<commit_before>
Feature: Parse GWP files

  GWP generates a range of files which we parse and turn into RDF

  @gwp
  Scenario: Parse digest 
    Given I have a digest file with name 'Ce_CDS' and contains
    """
cluster00396/results7*.txt
cluster00399/results7-8.txt M7-8  -1280.1  -1277.4      5.3
cluster00400/results7-8.txt M7-8   -857.0   -850.8     12.4 ++   6 sites (206 AA)
    """    
    Then I should fetch the cluster names 'cluster00399' and 'cluster00400'
    Then for cluster 400
    And I should be able to fetch the model 'M7-8'
    And I should be able to fetch the lnL '12.4'
    And I should be able to fetch sequence size as 206
    And I should be able to assert it is positively selected for 6 sites
    And I should be able to output RDF
      """
:Ce_CDS_cluster00400 rdf:label "Ce_CDS_cluster00400" ,
    a :cds ,
    a :family ,
    :model :M78 ,
    :lnL 12.4 ,
    :sites 6 ,
    :seq_size 206 .

"""

  Scenario: Parse BLAST results
    
    BLAST XML results are turned into a textual format

    Given I have a textual BLAST result with name 'Ce_CDS' in 'cluster00400'  which contains
    """
Caenorhabditis elegans\tNP_001251447\tProtein CDC-26, isoform c  > Protein CDC-26, isoform c\tgi|392887062|ref|NP_001251447.1|\t1.76535e-89
    """
    Then I should be able fetch the Species name 'Caenorhabditis elegans'
    Then I should be able fetch the gene name 'NP_001251447'
    Then I should be able fetch the description 'Protein CDC-262'
    Then I should be able fetch the E-value 1.76535e-89
    And I should be able to output RDF
    """
    """
<commit_msg>GWP digest feature to RDF<commit_after>
Feature: Parse GWP files

  GWP generates a range of files which we parse and turn into RDF

  @gwp
  Scenario: Parse digest 
    Given I have a digest file with name 'Ce_CDS' and contains
    """
cluster00396/results7*.txt
cluster00399/results7-8.txt M7-8  -1280.1  -1277.4      5.3
cluster00400/results7-8.txt M7-8   -857.0   -850.8     12.4 ++   6 sites (206 AA)
    """    
    Then I should fetch the cluster names 'cluster00399' and 'cluster00400'
    Then for cluster 400
    And I should be able to fetch the model 'M7-8'
    And I should be able to fetch the lnL '12.4'
    And I should be able to fetch sequence size as 206
    And I should be able to assert it is positively selected for 6 sites
    And I should be able to output RDF
      """
:Ce_CDS_cluster00400 rdf:label "Ce_CDS_cluster00400" ,
    a :cds ,
    a :family ,
    :species "Ce" ,
    :cluster "cluster00400"
    :model :M78 ,
    :lnL 12.4 ,
    :sites 6 ,
    :seq_size 206 .

"""

  Scenario: Parse BLAST results
    
    BLAST XML results are turned into a textual format

    Given I have a textual BLAST result with name 'Ce_CDS' in 'cluster00400'  which contains
    """
Caenorhabditis elegans\tNP_001251447\tProtein CDC-26, isoform c  > Protein CDC-26, isoform c\tgi|392887062|ref|NP_001251447.1|\t1.76535e-89
    """
    Then I should be able fetch the Species name 'Caenorhabditis elegans'
    Then I should be able fetch the gene name 'NP_001251447'
    Then I should be able fetch the description 'Protein CDC-262'
    Then I should be able fetch the E-value 1.76535e-89
    And I should be able to output RDF
      """
:Ce_CDS_cluster00400_NP_001251447 rdf:label "NP_001251447" ,
    a :homolog ,
    :family Ce_CDS_cluster00400,
    :model :M78 ,
    :lnL 12.4 ,
    :sites 6 ,
    :seq_size 206 .

"""


{'fraction_non_alphanumeric': 0.075713453698311, 'fraction_numerical': 0.10366919044845661, 'mean_word_length': 2.7623220153340635, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 5, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2624988', 'n_tokens_mistral': 1422, 'n_tokens_neox': 1162, 'n_words': 451}