Added new file types to the readme generation script

EBI-Metagenomics · Aug 8, 2024 · 1a673b7 · 1a673b7
1 parent 9e4dc96
commit 1a673b7
Showing 1 changed file with 4 additions and 0 deletions.
diff --git a/containers/genomes-catalog-update/scripts/generate_readme.py b/containers/genomes-catalog-update/scripts/generate_readme.py
@@ -133,10 +133,13 @@ def print_file(
 - genome/
  * [species_accession]_amrfinderplus.tsv : AMR annotations produced by AMRFinderPlus.
  * [species_accession]_annotation_coverage.tsv : A summary of annotation coverage.
+ * [species_accession]_antismash.gff : AntiSMASH output file containing biosynthetic gene cluster information.
  * [species_accession]_cazy_summary.tsv : CAZy summary parsed from the eggNOG annotation file.
  * [species_accession]_cog_summary.tsv : COG summary parsed from the eggNOG annotation file.
  * [species_accession]_crisprcasfinder.gff : Unfiltered CRISPRCasFinder results file, including calls that have evidence level 1 and are less likely to be genuine.
  * [species_accession]_crisprcasfinder.tsv : Additional data for CRISPRCasFinder records reported in [species_accession]_crisprcasfinder.gff.
+ * [species_accession]_dbcan.gff : dbCAN annotation file containing putative polysaccharide utilisation loci, predicted substrates and functions of member genes.
+ * [species_accession]_defense_finder.gff : Anti-phage system annotations.
  * [species_accession]_eggNOG.tsv : eggNOG annotations of the protein coding sequences.
  * [species_accession].faa : Protein sequence FASTA file of the species representative.
  * [species_accession].fna : DNA sequence FASTA file of the genome assembly of the species representative.
@@ -145,6 +148,7 @@ def print_file(
  * [species_accession]_InterProScan.tsv : InterProScan annotation of the protein coding sequences.
  * [species_accession]_kegg_classes.tsv : KEGG classes and their counts.
  * [species_accession]_kegg_modules.tsv : KEGG modules and their counts.
+ * [species_accession]_kegg_pathways.tsv : KEGG pathway completeness.
  * [species_accession]_mobilome.gff : Annotated viral sequence and mobile elements.
  * [species_accession]_rRNAs.fasta : rRNA sequence FASTA file.
  * [species_accession]_sanntis.gff : SanntiS output file containing biosynthetic gene cluster information.