submission code

08-submission/README.md

+# Submission
+
+Utility scripts for data upload to ENA.
+
+- [EMBL format conversion](convert_to_embl.sh) for an annotated genome (Fasta + GFF3) - inspired
+  from a [prokka issue](https://github.com/tseemann/prokka/issues/145), leading to
+  [GFF3toEMBL](https://github.com/sanger-pathogens/gff3toembl) and eventually to the real solution,
+  [EMBLmyGFF3](https://github.com/NBISweden/EMBLmyGFF3).
+- A [Python script](txome_manifest.py) to batch-create manifest files for de novo transcriptome
+  submissions to ENA.
\ No newline at end of file

08-submission/convert_to_embl.sh

+#!/usr/bin/env bash
+
+module load conda
+conda activate emblmygff3
+
+GENOME=/lisc/project/zoology/pycnogonum/paper/results/draft.fasta
+GFF=/lisc/project/zoology/pycnogonum/paper/results/merged_sorted.gff3
+RESDIR=/lisc/scratch/zoology/pycnogonum/genome/submission
+
+cd $RESDIR || exit
+
+EMBLmyGFF3 $GFF $GENOME \
+        --topology linear \
+        --molecule_type 'genomic DNA' \
+        --transl_table 1  \
+        --species 'Pycnogonum litorale' \
+        --taxonomy INV \
+        --locus_tag VPG \
+        --project_id PRJEB80537 \
+        --verbose \
+        -o result.embl
\ No newline at end of file

08-submission/txome_manifest.py

+#!/usr/bin/env python
+
+study = "PRJEB80537"
+
+samples = ["ERS21095029", "ERS21095030", "ERS21095031", "ERS21095032", "ERS21095033", "ERS21095034", "ERS21095035", "ERS21095036", "ERS21095037"]
+assembly_names = ["RNA_EMBRYO3", "RNA_INSTAR1", "RNA_INSTAR2", "RNA_INSTAR3", "RNA_INSTAR4", "RNA_INSTAR5", "RNA_INSTAR6", "RNA_JUV1", "RNA_SUBADULT"]
+base = "/lisc/scratch/zoology/pycnogonum/transcriptome/development"
+file_locs = ["embryonic_stage3-4", "instar_II", "instar_III", "instar_I-protonymphon", "instar_IV", "instar_V", "instar_VI", "juvenile_I", "subadult"]
+out_dir = "/lisc/scratch/zoology/pycnogonum/genome/submission/transcriptomes"
+
+for sample, name, loc in zip(samples, assembly_names, file_locs):
+    f = f"{out_dir}/{loc}.manifest"
+    with open(f, 'w') as manifest:
+        manifest.write(f"STUDY   PRJEB80537\n")
+        manifest.write(f"SAMPLE  {sample}\n")
+        manifest.write(f"ASSEMBLYNAME    {name}\n")
+        manifest.write(f"ASSEMBLY_TYPE isolate\n")
+        manifest.write(f"PROGRAM Trinity\n")
+        manifest.write(f"PLATFORM    ILLUMINA\n")
+        manifest.write(f"FASTA   {base}/{loc}/Trinity.fasta.gz\n")