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6 changes: 0 additions & 6 deletions
6
CHEWBBACA/tests/data/allelecall_data/test_genes_list/test_genes_results/logging_info.txt
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71 changes: 71 additions & 0 deletions
71
CHEWBBACA/tests/data/allelecall_data/test_results/cds_input/invalid_cds.txt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,71 @@ | ||
| GCA_000007265-protein1005: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein1038: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein1048: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein1095: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein1102: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein1104: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein1179: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein1218: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein1234: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein1247: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein1263: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein1265: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein126: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein1276: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein130: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein1350: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein1392: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein1408: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein1432: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein1434: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein1454: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein1455: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein155: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein1647: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein1734: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein1737: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein1779: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein1821: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein1883: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein1921: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein1923: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein1995: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein2016: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein2019: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein201: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein2040: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein2041: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein228: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein229: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein359: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein420: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein422: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein493: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein4: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein536: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein537: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein539: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein541: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein546: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein556: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein558: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein561: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein568: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein591: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein592: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein5: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein621: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein635: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein636: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein69: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein713: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein74: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein794: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein79: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein847: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein84: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein85: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein86: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein942: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein988: sequence shorter than 201 nucleotides | ||
| GCA_000007265-protein992: sequence shorter than 201 nucleotides |
11 changes: 11 additions & 0 deletions
11
CHEWBBACA/tests/data/allelecall_data/test_results/cds_input/loci_summary_stats.tsv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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| Locus EXC INF PLOT3 PLOT5 LOTSC NIPH NIPHEM ALM ASM PAMA LNF Total_CDS | ||
| sagalactiae-protein1 1 0 0 0 0 0 0 0 0 0 0 1 | ||
| sagalactiae-protein10 1 0 0 0 0 0 0 0 0 0 0 1 | ||
| sagalactiae-protein2 1 0 0 0 0 0 0 0 0 0 0 1 | ||
| sagalactiae-protein3 1 0 0 0 0 0 0 0 0 0 0 1 | ||
| sagalactiae-protein4 0 0 0 0 0 0 0 0 0 0 1 0 | ||
| sagalactiae-protein5 0 0 0 0 0 0 0 0 0 0 1 0 | ||
| sagalactiae-protein6 0 0 0 0 0 0 0 0 0 0 1 0 | ||
| sagalactiae-protein7 1 0 0 0 0 0 0 0 0 0 0 1 | ||
| sagalactiae-protein8 0 0 0 0 0 0 0 0 0 0 1 0 | ||
| sagalactiae-protein9 1 0 0 0 0 0 0 0 0 0 0 1 |
1 change: 1 addition & 0 deletions
1
CHEWBBACA/tests/data/allelecall_data/test_results/cds_input/paralogous_counts.tsv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| Locus Count |
1 change: 1 addition & 0 deletions
1
CHEWBBACA/tests/data/allelecall_data/test_results/cds_input/paralogous_loci.tsv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| Genome Loci CDS |
2 changes: 2 additions & 0 deletions
2
CHEWBBACA/tests/data/allelecall_data/test_results/cds_input/results_alleles.tsv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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| FILE sagalactiae-protein1 sagalactiae-protein10 sagalactiae-protein2 sagalactiae-protein3 sagalactiae-protein4 sagalactiae-protein5 sagalactiae-protein6 sagalactiae-protein7 sagalactiae-protein8 sagalactiae-protein9 | ||
| GCA_000007265 2 2 2 1 LNF LNF LNF 2 LNF 2 |
2 changes: 2 additions & 0 deletions
2
CHEWBBACA/tests/data/allelecall_data/test_results/cds_input/results_contigsInfo.tsv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| FILE sagalactiae-protein1 sagalactiae-protein10 sagalactiae-protein2 sagalactiae-protein3 sagalactiae-protein4 sagalactiae-protein5 sagalactiae-protein6 sagalactiae-protein7 sagalactiae-protein8 sagalactiae-protein9 | ||
| GCA_000007265 GCA_000007265-protein157 GCA_000007265-protein1138 GCA_000007265-protein1996 GCA_000007265-protein1371 LNF LNF LNF GCA_000007265-protein874 LNF GCA_000007265-protein1848 |
2 changes: 2 additions & 0 deletions
2
CHEWBBACA/tests/data/allelecall_data/test_results/cds_input/results_statistics.tsv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| FILE EXC INF PLOT3 PLOT5 LOTSC NIPH NIPHEM ALM ASM PAMA LNF Invalid CDSs Classified_CDSs Total_CDSs | ||
| GCA_000007265 6 0 0 0 0 0 0 0 0 0 4 71 6 2106 |
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