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ENH add readme.md for each folder
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‎General_Scripts/01_Taxonomy_mapping/README.md‎

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Codes for mapping taxonomy
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## 01_Taxonomy_mapping
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| **Code** | **Description** | **Input** | **Output** |
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| :---: | :---: | :---: | :---: |
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| 01_map_prog_taxa_dedup.py | Remove redundancy of smORFs from Progenomes and map specI taxonomy to genomes | genome_prog.tsv specI_genome_taxa.txt GMSC10.ProG_smorfs.faa.gz | prog_specI_genome_taxa.tsv prog_dedup_sort.faa.gz prog_redundant.tsv.gz |
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| 02_run_linclust.sh 03_lca_change_format.py | Cluster smORFs from Progenomes at 90% amino acid identity and 90% coverage and map taxonomy by LCA | prog_dedup.faa.gz prog_redundant.tsv.gz prog_specI_genome_taxa.tsv.gz | prog_taxonomy_change.tsv.gz |
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| 04_map_metag_taxid_full.py | Map taxid of smORFs from metaG based on contigs and et the fullname of taxid based on GTDB | mmseqs2.lca_taxonomy.full.tsv.xz GMSC10.metag_smorfs.rename.txt.xz gtdb_taxonomy.tsv | metag_taxid.tsv.xz taxid_fullname_gtdb.tsv |
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| 05_dedup_cluster.py | Get clusters at 100% identity of raw data | GMSC10.metag_ProG_smorfs.faa.gz | dedup_cluster.tsv.gz |
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| 06_map_taxonomy.py | Map taxonomy for all the smORFs from metaG | taxid_fullname_gtdb.tsv metag_taxid.tsv.xz dedup_cluster.tsv.gz prog_taxonomy_change.tsv.gz | metag_cluster_taxonomy.tsv.xz |
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| 07_deep_lca_100.py | Map taxonomy for 100% identity smORFs with LCA | metag_cluster_taxonomy.tsv.xz all_0.5_0.9.tsv.gz | 100AA_taxonomy.tsv.xz |
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| 08_map_cluster_tax.py | Map taxonomy for 90% identity smORFs with LCA | 100AA_taxonomy.tsv.xz all_cluster_0.9.tsv.xz | 90AA_tax.tsv.xz |
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| 09_fix_prog_tax.py | Make consistency between Progenomes2 taxonomy and GTDB taxonomy | 100AA_taxonomy.tsv.xz 90AA_tax.tsv.xz | GMSC10.100AA.taxonomy.tsv GMSC10.90AA.taxonomy.tsv |

‎General_Scripts/02_Habitat_mapping/README.md‎

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Codes for mapping habitat
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## 02_Habitat_mapping
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| **Code** | **Description** | **Input** | **Output** |
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| :---: | :---: | :---: | :---: |
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| 01_map_habitat.py | Map habitat for all the smORFs from metaG | metadata.tsv GMSC10.metag_smorfs.rename.txt.xz dedup_cluster.tsv.gz| metag_cluster_habitat.tsv.xz |
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| 02_multi_habitat.py | Combine multiple habitats for each smORF from the same cluster | metag_cluster_habitat.tsv.xz 100AA_rename.tsv.xz habitat_general.txt| 100AA_multi_general_habitat.tsv.xz |
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| 03_map_cluster_habitat.py | Map habitat to 90% identity smORFs clusters. | all_0.5_0.9.tsv.gz 100AA_multi_general_habitat.tsv.xz | cluster_multi_habitat_90.tsv.xz |
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|04_multi_habitat_90_50.py | Combine multiple habitats for each smORF from the same 90AA cluster |cluster_multi_habitat_90.tsv.xz habitat_general.txt | 90AA_multi_general_habitat.tsv.xz |

‎General_Scripts/03_Quality_control/Readme.md‎

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### Antifam
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| **Code** | **Description** | **Input** | **Output** |
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| :---: | :---: | :---: | :---: |
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| 01_run_antifam.sh | Map 100AA smORFs to antifam | AntiFam.hmm 100AA_GMSC_sort.faa | antifam_result.tsv |
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| 02_assign_all_level.py | Assign antifam results to 90AA smORFs. | antifam_result.tsv all_0.9_0.5_family.tsv.xz | antifam_90AA.tsv.gz |
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### Coordinates
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| **Code** | **Description** | **Input** | **Output** |
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| :---: | :---: | :---: | :---: |
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| 01_allcoordinate.py | Detect if there is a STOP codon on the upstream of the smORF in the contigs | GMSC10.metag_smorfs.rename.txt.xz ./contigs/ | result.tsv.gz |
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| 02_assign_all_level.py | Assign terminal checking results to 100AA and 90AA smORFs | result.tsv.gz 100AA_rename.tsv.xz all_0.9_0.5_family.tsv.xz | 100AA_coordinate.tsv.gz 90AA_coordinate.tsv.gz |
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### RNAcode
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| **Code** | **Description** | **Input** | **Output** |
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| :---: | :---: | :---: | :---: |
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| 01_filter8_addfna_split.py | Select clusters(>= 8 members) | all_0.5_0.9.tsv metag_ProG_smorfs.fna.xz | ./split/*.fna |
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| 02_run_MSA.sh | Multiple sequences alignment of each .fna file | ./split/*.fna | *.aln |
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| 03_run_RNAcode.sh | Run RNAcode | *.aln | *.tsv |
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| 04_filter_RNAcode.py | Filter RNAcode result | *.tsv | smORF_0.9_RNAcode.tsv |
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| 05_assign_all_level.py | Assign RNAcode results to 100AA and 90AA smORFs | smORF_0.9_RNAcode.tsv all_0.5_0.9_filter.tsv 100AA_rename.tsv.xz 90AA_rename.tsv.xz all_0.9_0.5_family.tsv.xz | rnacode_true_100AA.tsv.xz rnacode_false_100AA.tsv.xz rnacode_true_90AA.tsv.xz rnacode_false_90AA.tsv.xz |
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### metatranscriptomics
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| **Code** | **Description** | **Input** | **Output** |
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| :---: | :---: | :---: | :---: |
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| 01_run_bwa_ngless.sh | Map metatranscriptome reads to smORFs | 90AA_GMSC.fna *.fastq.gz | *.tsv |
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| 02_merge_filter.py | Merge and filter mapping results | *.tsv | metaT_result_filter.tsv |
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| 03_assign_all_level.py | Assign results to 100AA and 90AA smORFs | metaT_result_filter.tsv all_0.9_0.5_family.tsv.xz | metaT_100AA.tsv.gz metaT_90AA.tsv.gz |
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### riboseq
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| **Code** | **Description** | **Input** | **Output** |
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| :---: | :---: | :---: | :---: |
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| 01_run_bwa_ngless.sh | Map riboseq reads to smORFs | 90AA_GMSC.fna *.fastq.gz | *.tsv |
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| 02_merge_filter.py | Merge and filter mapping results | *.tsv | riboseq_result_filter.tsv |
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| 03_assign_all_level.py | Assign results to 100AA and 90AA smORFs | riboseq_result_filter.tsv all_0.9_0.5_family.tsv.xz | riboseq_100AA.tsv.gz riboseq_90AA.tsv.gz |
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### metaproteomics
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| **Code** | **Description** | **Input** | **Output** |
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| :---: | :---: | :---: | :---: |
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| 00_split_100AA.py 01_map.py | For each metaproteomes peptides from each project in PRIDE,find their exact match against 100AA smORFs | 100AA_GMSC.faa.xz *.fasta | *.tsv |
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| 02_merge.py | Calculate and filter peptide coverage rate of each smORF | *.tsv | coverage_analysis.tsv |
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| 03_assign_all_level.py | Assign results to 90AA smORFs | coverage_analysis.tsv all_0.9_0.5_family.tsv.xz | metaP_90AA.tsv.gz |
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### merge_quality_control
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| **Code** | **Description** | **Input** | **Output** |
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| :---: | :---: | :---: | :---: |
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| 01_merge.py | Merge all the quality control results | 100AA_rename.tsv.xz rnacode_true_100AA.tsv.xz rnacode_false_100AA.tsv.xz antifam_result.tsv coverage_analysis.tsv.gz riboseq_100AA.tsv.gz 100AA_coordinate.tsv.gz metaT_100AA.tsv.gz | allquality_100AA.tsv.gz allpass_100AA.txt |

‎General_Scripts/04_Frozen/05_sort_fna.py‎

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‎General_Scripts/04_Frozen/06_sort_faa_family.py‎

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‎General_Scripts/04_Frozen/07_habitat_100_50_90.py‎

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‎General_Scripts/04_Frozen/08_taxonomy_100_50_90.py‎

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‎General_Scripts/04_Frozen/README.md‎

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# 04_Frozen
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| **Code** | **Description** | **Input** | **Output** |
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| :---: | :---: | :---: | :---: |
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| 01_rename_list.py | Rename 100AA sequences | metag_ProG.raw_number.tsv.gz metag_ProG_nonsingleton.faa.gz singleton_0.5_0.9.tsv metag_ProG_singleton.faa.gz| nonsingleton_rename.tsv singleton_rename.tsv |
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| 02_100AA_faa_fna.py | Generate 100AA faa and fna file with new identifier | 100AA_rename.tsv.xz metag_ProG_dedup.faa.gz GMSC10.metag_smorfs.fna.xz GMSC.ProGenomes2.smorfs.fna.xz | 100AA_GMSC.faa.xz 100AA_metag.fna.xz 100AA_prog.fna.xz |
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| 03_90AA_faa_fna.py | Rename 90AA sequences and generate 90AA faa and fna file with new identifier | metag_ProG_nonsingleton_0.9_clu_rep.faa.gz metag_ProG_nonsingleton_0.9_clu.tsv.gz 100AA_rename.tsv.xz 100AA_GMSC.fna.xz | 90AA_rename.tsv.xz 90AA_rename_all.tsv.xz 90AA_GMSC.faa.xz 90AA_GMSC.fna.xz |
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| 04_family.py | Generate the cluster table | 90AA_rename_all.tsv.xz all_0.5_0.9_rename.tsv.gz | all_0.9_0.5_family.tsv.xz |

‎General_Scripts/06_Compare_with_other_datasets/Readme.md‎

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## 06_Compare_with_other_datasets
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| **Code** | **Description** |
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| :---: | :---: |
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| 01_download.sh 02_filter_sp_dedup.py | Download archaeal and bacterial proteins from Refseq, filter sequences (<100aa) and remove redundancy |
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| 03_align.sh | Use Diamond to align sequences to GMSC |

‎General_Scripts/07_GMSC_mapper_benchmark/Readme.md‎

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## 07_GMSC_mapper_benchmark
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### 01_sensitivity
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| **Code** | **Description** |
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| :---: | :---: |
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| 01_sensitivity.sh | Test the recovery of smORFs by different sensitivity of Diamond and MMseqs2 with different length |
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### 02_time
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| **Code** | **Description** |
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| :---: | :---: |
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| 01_time.sh | Test the time cost by Diamond and MMseqs2 |
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### 03_identity
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| **Code** | **Description** |
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| :---: | :---: |
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| 01_select_mutation.py | Randomly selected and mutated 10,000 sequences from 90AA smORFs with different length (20,30,40,60,80,all) at different identity. |
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| 02_identity.sh | Test the recovery of smORFs between Blast,Diamond,MMseqs with different length (20,30,40,60,80,all) and different identity |

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