🧬 superdarks: Code files : 3-post_query_informatics

• 📁 7-clusterupdate_branch/
• 📁 library/
• 📄 1-listing_parse.py – Download
• 📄 10-goFo_one_node.py – Download
• 📄 11-reduce_for_cytoscape_strict.py – Download
• 📄 12-clustalo_pairwise_traceback_map_con_to_structure.py – Download
• 📄 2-uniprot_parse.py – Download
• 📄 3-listing_uniprot_merge.py – Download
• 📄 4-uniprot_interpro_merge.py – Download
• 📄 5-gpcr_filtering.py – Download
• 📄 6-sequence_chunkify_and_collect.py – Download
• 📄 8-chunkify_and_blastp.py – Download
• 📄 9-blastp_chunks_to_network_fast.py – Download

📜 Scripts in this folder

• 1-listing_parse.py — Parses rank / coverage / TM-score / UniProt-ID tuples out of the rank--coverage-tm--UNIPROT-…-full.pdb filenames produced upstream.
• 2-uniprot_parse.py — Streaming parser for Swiss-Prot / TrEMBL .dat flat-file entries, one protein record at a time (memory-safe).
• 3-listing_uniprot_merge.py — Streams the full Swiss-Prot and TrEMBL .dat.gz archives via pigz / gzip and merges them with the hit listing into a unified TSV (gene, organism, superkingdom, and protein-function columns).
• 4-uniprot_interpro_merge.py — Joins the merged UniProt TSV with InterPro’s protein2ipr.dat.gz, emitting one combined TSV per hit (UPPERCASE-normalized for downstream matching).
• 5-gpcr_filtering.py — Pandas-based 7TM + GPCR keyword filter over the InterPro-enriched TSV (with a special GCR-\d+ family rule), writing per-match Excel workbooks up to the 1,048,576-row sheet limit.
• 6-sequence_chunkify_and_collect.py — Rewrites FASTA headers into the canonical superkingdom|uniprot_id|gene|organism|rank form and chunks sequences into downstream-ready files.
• 7-clusterupdate_branch/ — Optional pre-BLASTP reduction: splits the FASTA by superkingdom and runs MMseqs2 linclust + clusterupdate to produce priority representatives (Archaea → Bacteria → Eukaryota).
• 8-chunkify_and_blastp.py — Splits one FASTA into N whole-record chunks and submits one all-vs-all BLASTP LSF job per chunk (no CLI — edit the CONFIG block).
• 9-blastp_chunks_to_network_fast.py — Unified network builder (FAST in-process, or TURBO / LSF cluster) that turns per-chunk BLASTP TSVs into gzipped nodes + edges tables ready for Cytoscape.
• 10-goFo_one_node.py — Isom-Lab “go-forward” BFS walk over the thresholded BLAST similarity graph (by % identity plus e-value or bitscore), producing a no-rings, strongest-edges-first subgraph.
• 11-reduce_for_cytoscape_strict.py — Reduces a very large network to a Cytoscape-friendly subset by keeping the largest components, extracting a Maximum Spanning Forest backbone, and pruning by node-importance score.
• 12-clustalo_pairwise_traceback_map_con_to_structure.py — Clustal-Omega pairwise traceback that maps sequence conservation onto a reference PDB, enabling 3D visualization of evolutionary signal.

⚠️ Disclaimer

This is research-grade code provided for academic and exploratory purposes only. It is not intended for professional or clinical deployment.