTable.txt

# Directories
workdir: ~/dissertation-project/seqs

outdir: dissertation-project/seqs

prevent_sra_download: False

# The kmer size within the database (`sourmash sig fileinfo`)
k_size:
  - 21
  - 31
#  - 51 is too large for khmer abundtrimming

# Query genomes for spacegraphcats
query_genomes:
 - GCA_000143535.4
 - GCF_000143535.2
 - GCA_019186565.1
 - GCA_019186575.1
 - GCA_031205075.1
 - GCA_015148055.1
 - GCA_000349525.1

query_radius:
  - 1
  - 5
  - 10

# The amount to scale representative kmer set
scale:
  - 1000