Map NCBI and Ensembl files #24
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| name: Map NCBI and Ensembl files | |
| on: | |
| schedule: | |
| - cron: '0 0 * * 1' | |
| workflow_dispatch: | |
| jobs: | |
| map-files: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| - name: Install Dependencies | |
| run: | | |
| curl -O 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-amd64/dataformat' | |
| curl -O 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-amd64/datasets' | |
| chmod +x datasets dataformat | |
| - name: Set Environment Variables | |
| run: | | |
| #datasets | |
| fields=accession,assminfo-name,organism-name,organism-tax-id | |
| echo "FIELDS=$fields" >> $GITHUB_ENV | |
| #input files | |
| echo "NCBI=ncbi.tsv" >> $GITHUB_ENV | |
| echo "ENSEMBL_RR=ensembl_rapid_release.tsv" >> $GITHUB_ENV | |
| #assembly info | |
| echo "ASSEMBLY_TABLE=assemblies_table.tsv" >> $GITHUB_ENV | |
| #output file header | |
| header="annotation_name\t$(echo $fields | tr ',' '\t')\tfull_path" | |
| echo "HEADER=$header" >> $GITHUB_ENV | |
| #output file name | |
| echo "OUTPUT=mapped_annotations.tsv" >> $GITHUB_ENV | |
| #tmp files | |
| echo "MERGED_TABLE=merged_table.tsv" >> $GITHUB_ENV | |
| echo "NEW_ANNOTATIONS=new_annotations.tsv" >> $GITHUB_ENV | |
| - name: Init Output File | |
| run: | | |
| output="${{env.OUTPUT}}" | |
| # Initialize the output file for FTP paths if it doesn't exist | |
| if [[ ! -f "$output" ]]; then | |
| echo -e "${{env.HEADER}}" > "$output" | |
| fi | |
| - name: Collect and Filter Data from TSVs | |
| run: | | |
| # Define the input files (two TSVs) and output file | |
| ncbi="${{env.NCBI}}" | |
| ensembl_rr="${{env.ENSEMBL_RR}}" | |
| #format name accession path | |
| merged_table="${{env.MERGED_TABLE}}" | |
| # Merge two TSVs, process columns, and save to output | |
| { tail -n +2 "$ncbi"; tail -n +2 "$ensembl_rr"; } | awk -F'\t' '{ | |
| # Get the accession (first column) | |
| accession = $1; | |
| # Extract the filename from the full path (second column), remove .gff.gz or .gff3.gz extension | |
| match($2, /([^\/]+)\.(gff3?|gff)\.gz$/, arr); | |
| filename = arr[1]; | |
| # Print accession, filename without extension, and full URL (second column) | |
| print filename "\t" accession "\t" $2; | |
| }' > "$merged_table" | |
| - name: Filter Out Existing Annotations | |
| run: | | |
| new_annotations="${{env.NEW_ANNOTATIONS}}" | |
| merged_table="${{env.MERGED_TABLE}}" | |
| existing_annotations="${{env.OUTPUT}}" | |
| awk 'NR==FNR {if (FNR > 1) exclude[$1]; next} FNR > 1 && !($1 in exclude)' "$existing_annotations" "$merged_table" > "$new_annotations" | |
| # Check if the output file is empty | |
| if [ ! -s "$new_annotations" ]; then | |
| echo "Output file is empty. Exiting.." | |
| exit 0 | |
| fi | |
| rm "$merged_table" | |
| - name: Get New Assemblies NCBI Metadata | |
| run: | | |
| tmp=tmp.txt | |
| cat "${{env.NEW_ANNOTATIONS}}" | | |
| awk -F'\t' '{print $2}' > "$tmp" | |
| ./datasets summary genome accession --inputfile "$tmp" --as-json-lines | | |
| ./dataformat tsv genome --fields "${{env.FIELDS}}" > "${{env.ASSEMBLY_TABLE}}" | |
| rm "$tmp" | |
| - name: Insert new annotations | |
| run: | | |
| new_annotations="${{env.NEW_ANNOTATIONS}}" | |
| existing_annotations="${{env.OUTPUT}}" | |
| assembly_table="${{env.ASSEMBLY_TABLE}}" | |
| # Process new annotations | |
| awk 'NR==FNR {if (FNR > 1) assembly[$1] = $0; next} FNR > 1 { | |
| accession = $2; # Get the second column (accession) from new_annotations | |
| full_path = $3; # Get the third column (full path) from new_annotations | |
| if (accession in assembly) { # If accession matches a line in assembly_table | |
| # Print formatted output with new_annotations first column, full_path, and the rest of assembly_table | |
| match(assembly[accession], /^[^\t]+\t(.+)/, arr); | |
| print $1 "\t" arr[0] "\t" full_path; | |
| } | |
| }' "$assembly_table" "$new_annotations" >> "$existing_annotations" | |
| # Display the final output for debugging purposes | |
| rm "$assembly_table" | |
| rm "$new_annotations" | |
| rm datasets | |
| rm dataformat | |
| - name: Commit & Push changes | |
| uses: actions-js/push@master | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} |