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useful_cmds.txt
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# Populate with stage database
time python populate_db.py --sample_info data/stage/lmo/sample_info.csv \
--pfam_annotation_info data/stage/annotation_info/all_pfam_annotation_info.tsv \
--eggnog_category_info data/stage/annotation_info/eggnog_categories.tsv \
--eggnog_annotation_info data/stage/annotation_info/all_EggNOG_annotation_info.tsv \
--ec_annotation_info data/stage/annotation_info/all_EC_annotation_info.tsv \
--tigrfam_annotation_info data/stage/annotation_info/all_TIGRFAM_annotation_info.tsv \
--annotation_source_info data/stage/annotation_source_info.csv \
--gene_annotations_pfam data/stage/annotations/all.pfam.standardized.tsv \
--gene_annotations_eggnog data/stage/annotations/all.EggNOG.standardized.tsv \
--gene_annotations_ec data/stage/annotations/all.EC.standardized.tsv \
--gene_annotations_tigrfam data/stage/annotations/all.TIGRFAM.standardized.tsv \
--reference_assembly "megahit_coassembly.0" \
--gene_counts data/stage/lmo/all_genes.tpm.tsv.gz \
--metadata_reference data/stage/metadata_reference.tsv \
--tmp_file /Users/johannes.alneberg/repos/BARM_web_server/data/stage/tmp_file.csv \
--taxonomy_per_gene ~/repos/BARM_web_server/data/stage/lca_megan.tsv
# Old, missing tigrfam
time python populate_db.py --sample_info data/real/lmo/sample_info.csv \
--pfam_annotation_info data/real/annotation_info/all_pfam_annotation_info.tsv \
--eggnog_category_info data/real/annotation_info/eggnog_categories.tsv \
--eggnog_annotation_info data/real/annotation_info/all_EggNOG_annotation_info.tsv \
--ec_annotation_info data/real/annotation_info/all_EC_annotation_info.tsv \
--annotation_source_info data/real/annotation_source_info.csv \
--gene_annotations_pfam data/real/annotations/all.pfam.standardized.tsv \
--gene_annotations_eggnog data/real/annotations/all.EggNOG.standardized.tsv \
--gene_annotations_ec data/real/annotations/all.EC.standardized.tsv \
--reference_assembly "megahit_coassembly.0" \
--gene_counts data/real/lmo/all_genes.tpm.tsv.gz \
--metadata_reference data/real/metadata_reference.tsv \
--tmp_file /Users/johannesalneberg/repos/BARM_web_server/data/real/tmp_file.csv \
--taxonomy_per_gene ~/repos/BARM_web_server/data/real/lca_script.tsv
# Adding tigrfam to stage:
time python add_TigrFam_to_db.py --annotation_source_info data/stage/annotation_source_info.csv \
--tigrfam_annotation_info data/stage/annotation_info/all_TIGRFAM_annotation_info.tsv \
--gene_annotations_tigrfam data/stage/annotations/all.TIGRFAM.standardized.tsv \
--tmp_file /Users/johannesalneberg/repos/BARM_web_server/data/real/tmp_file.csv \
--reference_assembly "megahit_coassembly.0" \
--gene_counts data/stage/merged/merged2.tsv.gz
# Adding tigrfam to real:
time python add_TigrFam_to_db.py --annotation_source_info data/real/annotation_source_info.csv \
--tigrfam_annotation_info data/real/annotation_info/all_TIGRFAM_annotation_info.tsv \
--gene_annotations_tigrfam data/real/annotations/all.TIGRFAM.standardized.tsv \
--tmp_file /tmp/tmp_file.csv \
--reference_assembly "megahit_coassembly.0" \
--gene_counts data/real/merged/merged.tsv.gz
time python populate_db.py --sample_info data/test/lmo/sample_info.csv \
--pfam_annotation_info data/test/annotation_info/all_pfam_annotation_info.tsv \
--eggnog_category_info data/test/annotation_info/eggnog_categories.tsv \
--eggnog_annotation_info data/test/annotation_info/all_EggNOG_annotation_info.tsv \
--ec_annotation_info data/test/annotation_info/all_EC_annotation_info.tsv \
--dbcan_annotation_info data/test/annotation_info/all_dbCAN_annotation_info.tsv \
--annotation_source_info data/test/annotation_source_info.csv \
--gene_annotations_pfam data/test/annotations/all.pfam.standardized.tsv \
--gene_annotations_eggnog data/test/annotations/all.EggNOG.standardized.tsv \
--gene_annotations_ec data/test/annotations/all.EC.standardized.tsv \
--gene_annotations_dbcan data/test/all.dbCAN.standardized.tsv \
--reference_assembly "megahit_coassembly.0" \
--gene_counts data/test/lmo/all_genes.tpm.tsv.gz \
--metadata_reference data/test/metadata_reference.tsv \
--tmp_file /Users/johannesalneberg/repos/BARM_web_server/data/test/tmp_file.csv \
--taxonomy_per_gene ~/repos/BARM_web_server/data/test/lca_megan.tsv
time python add_sample_set_to_db.py --sample_info data/test/baltic_redox_cline_2014/sample_info.csv \
--gene_counts data/test/baltic_redox_cline_2014/all_genes.tpm.tsv.gz \
--metadata_reference data/test/metadata_reference.tsv \
--tmp_file /Users/johannesalneberg/repos/BARM_web_server/data/test/tmp_file.csv
time python add_sample_set_to_db.py --sample_info data/real/baltic_redoxcline_2014/sample_info.csv \
--gene_counts data/real/baltic_redoxcline_2014/all_genes.tpm.tsv.gz \
--metadata_reference data/real/metadata_reference.tsv \
--tmp_file /Users/johannesalneberg/repos/BARM_web_server/data/real/tmp_file.csv
time python add_sample_set_to_db.py --sample_info data/real/baltic_transect_2014/sample_info.csv \
--gene_counts data/real/baltic_transect_2014/all_genes.tpm.tsv.gz \
--metadata_reference data/real/metadata_reference.tsv \
--tmp_file /Users/johannesalneberg/repos/BARM_web_server/data/real/tmp_file.csv