/usr/local/lib/python3.6/dist-packages/fuzzywuzzy/fuzz.py:11: UserWarning: Using slow pure-python SequenceMatcher. Install python-Levenshtein to remove this warning
  warnings.warn('Using slow pure-python SequenceMatcher. Install python-Levenshtein to remove this warning')


-------------------------------- PARAMETERS --------------------------------

--inputPath          Path of npl tagged file (crf output): /home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/
--iAnnotatedFile     Input file of npl tagged file (crf output: srr_htregulondb_model_Run3_v10_S1_False_S2_True_S3_False_S4_False_Run3_v10.tsv
--iOntoFile          Input file with the ontology entities (MCO-terms): gc_ontology_terms_v2.txt
--iLinksFile         Input file with links and id for the ontology (MCO-type-links): None
--iSynFile           Input file for the additional ontology of synonyms (MCO-syn-json): mco_terms_v0.2.json
--outputPath         Output path to place output files: /home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/output/
--outputFile         Output of the mapping process: srr_htregulondb_mapped.tsv
--minPerMatch        Minimal string matching percentage: 80
--minCRFProbs        Minimal crf probabilities allowed: 0.9



set()
{'SRR  GSE   GSM GPL  PMID  GSM_NAME  FULLTEXT  BANGLINE  SOURCE_TEXT_CTRL  FULL_TEXT  TERM_NAME TERM_TYPE   PROB'}
GSE, BANGLINE, GSM, FULL_TEXT, PROB, TERM_NAME, GPL, SRR, TERM_TYPE, PMID expected columns for iAnnotatedFile