diff --git a/.github/labeler.yml b/.github/labeler.yml index 109d044..bf3373e 100644 --- a/.github/labeler.yml +++ b/.github/labeler.yml @@ -71,6 +71,11 @@ area:packaging: - "src-tauri/tauri.conf.json" - "CITATION.cff" +area:galaxy: + - changed-files: + - any-glob-to-any-file: + - "galaxy/**" + # Everything under .github, not a list of the files there. Naming them one by one # would leave this file itself uncovered, so the pull request adding a rule would # arrive with no label, which is a small thing that says exactly how such a list diff --git a/galaxy/tools/pathotypr/.shed.yml b/galaxy/tools/pathotypr/.shed.yml new file mode 100644 index 0000000..17a0a0f --- /dev/null +++ b/galaxy/tools/pathotypr/.shed.yml @@ -0,0 +1,21 @@ +name: pathotypr +owner: iuc +description: Lineage classification and marker-driven genotyping from assemblies or raw reads +long_description: | + pathotypr classifies microbial genomes into lineages and genotypes them + against user-defined marker panels. It works from assembled genomes (FASTA) + and from raw reads (FASTQ) without aligning them, and it carries no assumption + about the organism: the marker panel supplied defines what is typed. +categories: +- Sequence Analysis +- Variant Analysis +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathotypr +homepage_url: https://pathogenomics-lab.github.io/pathotypr/ +type: unrestricted +auto_tool_repositories: + name_template: "{{ tool_id }}" + description_template: "Wrapper for the pathotypr tool {{ tool_name }}." +suite: + name: "suite_pathotypr" + description: A suite of Galaxy tools for the five pathotypr commands. + type: repository_suite_definition diff --git a/galaxy/tools/pathotypr/README.md b/galaxy/tools/pathotypr/README.md new file mode 100644 index 0000000..a4733cc --- /dev/null +++ b/galaxy/tools/pathotypr/README.md @@ -0,0 +1,74 @@ +# Galaxy wrappers for pathotypr + +Five tools, one per subcommand, sharing `macros.xml`. + +| Tool | Wraps | Outputs | +|---|---|---| +| `pathotypr_train` | `train` | model, and optionally the two feature-importance reports | +| `pathotypr_predict` | `predict` | predictions TSV | +| `pathotypr_classify` | `classify` | per-marker hits, summary, optionally masked FASTA | +| `pathotypr_split_fastq` | `split-fastq` | per-marker calls, summary | +| `pathotypr_match` | `match` | best-match report | + +## Running the tests + +```bash +python3 -m venv .venv && .venv/bin/pip install planemo +.venv/bin/planemo lint tools/pathotypr/*.xml +.venv/bin/planemo test tools/pathotypr/ +``` + +`planemo test` resolves `pathotypr` from Bioconda. On a machine where that +package has no build for the local platform, put a `pathotypr` binary on `PATH` +and add `--no_dependency_resolution`; that still exercises the command lines, +the outputs and the assertions, and leaves only the dependency resolution to CI. + +## The test data + +Everything under `test-data/` is synthetic and generated deterministically: +a 2 kb reference, eight markers, two samples, paired reads at about 18x, and a +twelve-genome training set in two classes. 64 KB in total. + +It is not filler. The generator asserts that **every marker k-mer occurs exactly +once in the reference**, in both orientations, because a marker that matched in +two places would make the tests pass for the wrong reason. The expected calls +follow from how the samples were built: + +- `sample1` carries the L2 to L2.1 to L2.1.1 path plus the RIF marker, so + `classify` calls L2 and reports `rpoB` / `S450L`. +- `sample2` carries L3 to L3.2 plus the INH marker. +- `split-fastq` on `sample1`'s reads produces the **same summary** as `classify` + on its assembly, which is the property the marker format promises. +- `predict` assigns the two held-out queries to L2 and L3. +- `match` picks `ref_A`, which is `sample1`'s own genome. + +## Three things the wrappers have to work around + +1. **Sample names come from filenames.** Galaxy datasets arrive as + `dataset_NNN.dat`, so `classify` and `split-fastq` would name their outputs + after a Galaxy id. Each input is symlinked to a stable name first. +2. **`match` echoes input paths into its report.** Same fix, otherwise the first + column is full of absolute paths that differ between instances. +3. **`--min-alt-percent` is an integer.** A Galaxy `float` parameter renders + `95.0`, which the tool rejects outright. It is declared as an integer, so + fractional thresholds such as 99.5% are not available. + +## Submitting to the IUC + +The directory layout matches `galaxyproject/tools-iuc`, so submission is a copy: + +```bash +cp -r galaxy/tools/pathotypr /tools/pathotypr +``` + +then a pull request against that repository. Their CI runs the same planemo +lint and tests on Linux, where the Bioconda package resolves. + +## Not done yet + +Marker panels and models come from the history. A **data manager** plus a +`.loc` table would let an administrator install the published MTBC panels once +so users pick them from a dropdown, which is how Galaxy normally handles +reference data. That is a separate piece of work and was left out deliberately +rather than half-built: shipping a data table with nothing to populate it moves +the burden to administrators without helping anyone. diff --git a/galaxy/tools/pathotypr/macros.xml b/galaxy/tools/pathotypr/macros.xml new file mode 100644 index 0000000..c42bac2 --- /dev/null +++ b/galaxy/tools/pathotypr/macros.xml @@ -0,0 +1,85 @@ + + 1.0.2 + 0 + 23.0 + + + + pathotypr + + + + + + pathotypr + + + + + pathotypr --version + + + + + 10.64898/2026.03.24.714002 + 10.5281/zenodo.19210044 + + + + + -t \${GALAXY_SLOTS:-1} + + + + + + + + + + + + + + + + +**Marker file format** + +Tab-separated, no header required. Column order: + +:: + + position REF ALT level1 level2 ... (empty) gene mutation + +Positions are 1-based on the reference genome you supply. The lineage hierarchy +runs from column 4 until the first empty cell; whatever follows that empty cell +is read as gene and mutation. SNPs and equal-length MNVs work everywhere; +indels are accepted by *classify* and skipped by *split-fastq*. + +The full rules are at +https://pathogenomics-lab.github.io/pathotypr/marker_format/ + +Ready-made panels for the *M. tuberculosis* complex, and a pre-trained model, +are published on Zenodo: https://doi.org/10.5281/zenodo.19210044 + + + +**A note on other organisms** + +Nothing in pathotypr is hard-coded to one organism: the panel you supply defines +what is typed. In practice it has only been validated on the *M. tuberculosis* +complex, so treat other organisms as exploratory and check the calls against a +truth set you trust. + + diff --git a/galaxy/tools/pathotypr/pathotypr_classify.xml b/galaxy/tools/pathotypr/pathotypr_classify.xml new file mode 100644 index 0000000..cf3daaf --- /dev/null +++ b/galaxy/tools/pathotypr/pathotypr_classify.xml @@ -0,0 +1,160 @@ + + genotypes assembled genomes against a marker panel + + macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + output_masked_fasta + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/galaxy/tools/pathotypr/pathotypr_match.xml b/galaxy/tools/pathotypr/pathotypr_match.xml new file mode 100644 index 0000000..17c4209 --- /dev/null +++ b/galaxy/tools/pathotypr/pathotypr_match.xml @@ -0,0 +1,128 @@ + + finds which reference genome a set of reads is closest to + + macros.xml + + + + + 0 + --early-stop-confidence $early_stop_confidence + --early-stop-min-kmers $early_stop_min_kmers +#end if + $strict_percentages + @THREADS@ + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/galaxy/tools/pathotypr/pathotypr_predict.xml b/galaxy/tools/pathotypr/pathotypr_predict.xml new file mode 100644 index 0000000..a384f06 --- /dev/null +++ b/galaxy/tools/pathotypr/pathotypr_predict.xml @@ -0,0 +1,78 @@ + + assigns lineages to genomes using a trained model + + macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/galaxy/tools/pathotypr/pathotypr_split_fastq.xml b/galaxy/tools/pathotypr/pathotypr_split_fastq.xml new file mode 100644 index 0000000..a85256c --- /dev/null +++ b/galaxy/tools/pathotypr/pathotypr_split_fastq.xml @@ -0,0 +1,144 @@ + + genotypes raw reads against a marker panel without aligning them + + macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/galaxy/tools/pathotypr/pathotypr_train.xml b/galaxy/tools/pathotypr/pathotypr_train.xml new file mode 100644 index 0000000..f8a22d3 --- /dev/null +++ b/galaxy/tools/pathotypr/pathotypr_train.xml @@ -0,0 +1,135 @@ + + fits a Random Forest lineage classifier on labelled genomes + + macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + want_reports + + + want_reports + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + GCF_000195955.2 Mycobacterium tuberculosis H37Rv``, which yields one +class per accession rather than one class per group, and nothing warns you. +Rewrite the headers to the labels you actually want predicted:: + + >L2 sample_A collected_2021 + >L2 sample_B + >L4.3 sample_C + +Labels are compared as flat strings. ``L4`` and ``L4.1`` are two unrelated +classes; the tool knows nothing about the hierarchy in the name. If you want +hierarchical calls, use a marker panel with *pathotypr classify* or +*pathotypr split-fastq* instead. + +**How much data** + +Nothing enforces a minimum per class, but a class represented by one or two +genomes contributes almost nothing the forest can generalise from. Aim for ten +or more per class, and prefer cross-validation over a single split when the set +is small or imbalanced. + +@ORGANISM_NOTE@ + ]]> + + diff --git a/galaxy/tools/pathotypr/test-data/make_testdata.py b/galaxy/tools/pathotypr/test-data/make_testdata.py new file mode 100644 index 0000000..32ebf29 --- /dev/null +++ b/galaxy/tools/pathotypr/test-data/make_testdata.py @@ -0,0 +1,178 @@ +#!/usr/bin/env python3 +"""Generate the smallest test data that still exercises every pathotypr module. + +Everything is deterministic: a fixed seed, and every derived file is built from +the same reference so the expected calls can be reasoned about rather than +copied out of a run. + +Size matters here. tools-iuc carries this data forever, so the reference is a +couple of kb rather than a genome. +""" +import gzip +import os +import random +import sys + +random.seed(20260816) + +OUT = sys.argv[1] if len(sys.argv) > 1 else "test-data" +os.makedirs(OUT, exist_ok=True) + +REF_LEN = 2000 +K = 31 # default --kmer-size +FLANK = 10 # default --min-flank-bases +READ_LEN = 100 +DEPTH = 20 # comfortably above the default --min-depth of 10 + + +def w(name, text): + with open(os.path.join(OUT, name), "w") as fh: + fh.write(text) + return os.path.join(OUT, name) + + +def revcomp(s): + return s.translate(str.maketrans("ACGT", "TGCA"))[::-1] + + +# ---------------------------------------------------------------- reference +# Random sequence, but every k-mer window around a marker has to be unique or +# the diagnostic k-mers match in more than one place. Random 2 kb over a 31-mer +# window is unique with overwhelming probability; asserted below rather than +# assumed. +ref = "".join(random.choice("ACGT") for _ in range(REF_LEN)) + +# Marker positions are 1-based. Keep them clear of the ends so a centred 31-mer +# with 10 flanking bases always fits. +MARKERS = [ + # pos, alt, lineage levels, gene, mutation + (200, "L1",), + (400, "L2",), + (600, "L2", "L2.1"), + (800, "L2", "L2.1", "L2.1.1"), + (1000, "L3",), + (1200, "L3", "L3.2"), +] +ANNOTATED = [ + (1400, "RIF", "rpoB", "S450L"), + (1600, "INH", "katG", "Ser315Thr"), +] + + +def alt_of(base): + return {"A": "G", "G": "A", "C": "T", "T": "C"}[base] + + +rows = ["#position\tref\talt\tlevel1\tlevel2\tlevel3"] +marker_alts = {} +for m in MARKERS: + pos, levels = m[0], list(m[1:]) + r = ref[pos - 1] + a = alt_of(r) + marker_alts[pos] = (r, a) + rows.append("\t".join([str(pos), r, a] + levels)) +for pos, lineage, gene, mut in ANNOTATED: + r = ref[pos - 1] + a = alt_of(r) + marker_alts[pos] = (r, a) + # The empty cell after the lineage is what makes gene and mutation be read + # as annotations rather than as two more lineage levels. + rows.append("\t".join([str(pos), r, a, lineage, "", gene, mut])) + +# Every marker k-mer must be unique in the reference, otherwise a hit is +# ambiguous and the test data would be testing the wrong thing. +half = K // 2 +for pos in marker_alts: + kmer = ref[pos - 1 - half: pos + half] + assert len(kmer) == K, f"marker {pos} too close to the end" + assert ref.count(kmer) == 1 and ref.count(revcomp(kmer)) == 0, ( + f"marker k-mer at {pos} is not unique") + assert pos - 1 - half >= FLANK and pos + half <= REF_LEN - FLANK + +w("reference.fasta", ">MTB_test_ref synthetic 2 kb reference\n" + + "\n".join(ref[i:i + 60] for i in range(0, len(ref), 60)) + "\n") +w("markers.tsv", "\n".join(rows) + "\n") + + +def genome_with(alt_positions, name, desc): + """The reference with the ALT allele substituted at the given positions.""" + g = list(ref) + for pos in alt_positions: + g[pos - 1] = marker_alts[pos][1] + seq = "".join(g) + w(name, f">{desc}\n" + "\n".join(seq[i:i + 60] for i in range(0, len(seq), 60)) + "\n") + return seq + + +# sample1 carries the full L2 -> L2.1 -> L2.1.1 path plus the RIF marker. +s1 = genome_with([400, 600, 800, 1400], "sample1.fasta", "sample1") +# sample2 carries L3 -> L3.2 and the INH marker. +s2 = genome_with([1000, 1200, 1600], "sample2.fasta", "sample2") + +# ------------------------------------------------------------------- FASTQ +def reads(seq, path, depth=DEPTH, read_len=READ_LEN, paired=True): + """Tile the genome so every position, markers included, is covered `depth` + times. Tiling rather than random sampling keeps the file small and the + coverage guaranteed.""" + step = max(1, (read_len * 2) // depth) + r1, r2 = [], [] + n = 0 + for start in range(0, len(seq) - read_len * 2, step): + f = seq[start:start + read_len] + rc = revcomp(seq[start + read_len: start + read_len * 2]) + if len(f) < read_len or len(rc) < read_len: + continue + n += 1 + q = "I" * read_len + r1.append(f"@read{n}/1\n{f}\n+\n{q}\n") + r2.append(f"@read{n}/2\n{rc}\n+\n{q}\n") + if paired: + with gzip.open(path + "_R1.fastq.gz", "wt") as fh: + fh.write("".join(r1)) + with gzip.open(path + "_R2.fastq.gz", "wt") as fh: + fh.write("".join(r2)) + return n + + +n1 = reads(s1, os.path.join(OUT, "sample1")) + +# ---------------------------------------------------------------- training +# train takes the label from the first whitespace-separated token of the +# header. Several genomes per class, each a mutated copy, so the forest has +# something to separate. +def mutate(seq, n_changes, rng): + g = list(seq) + for _ in range(n_changes): + i = rng.randrange(len(g)) + g[i] = alt_of(g[i]) + return "".join(g) + + +rng = random.Random(7) +train_records = [] +for i in range(6): + train_records.append((f"L2 train_L2_{i}", mutate(s1, 20, rng))) +for i in range(6): + train_records.append((f"L3 train_L3_{i}", mutate(s2, 20, rng))) + +w("training.fasta", "".join( + f">{h}\n" + "\n".join(s[j:j + 60] for j in range(0, len(s), 60)) + "\n" + for h, s in train_records)) + +# query set for predict: two unseen genomes, one per class +w("query.fasta", "".join( + f">{h}\n" + "\n".join(s[j:j + 60] for j in range(0, len(s), 60)) + "\n" + for h, s in [("query_a", mutate(s1, 20, rng)), ("query_b", mutate(s2, 20, rng))])) + +# ------------------------------------------------------------- match refs +w("references.fasta", + ">ref_A\n" + "\n".join(s1[i:i + 60] for i in range(0, len(s1), 60)) + "\n" + + ">ref_B\n" + "\n".join(s2[i:i + 60] for i in range(0, len(s2), 60)) + "\n") + +print(f"reference {REF_LEN} bp") +print(f"markers {len(marker_alts)} ({len(MARKERS)} lineage, {len(ANNOTATED)} annotated)") +print(f"reads {n1} pairs, ~{n1 * READ_LEN * 2 / REF_LEN:.0f}x") +print(f"training {len(train_records)} records, 2 classes") +print() +for f in sorted(os.listdir(OUT)): + print(f" {os.path.getsize(os.path.join(OUT, f)):>8} B {f}") diff --git a/galaxy/tools/pathotypr/test-data/markers.tsv b/galaxy/tools/pathotypr/test-data/markers.tsv new file mode 100644 index 0000000..a0d38c5 --- /dev/null +++ b/galaxy/tools/pathotypr/test-data/markers.tsv @@ -0,0 +1,9 @@ +#position ref alt level1 level2 level3 +200 C T L1 +400 G A L2 +600 G A L2 L2.1 +800 T C L2 L2.1 L2.1.1 +1000 A G L3 +1200 C T L3 L3.2 +1400 A G RIF rpoB S450L +1600 A G INH katG Ser315Thr diff --git a/galaxy/tools/pathotypr/test-data/model.pathotypr.zst b/galaxy/tools/pathotypr/test-data/model.pathotypr.zst new file mode 100644 index 0000000..d1a7536 Binary files /dev/null and b/galaxy/tools/pathotypr/test-data/model.pathotypr.zst differ diff --git a/galaxy/tools/pathotypr/test-data/query.fasta b/galaxy/tools/pathotypr/test-data/query.fasta new file mode 100644 index 0000000..ccc6788 --- /dev/null +++ b/galaxy/tools/pathotypr/test-data/query.fasta @@ -0,0 +1,70 @@ +>query_a +CGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA +GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCCGGGGGATGCGTT +AATGAAACTCCTTAGAATAGAGTTAGATTCCTACCTTTGTGGGGTGGTGCTTCACCAGGG +TCTGTGACCACTCGACCCGCGCTAGATTTTCGGCGTCTACCTGTATAACTTATGTCCGCT +CGCGGTACCTAGTATTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT +AAAGGGTGTCAAGTAGTTTTCCTATGGGGGATTGCTCGGCTGGAGGAACACATCGTGATA +CTACTAATATTTCCTTCACCGACCCTATGCCGTATCCCCACAGATTAATCGTTTGTCATC +AGGGGCTGGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGCAG +AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC +GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGAAGTGGCTCTA +GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCTGGAACTT +GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACAGATTCAAAGAATCCCATGCCCCA +GGCGTACGTACGGTCTGGGAGTGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCT +TTTATGTAGGCGCGTTGTACCAACCGATACGTGCTAGTTCGTCACAATTCCCGTTATACA +TCGCTGGGGTGGACAACACCTTTGAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA +ATGGTAGAGAAGTGGCAGGTTGGATTACAGCGCCATATACGGTTGCGTACTGCTGTCTCA +GAATTTCTAACATAGTAAATCGTCTTGATCTAGCGGAATATGCCGACGCCAAGTTTCGGT +CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA +CGGAGCGACTTAATGCGTCCCAGGTCTCTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA +AAAACTGCACCTCTTATCGCGCTTAGGGCCGACGTGCACTATCTTCTCCGCCCCAGACAC +CGATTGGAACTGATGATCGCGAGAAACTCTACTGTACTTGGAGATAGGCTATTCATCACC +CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCCGGGTCACAGAAGCTGCAGGG +GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATATGCTACCCTATC +TGCGTCCTCAGGAAACCCCGCGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC +ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT +GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA +ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTTGATCCGTTAAAGCCTGCGGCCC +CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA +CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA +TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTATCCAATGCTG +GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG +GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC +GCTGGGTGTCTCGTCGGACGATAATTCACATTGCTGGTTCCTATAGTCTCCTGTCACAGG +ATCACGGCAGAAAGGAGGGG +>query_b +TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAGCTTCCCA +GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCTGGGGGATGCGTT +AATGAAATTCCTTAGAACAGAGTTGGATTCCTACCTTTGTGGGGTGGTGCTTCACCAGGG +TCTGTGACCACTCGACCCGCGCTAGATCTCCGACGTCTACCTGTACAACTTATGTCTGCT +CGCGGTACCTAATATTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT +AAAGAGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA +CTACTAATATTTCCTTCACCGACCCTATGCTGTATCCCCGCAGATTAATCGTTTGTCATC +AGGGGTTAGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGCAG +AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGACCTCCGACCCGGGTAGTAAAATCC +GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGAAGTGGCTCTG +GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCTGGAACTT +GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCCTATGCCCCA +GGCGTACGTACGGTCTGGGAGTGCCAGCGAGCGATCCTATAGAAGGCCTGCATGACACCT +TTTATGTAGGCGCGTTGTATCAACCGACACGTGCTAGTTCATCACAATTCCCGTTATACA +TCGCTGGGGTGGACAACACCTTTGAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA +ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCATATACGGTTGCGTACTGCTGTCTCA +GAATTTCTAACGTAGTAAATCGTCTTAATCTAGCGGAATGTGCCGACGCCAAGTTTCGGT +CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA +CGGAGCGACTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA +AAAACTGCACCTCTTATCGCACTTAGGGCCGACGTGCACTATCTTCTCCGCCCCAGACAT +CGATTGGAACTGATGATCGCGAGAAACTCTGCTATACTTGGAGATAGGCTATTCATTGCC +CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCCGGGTCACAGAAGCTGCAGGG +GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATATGCTACCCTATC +TGCGTCCTCAGGAAACCCCACGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC +ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT +GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA +ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTTGGTCCGTTAAAGCCTGCGGCCC +CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA +CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA +TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTACCCAATGCTG +GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG +GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC +GCTGGGTGTCTCGTCGGACGATAGTTCACATTGCTGATTCCTATAGTCTCCTGTCACAGG +ATCACGGCAGAAAGGAGGGG diff --git a/galaxy/tools/pathotypr/test-data/reference.fasta b/galaxy/tools/pathotypr/test-data/reference.fasta new file mode 100644 index 0000000..258cfee --- /dev/null +++ b/galaxy/tools/pathotypr/test-data/reference.fasta @@ -0,0 +1,35 @@ +>MTB_test_ref synthetic 2 kb reference +TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA +GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCTGGGGGATGCGTT +AATGAAATTCCTTAGAACAGAGTTAGATTCCTACCTTTGTGGGGTGGTGCTTCACCAGGG +TCTGTGACCACTCGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT +CGCGGTACCTAGTATTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT +AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA +CTACTAATATTTCCTTCACCGACCCTATGCTGTATCCCCGCAGATTAATCGTTTGTCATC +AGGGGCTAGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGCAG +AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC +GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGAAGTGGCTCTG +GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCTGGAACTT +GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCCCATGCCCCA +GGCGTACGTACGGTCTGGGAGTGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCT +TTTATGTAGGCGCGTTGTATCAACCGACACGTGCTAGTTCATCACAATTCCCGTTATACA +TCGCTGGGGTGGACAACACCTTTGAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA +ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCATATACGGTTGCGTACTGCTGTCTCA +GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATATGCCGACGCCAAGTTTCGGT +CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA +CGGAGCGACTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA +AAAACTGCACCTCTTATCGCACTTAGGGCCGACGTGCACTATCTTCTCCGCCCCAGACAC +CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGCTATTCATCACC +CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG +GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATATGCTACCCTATC +TGCGTCCTCAGGAAACCCCACGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC +ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT +GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA +ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTTGATCCGTTAAAGCCTGCGGCCC +CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA +CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA +TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTATCCAATGCTG +GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG +GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC +GCTGGGTGTCTCGTCGGACGATAATTCACATTGCTGGTTCCTATAGTCTCCTGTCACAGG +ATCACGGCAGAAAGGAGGGG diff --git a/galaxy/tools/pathotypr/test-data/references.fasta b/galaxy/tools/pathotypr/test-data/references.fasta new file mode 100644 index 0000000..4022036 --- /dev/null +++ b/galaxy/tools/pathotypr/test-data/references.fasta @@ -0,0 +1,70 @@ +>ref_A +TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA +GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCTGGGGGATGCGTT +AATGAAATTCCTTAGAACAGAGTTAGATTCCTACCTTTGTGGGGTGGTGCTTCACCAGGG +TCTGTGACCACTCGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT +CGCGGTACCTAGTATTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT +AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA +CTACTAATATTTCCTTCACCGACCCTATGCTGTATCCCCACAGATTAATCGTTTGTCATC +AGGGGCTAGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGCAG +AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC +GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGAAGTGGCTCTA +GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCTGGAACTT +GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCCCATGCCCCA +GGCGTACGTACGGTCTGGGAGTGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCT +TTTATGTAGGCGCGTTGTACCAACCGACACGTGCTAGTTCATCACAATTCCCGTTATACA +TCGCTGGGGTGGACAACACCTTTGAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA +ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCATATACGGTTGCGTACTGCTGTCTCA +GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATATGCCGACGCCAAGTTTCGGT +CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA +CGGAGCGACTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA +AAAACTGCACCTCTTATCGCACTTAGGGCCGACGTGCACTATCTTCTCCGCCCCAGACAC +CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGCTATTCATCACC +CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG +GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATATGCTACCCTATC +TGCGTCCTCAGGAAACCCCGCGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC +ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT +GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA +ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTTGATCCGTTAAAGCCTGCGGCCC +CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA +CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA +TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTATCCAATGCTG +GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG +GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC +GCTGGGTGTCTCGTCGGACGATAATTCACATTGCTGGTTCCTATAGTCTCCTGTCACAGG +ATCACGGCAGAAAGGAGGGG +>ref_B +TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA +GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCTGGGGGATGCGTT +AATGAAATTCCTTAGAACAGAGTTAGATTCCTACCTTTGTGGGGTGGTGCTTCACCAGGG +TCTGTGACCACTCGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT +CGCGGTACCTAGTATTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT +AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA +CTACTAATATTTCCTTCACCGACCCTATGCTGTATCCCCGCAGATTAATCGTTTGTCATC +AGGGGCTAGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGCAG +AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC +GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGAAGTGGCTCTG +GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCTGGAACTT +GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCCCATGCCCCA +GGCGTACGTACGGTCTGGGAGTGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCT +TTTATGTAGGCGCGTTGTATCAACCGACACGTGCTAGTTCATCACAATTCCCGTTATACA +TCGCTGGGGTGGACAACACCTTTGAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA +ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCATATACGGTTGCGTACTGCTGTCTCA +GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATGTGCCGACGCCAAGTTTCGGT +CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA +CGGAGCGACTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA +AAAACTGCACCTCTTATCGCACTTAGGGCCGACGTGCACTATCTTCTCCGCCCCAGACAT +CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGCTATTCATCACC +CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG +GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATATGCTACCCTATC +TGCGTCCTCAGGAAACCCCACGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC +ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT +GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA +ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTTGGTCCGTTAAAGCCTGCGGCCC +CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA +CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA +TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTATCCAATGCTG +GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG +GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC +GCTGGGTGTCTCGTCGGACGATAATTCACATTGCTGGTTCCTATAGTCTCCTGTCACAGG +ATCACGGCAGAAAGGAGGGG diff --git a/galaxy/tools/pathotypr/test-data/sample1.fasta b/galaxy/tools/pathotypr/test-data/sample1.fasta new file mode 100644 index 0000000..d29bd70 --- /dev/null +++ b/galaxy/tools/pathotypr/test-data/sample1.fasta @@ -0,0 +1,35 @@ +>sample1 +TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA +GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCTGGGGGATGCGTT +AATGAAATTCCTTAGAACAGAGTTAGATTCCTACCTTTGTGGGGTGGTGCTTCACCAGGG +TCTGTGACCACTCGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT +CGCGGTACCTAGTATTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT +AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA +CTACTAATATTTCCTTCACCGACCCTATGCTGTATCCCCACAGATTAATCGTTTGTCATC +AGGGGCTAGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGCAG +AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC +GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGAAGTGGCTCTA +GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCTGGAACTT +GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCCCATGCCCCA +GGCGTACGTACGGTCTGGGAGTGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCT +TTTATGTAGGCGCGTTGTACCAACCGACACGTGCTAGTTCATCACAATTCCCGTTATACA +TCGCTGGGGTGGACAACACCTTTGAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA +ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCATATACGGTTGCGTACTGCTGTCTCA +GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATATGCCGACGCCAAGTTTCGGT +CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA +CGGAGCGACTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA +AAAACTGCACCTCTTATCGCACTTAGGGCCGACGTGCACTATCTTCTCCGCCCCAGACAC +CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGCTATTCATCACC +CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG +GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATATGCTACCCTATC +TGCGTCCTCAGGAAACCCCGCGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC +ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT +GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA +ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTTGATCCGTTAAAGCCTGCGGCCC +CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA +CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA +TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTATCCAATGCTG +GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG +GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC +GCTGGGTGTCTCGTCGGACGATAATTCACATTGCTGGTTCCTATAGTCTCCTGTCACAGG +ATCACGGCAGAAAGGAGGGG diff --git a/galaxy/tools/pathotypr/test-data/sample1_R1.fastq.gz b/galaxy/tools/pathotypr/test-data/sample1_R1.fastq.gz new file mode 100644 index 0000000..46a9493 Binary files /dev/null and b/galaxy/tools/pathotypr/test-data/sample1_R1.fastq.gz differ diff --git a/galaxy/tools/pathotypr/test-data/sample1_R2.fastq.gz b/galaxy/tools/pathotypr/test-data/sample1_R2.fastq.gz new file mode 100644 index 0000000..cedc88d Binary files /dev/null and b/galaxy/tools/pathotypr/test-data/sample1_R2.fastq.gz differ diff --git a/galaxy/tools/pathotypr/test-data/sample2.fasta b/galaxy/tools/pathotypr/test-data/sample2.fasta new file mode 100644 index 0000000..d5ce268 --- /dev/null +++ b/galaxy/tools/pathotypr/test-data/sample2.fasta @@ -0,0 +1,35 @@ +>sample2 +TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA +GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCTGGGGGATGCGTT +AATGAAATTCCTTAGAACAGAGTTAGATTCCTACCTTTGTGGGGTGGTGCTTCACCAGGG +TCTGTGACCACTCGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT +CGCGGTACCTAGTATTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT +AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA +CTACTAATATTTCCTTCACCGACCCTATGCTGTATCCCCGCAGATTAATCGTTTGTCATC +AGGGGCTAGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGCAG +AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC +GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGAAGTGGCTCTG +GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCTGGAACTT +GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCCCATGCCCCA +GGCGTACGTACGGTCTGGGAGTGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCT +TTTATGTAGGCGCGTTGTATCAACCGACACGTGCTAGTTCATCACAATTCCCGTTATACA +TCGCTGGGGTGGACAACACCTTTGAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA +ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCATATACGGTTGCGTACTGCTGTCTCA +GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATGTGCCGACGCCAAGTTTCGGT +CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA +CGGAGCGACTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA +AAAACTGCACCTCTTATCGCACTTAGGGCCGACGTGCACTATCTTCTCCGCCCCAGACAT +CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGCTATTCATCACC +CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG +GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATATGCTACCCTATC +TGCGTCCTCAGGAAACCCCACGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC +ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT +GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA +ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTTGGTCCGTTAAAGCCTGCGGCCC +CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA +CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA +TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTATCCAATGCTG +GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG +GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC +GCTGGGTGTCTCGTCGGACGATAATTCACATTGCTGGTTCCTATAGTCTCCTGTCACAGG +ATCACGGCAGAAAGGAGGGG diff --git a/galaxy/tools/pathotypr/test-data/training.fasta b/galaxy/tools/pathotypr/test-data/training.fasta new file mode 100644 index 0000000..e878ffe --- /dev/null +++ b/galaxy/tools/pathotypr/test-data/training.fasta @@ -0,0 +1,420 @@ +>L2 train_L2_0 +TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA +GTAGCGCTGATAGGGAGGGACTGACAGGCGTGAACCGGATCCAGCGCTGGGGGATGCGCT +AATGAAATTCCTTAGAACAGAGTTAGATCCCTACCTTTGTGGGGTGGTGCTTCACCGGGG +TCTGTGACCACTTGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT +CGCGGTACCTAGTATTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT +AAAGGGTGCTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA +CTACTAATATTTCCTTCACCGACCCTATGCTGTATCCCCACAGATTAATCGTTTGTCATC +AGGGGCTAGTACGATTTTCACTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGCAG +AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC +GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGAAGTGGCTCTA +GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCTGGAACTT +GGGTAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCCCATGCCCCA +GGCGTACGTACGGTCTGGGAGTGCTGGCAAGCGATCCTATAGAAGGCCTGTATGACACCT +TTTATGTAGGCGCGTTGTACCAACCGACGCGTGCTAGTTCATCACAATTCCCGTTATACA +TCGCTGGGGTGGACAATACCTTTGAAAGGAACAAATCCGGAACGATGTTCCGTCACTGCA +ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCATATACGGTTGCGTACTGCTGTCTCA +GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATATGCCGACGCCAAGTTTCGGT +CATAGTAAGGTGTGGTGCTGGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA +CGGAGCGACTTAATGCGCTCCAGGTCTCTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA +AAAACTGCACCTCTTATCGCACTTAGGGCCGACGTGCACTATCTTCTCCGCCCTAGACAC +CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGCTATTCATCACC +CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG +GGTCGTCCATGACGTGGATGGGCTAGCTAGATACATGCAACGGTCATATGCTACCCTATC +TGCGTCCTCAGGAAACCCCGCGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC +ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT +GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA +ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTTGATCCGTTAAAGCCTGCGGCCC +CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA +CTTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA +TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTATCCAATGCTG +GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG +GAACCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC +GCTGGGTGTCTCGTCGGACGACAATTCACATTGCTGGTTCCTATAGTCTCCTGTCACAGG +ATCACGGCAGAAAGGAGGGG +>L2 train_L2_1 +TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA +GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCTAGCGCTGGGGGATGCGTT +AGTGAAGTTCCTTAGAACAGAGTCAGATTCCTACCTTTGTGGGGTGGTGCTTCACCAGGG +TCTGTAACCACTCGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT +CGCGGTACCTAGTGTTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT +AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA +CTACTAATATTTCCTTCACCGACCCTATGCTGTATCCCCACAGATTAATCGTTTGTCATC +AGGGGCTAGTACGATTTTCGCTTTGTCGAAGATATTTTCCCGTTAACTTTATTCTGGCAG +AAGTCTCATGTCTGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC +GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGAAGTGGCTCTA +GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCTGGAACTT +GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCCCATGCCCCA +GGCGTACGTACGGTCTGGGAGTGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCT +TTTATGTAGGCGCGTTGTACCAACCGACACGTACTAGTTCATCACAATTCCCGTTATACA +TCGCTGGGGTGGACAACACCTTTGAAAGGGACAAATCCGGAACGATGTCCCGTCACTGCA +ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCATATACGGTTGCGTACTGCTGTCTCA +GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATATGCCGACGCCAAGTTTCGGT +CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA +CGGAGCGACTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTTGCCTTCGATGTCGGGGCA +AAAACTGCACCTCTTATCACACTTAGGGCCGACGTGCACTACCTTCTCCGCCCTAGACAT +CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGCTATTCATCACC +CGCTGCACGATCGGTCATCGAGGGACGGGAGAGATAGCCTGGGTCACAGAAGCTGCAGGG +GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATATGCTACCCTATC +TGCGTCCTCAGGAAACCCCGCGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC +ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT +GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA +ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTTGATCCGTTAAAGCCTGCGGCCC +CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA +CCTTGCACCATGATTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA +TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTATCCAATGCTG +GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG +GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC +GCTGGGTGTCTCGTCGGACGATAATTCACATTGCTGGTTCCTATAGTCTCCTGTCACAGG +ATCACGGCAGAAAGGAGGGG +>L2 train_L2_2 +TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA +GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACTGGGTCCAGCGCTGGGGGATGCGTT +AATGAAATTCCTTAGAACAGAGTTAGATTCCTACCTTTGTGGGGTGGTGCTTCACCAGGG +TCTGTGACCACTCGACCCGCGCTAGATTTCCAACGTCTACCTGTACAACTTATGTCCGCT +CACGGTACCTAGTATTGTGTTGGACCTCCACTTTCGAAGTCGAGATAAGAACATCTACTT +AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA +CTACTAATATCTCCTTCACCGACCCTATGCTGTATCCCCACAGATTAATCGTTTGTCATC +AGGGGCTAGTACGATTTTCGCTTTGTCGAAGACATTTCCCCGTTAACTTTATTCTGGCAG +AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC +GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGAAGTAGCTCTA +GTCGGAATAAACTTGAAAAAGGACAGCGGCAGCGATACTCTTGCTAGACGCCTGGAACTT +GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCCCATGCCCCA +GGCGTACGTACGGTCTGGGAGTGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCT +TTTATGTAGGCGCGTTGTACCAACCGACACGTGCTAGTTCATCACAATTCCCGTTATACA +TCGCTGGGGTGGACAACATCTTTGAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA +ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCATATACGGTTGCGTACTGCTGTCTCA +GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATATGCCGACGCCAAGTTTCGGT +CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA +CGGAGCGACTTAATGCGTTCCAGGTCTTTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA +GAAACTGTACCTCTTATCGCACTTAGGGCCGACGTGCACTATCTTCTCCGCTCCAGACAC +CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGCTATTCATCACC +CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG +GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATATGCTACCCTATC +TGCGTCCTCAGGAAACTCCGCGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC +ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT +GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA +ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTTGATCCGTTAAAGCCTGCGGCCC +CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGACGCTTATA +CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA +TGATTAGCAATCTCCGGCCAAGAGATGAGCAGTACACGCGTGGCTACCTATCCAATGCTG +GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG +GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC +GCTGGGTGTCTCGTCGGACGATAATTCACATTGCTGGTTCCTATAGTCTCCTGTCACAGG +ATCACGGCAGAAAGGAGGGA +>L2 train_L2_3 +TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA +GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCTGGGGGATGCGTT +AACGAAATCCCTTAGAACAGAGTTAGATTCCTACCTTTGTGGGGTGGTGCTTCACCAGGG +TCTGTGACCACTCGACCCGTGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT +CGCGGTACCTAGTATTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT +AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA +CTACTAATATTTCCTTCACCGACCTTATGCTGTATCCCCACAGATTAATCGTTTGTCATC +AAGGGCTAGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGCAG +AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC +GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGAAGTGGCTCTA +GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGTTAGACGCCTGGAACTT +GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCCCATGCCCCA +GGCGTACGTACGGTCTGGGAGTGCTGGCGAGCGATCCTATAGGAGGCCTGTATGACACCT +TTTATGTAGGCGCGTTGTACCAACCGACACGTGCTAGTTCATCACAATTCCCGTTATACA +TCGCTGGGGTGGACAACACCTTTGAAAGGAACAAACCCGGAACGATGTCCCGTCACTGCA +ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCATATACGGTTGCGTACTGCCGTCTCA +GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATATGCCGACGCCAAGTTTTGGT +CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA +CGGAGCGATTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTCGCCTTCAATGTCGGGGCA +AAAACTGCACCTCTTGTCGCACTTAGGGCCGACGTGCACTATCTTCTCCGCCCCAGACAT +CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGCTATTCATCACC +CGCTGCATGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAAAAGCTGCAGGG +GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATATGCTACCCTATC +TGCGTCCTCAGGAGACCCCGCGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC +ATTTTTTTAACTAAATCTTAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT +GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA +ATGGCTTCCACGCCTGCTATAGCGGCCCAAATATCTTTGATCCGTTAAAGCCTGCGGCCC +CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA +CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA +TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTATCCAATGCTG +GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG +GAATCCATGCGCGGAGTACCTGGCTGCAAGCAGCATACTGATCCGTGTTGTTCCCTAGAC +GCTGGGTGTCTCGTCGGACGATAATTCACATTGCTGGTTCCTATAGTCTCCTGTCACAGG +ATCACGGCAGAAAGGAGGGG +>L2 train_L2_4 +TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA +GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCTGGGGGATGCGTT +AATGAAATTCCTTAGAACAGAGTTAGATTCCTACCTTTGTGGGGTGGCGCTTCACCAGGG +TCTGTGACCACTCGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT +CGCGGTACCTAGTATTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT +AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA +CTACTAATGTTTCCTTCACCGACCCTATGCTGTATCCCCACAGATTAATCGTTTGTCATC +AGGGGCTAGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGCAG +AAGTCTCATGTCCGATATATTAAGTCATATTAAAGATCTCCGACCCGGGTAGTAAAATCC +GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGGAGTGGCTCTA +GTCGGAATAAACTCAAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCTGGAACTT +GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAGAGAATCCCATGCCCCA +GGCGTACGTACGGTCTGGGAATGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCT +TTTATGTAGGCGCGTTGTACCAACCGACACGTGCTAGTTCATCACAATTCCCGTTATACA +TCGCTGGGGTGGACAACACCTTTGAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA +ATAGTAGAGAAGTGGCAGGCTGGATTACGGCGCCATATACGGTTGCGTACTGCTGTCTCA +GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATATGCCGACGCCAAGCTTCGGT +CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTACGTA +CGGAGCGACTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA +AAAACTGCACCTCTTATCGCACTTAGGGCCGACGTGTACTATCTTCTCCGCCCCAGACAC +CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGACTATTCATCACC +CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG +GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATATGCTACCCTATC +TGCGTCCTCAGGAAACCCCGCGTAAATTAATACAGTGAATATTTCTCACAAGTATAGCAC +ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTCACGTGT +GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA +ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTCGATCCGTTAAAGCCTGCGGCCC +CCATCCCAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA +CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA +TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTATCTAATGCTG +GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG +GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC +GCTGGGTGTCTCGTCGGACGATAATTCACATTGCTGGTTCCTATAGTCTCCTGTCACAGG +ATCACGGCAGAAAGGAGGGG +>L2 train_L2_5 +TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA +GTAGCGCTGATAGGGAAGGATTGACAGGCGTGAACCGGGTCCAGCGCTGGGGGATGCGTT +AATGAAATTCCTTAGAACAGAGTTAGATTTCTACCTTTATGGGGTGGTGCTTCACCAGGG +TCTGTGACCACTCGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT +CACGGTACCTAGTATTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT +AAAGGGTGTTAGGTAGTTTTCCTATGGGGGATCGCTCAGCTGGAGGAACACATCGTGATA +CTACTAATATTTCCTTCACCGACCCTATGCTGTATCCCCACAGATTAATCGTTTGTCATC +AGGGGCTAGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGCAG +AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC +GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGAAGTGGCTCTA +GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCTGGAACTT +GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATCCAAAGAATCCCATGCCCCA +GGCGTACGTACGGTCTGGGAGTGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCT +TTTATGTAGGCGCGTTGTACCAACCGACACGTGCTAGTTCATCACAATTCCCGTTATACA +TCGCTGGGGTGGACAATACCTTTAAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA +ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCATATACGGTTGCGTACTGCTGTCTCA +GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATATACCGACGCCAAGTTTCGGT +CATAGTAAGGTGTGGTGCTAGGGGCTCCCATACGCCCAGTGTGGGCGACTGATTTGCGTA +CGGAGCGACTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA +AAGACTGCACCTCTTATCGCACTTAGGGCCGACATGCACTATCTTCTCCGCCCCAGACAC +CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGCTATTCATCACC +CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG +GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATACGCTACCCTATC +TGCGTCCTCAGGAAACCCCGCGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC +ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT +GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCATCAATTTAAA +ATGGCCTCCACGCCTGCTATAGCGGCCCAAACATCTTTGATCCGTTAAAGCCTGCGACCC +CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA +CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA +TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTATCTAATGCTG +GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG +GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTCCCCTAGAC +GCTGGGTGTCTCGTCGGACGATAATTCACATTGCTGGTTCCTATAGTCTCTTGTCACAGG +ATCACGGCAGAAAGGAGGGG +>L3 train_L3_0 +TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA +GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCTGGGGGATGCGTT +AATGGAATTCCTTGGAACAGGGTTAGATTCCTACCTTTGTGGGGTGGTGCTTCACCAGGG +TCTGTGACCACCCGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT +CGCGGTACCTAGTATTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT +AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA +CTACTAATATTTCCTTCACCGACCCTATGCTGTATCCCCGCAGATTAATCGTTTGTCATC +AGGGGCTAGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGCAG +AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC +GTTTGACAACTAGGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGAAGTGGCTCTG +GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTACTAGACGCCTGGAACTT +GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACAGATTCAAAGAATCCCATGCCTCA +GGCGTACGTACGGTCTGGGAGTGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCT +TTTATGTAGGCGCGTTGTATCAACCGACACGTGCTAGTTCATCACAATTCCCGTTATACA +TCGCTGGGGTGGACAACACCTTTGAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA +ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCGTATACGGTTGCGTACTGCTGTCTCA +GAATTTCTAATATAGTAAATCGTCTTAATCTAGCGGAATGTGCCGACGCCAAGTTTCAGT +CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA +CGGAGCGACTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA +AAAACTGCACCTCTTATCGCACTTAGGGCCGACGTGCACTATCTTCTTCGCCCCAGACAT +CGATTGGAACTGATGATTGCGAGAAACTCTGCTGTACTTGGAGATAGGCTATTCATCACC +CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG +GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAATGGTCATATGCTACCCTATC +TGCGTCCTCAGGAAACCCCACGTAAATTAATACAGTGAATATTCCTCGCAAATATAGCAC +ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT +GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA +ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTTGGTCCGTTAAAGCCTGCGGCCC +CCATCCTAGCGTCGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCCTATA +CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCAAGCGCTGCCAGCGCTCATA +TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTATCCAATGCTG +GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG +GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC +GCTGGGTGTCTCGTTGGACGATAATTCACATTGCTGGTTCCTATAGTCTCCTGTCACAGG +ATCACGGCAGAAAGGAGGGG +>L3 train_L3_1 +TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGATACTCAACTTCCCA +GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCTGGGGGATGCGTT +AATGAAATTCCTTAGAACAGAGTTAGATTCCTACCTTTGTGGGGTGGTGCTTCACCAGGG +TCTGTGACCACTCGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT +CGCGGTACCTAGTATTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT +AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAAGAACACATCGTGATA +CTACTAATATTTCCTTCACCGACCCTATGCTGTATCCCCGCAGATTAATCGTTTGTCATC +AGGGGCTAGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGCAG +AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC +GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGTCGTCAGAAGTGGCTCTG +GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGGTACTCTTGCTAGACGCCTGGAACTT +GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCTCATGCCCCA +GGCGTACATACGGTCTGGGAGTGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCT +TTTATGTAGGTGCGTTGTATCAACCGACACGTGCTAGTTCATCACAATTCCCGTTATACA +TCGCTGGGGTGGACAACACCTTTGAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA +ATAGTAGAGAAGCGGCAGGTTGGATTACAGCGCCATATACGGTTGTGTACTGCTGTCTCA +GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATGTGCCGACGCCAAGTTTCGGT +CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA +CGGAGCGACTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA +AAAACTGCACCTCTTATCGCACTTAGGGCCGACGTGCACTATCCTCTCCGCCCCAGACAT +CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGCTACTCATCACC +CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG +GGTCGCCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATATACTACCCTATC +TGCGTCCTCAGGAAATCCCACGTAAATTAATACAGTGAATATTTCTCACAAATATAACAC +ATTTTTTTAACTAAATCTCAGCGAATGACGACGAGTGATGCTTAAACAATGGTTACGCGT +GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA +ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTTGGTCCGTTAAAGCCTGCGGCCC +CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA +CCTCGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA +TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTATCCAATGCTG +GCTACGCTAGTGGTAATAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG +GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC +GCTGGGCGTCTCGTCGGACGATAATTCACATTGCTGGTTCCTATAGTCTCCTGTCACAGG +ATCACGGCAGAAAGGAGGGG +>L3 train_L3_2 +TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA +GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCTGGGGGATGCGTT +GATGAAATTCCTTAGAACAGAGTTAGATTCCTACCTTTGTGGGGTAGTGCTTCACCAGGG +TCTGTGACCACTCGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCC +CGCGGTACCTAGTATTGTGTTGGATCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT +AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCCGGAGGAACACATCGTGATA +CTACTAATATTTCCTTCACCGACCCTATGCTGTATCCCCGCAGATTAATCGTTTGTCATC +AGGGGCTAGTACGATTTTCGCTTTGTTGAAGATATTTCCCCGTTAACTTTATTCTGGCAG +AAGTCTCATGTCCGATATACTAAGTCACGTTAAAGATCTCCGACCCGGGTAGTAAAATCC +GTTTGACAACTAAGTACAAGCAGGTTAAGTAACTAGGTTGCGCCGTCAAAAGTGGCTCTG +GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCTGGAACTT +GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCCCATGCCCCA +GGCGTACGTACGGTCTGGGAGTGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCT +TTTATGTAGGCGCGTTGTATTAACCGACACGTGCCAGTTCATTACAATTCCCGTTATACA +TCGCTGGGGTGGACAACACCTTTGAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA +ATAGTAGAGAAGTGGCAGGCTGGATTACAGCGCCATATACGGTTGCGTACTGCTGTCTCA +GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATGTGCCGACGCCAGGTTTTGGT +CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA +CGGAGCGACTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTTGCCCTCAATGTCGGGGCA +AAAACTGCACCTCTTATCGCACTTAGGGCCGACGTGCACTATCTTCTCCGCCCCAGACAT +CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGCTATTCATCACC +CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG +GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATATGCTACCCTATC +TGCGTCCTCAGGAAACCCCACGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC +ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT +GCTCTAAGCTACCCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA +ATGGCTTCCACGCTTGCTATAGCGGCCCAAACATCTTTGGTCCGTTAAAGCCTGCGGCCC +CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA +CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA +TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCCACCTATCCAATGCTG +GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG +GAATCCATGCGCGGAGTGCCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC +GCTGGGTGTCTCGTCGGACGATAATTCACATTGCTGGTTCCTATAGTCTCCTGTCACAGG +ATCACGGCAGAAAGGAGGGG +>L3 train_L3_3 +TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA +GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCTGGGGGATGCGTT +AATGAAATTCCTTAGAACAGAGTTAGATTCCTACCTTTGTGGGGTGGTGTTTCACCAGGG +TCTGTGACCACTCGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT +CGCGGTACCTAGTATTGTGTTGGACCTCCACTCTCGAAGTTGAGATAAGAACATCCACTT +AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA +TTACTAATATTTCCTTCACCGACCCTATGCTGTATCCCCGCAGATTAATCGTTTGTCATC +AGGGGCTAGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATCCTAGCAG +AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC +GTTTGACAACTAAGTACAAGCAGGTTAAGCGACTAGGTTGCGCCGTCAGAAGTGGCTCTG +GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCTGGAACTT +GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCCCATGCCCCA +GGCGTACGTACGGTTTGGGAGTGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCC +TTTATGTAGGCGCGTTGTATCAACCGACACGTGCTAGTTCATCACAATTCCCGTTATACA +TCGCTGGGGTAGACAACACCTTTGAAAGGAACAAATCCGGAGCGATGTCCCGTCACTGCA +ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCATATACGGTTGCGTACTGCTGTCTCA +GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATGTGCCGACGCCAAGTTTCGGT +CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA +CGGAGCGACTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTTGCCTCCAATGTCGGGGCA +AAAACTGCACCTCTTATCGCACTTAGGGCCGACGTGCACTATCTTCTCCGCCCCAGACAT +CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGCTATTCATCACC +CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG +GGTCGTCCATGACATGGATGGGCTAGCTAGATACATGCAACGGTCATATGCTACCCTATC +TGCGTCCTCAGGAAACCCTACGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC +ATTTTTCTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT +GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA +ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTTGGTCCGTTAAAGCCTGCGGCCC +CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTGTA +CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA +TGATTAGCAATCTCCGGCTAAGAGATGAGTAGTACACGCGTGGCTACCTATCCAATGCTG +GCTACGCTAACGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG +GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC +GCTGGGTGTCTCGTCGGACGATAATTCACATTGCTGGTTCCCATAGTCTCCTGTCACAGG +ATCACGGCAGAAAGGAGGGG +>L3 train_L3_4 +TGTGAGTCATGTTCACCTCGGTACGGGACGACAATGCTGGCACAGACACTCAACTTCCCA +GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCTGGGGGATGCGTT +AATGAAATTCCTTAGAACAGAGTTAGATTCCTACCTTTGTGGGGTGGTGCTTCACCAGGG +TCTGTGACCACTCGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT +CGCGGTACCTAGTATTGCGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACCT +AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA +CTACTAATATTTCTTTCACCGACCCTATGCTGTATCCCCGCAGATTAATCGTTTGTCATC +AGGGGCTAGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGTAG +AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATTC +GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGCTGCGCCGTCAGAAGTGGCTCTG +GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCCGGAACTT +GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCCCATGCCCCA +GGCGTACGTACGGTCTGGGAGTGCTGGCGAGCGATCTTATAGAAGGCCTGTATGACACCT +TTTATGTAGGCGCGTTGTATCAACCGACACGTGCTAGTTCATCACAATTCCCGTTATACA +TCGCTGGGGTGGACAACATCTTTGAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA +ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCATATACGGTTGCGTACTGCTGTCTCA +GAATTTCTAACATAGTAAATCGTCTTAATCTAGTGGAATGTGCCGACGCCAAGTTTCGGT +CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCCCAGTGTGGGCGACTGATTTGCGTA +CGGAGCGACTTAATACGTTCCAGGTCTCTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA +AAAACTGCACCTCTTATCGTACTTAGGGCCGACGTGCACTATCTTCTCCGCCCCAGACAT +CGATTGAAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGTTATTCATCACC +CGCTGCACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG +GGTCGTCCATGACATGGATGGGCTAGCTGGATACATGCAACGGTCATATGCTACCCTATC +TGCGTCCTCAGGAAACCCCACGTAAATTAATACAATGAATATTTCTCACAAATATAGCAC +ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT +GCTCTAAGCTACTCCTTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA +ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTTGGTCCGTTAAAGCCTGCGGCCC +CCATCCTAGCGTTGTCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA +CCTTGCACCATGACTTCAGTCCCGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA +TGATTAGCAATCTCCGGCTAAGAGATGAGCAGTACACGCGTGGCTACCTATCCAATGCTG +GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGTTGGGAGTAATCGTCTCG +GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC +GCTGGGTGTCTCGTCGGACGATAATTCACATCGCTGGTTCCTATAGTCTCCTGTCACAGG +ATCACGGCAGAAAGGAGGGG +>L3 train_L3_5 +TGTGAGTCGTGTTCACCTCGGTACAGGACGACAATGCTGGCACAGACACTCAACTTCCCA +GTAGCGCTGATAGGGAAGGACTGACAGGCGTGAACCGGGTCCAGCGCTGGAGGATGCGTT +AATGAAATTCCTTAGAACAGAGTTAGATTCCTACCTTTGTGGGGTGGTGCTTCACCAGGG +TCTGTGACCACTCGACCCGCGCTAGATTTCCGACGTCTACCTGTACAACTTATGTCCGCT +CGCGGTACCTAGTATTGTGTTGGACCTCCACTCTCGAAGTCGAGATAAGAACATCCACTT +AAAGGGTGTTAAGTAGTTTTCCTATGGGGGATCGCTCGGCTGGAGGAACACATCGTGATA +CTACTAATATTTCCTTCACCGACCCTATGCTGTATCCCCGCAGATTAATCGTTTGTCATC +AGGGGCTAGTACGATTTTCGCTTTGTCGAAGATATTTCCCCGTTAACTTTATTCTGGCAG +AAGTCTCATGTCCGATATACTAAGTCATGTTAAAGATCTCCGACCCGGGTAGTAAAATCC +GTTTGACAACTAAGTACAAGCAGGTTAAGCAACTAGGTTGCGCCGTCAGAAGTGGCTCTG +GTCGGAATAAACTTGAAAAAGGACAGCGGCAACGATACTCTTGCTAGACGCCTGGAACTT +GGGCAGGCTCATACCTCATGCACCAGCCCCCTAAACGGATTCAAAGAATCCCATGCCCCA +GGCGTACGTACGGTCTGGGAGTGCTGGCGAGCGATCCTATAGAAGGCCTGTATGACACCT +TTTATGTAGGCGCGTTGTATCAATCGACACGTGCTGGCTCATCACAATTCCCGTTATACA +TCGCTGGGGTGGACAACACCTTTGAAAGGAACAAATCCGGAACGATGTCCCGTCACTGCA +ATAGTAGAGAAGTGGCAGGTTGGATTACAGCGCCACATACGGTTGCGTACTGCTGTCTCA +GAATTTCTAACATAGTAAATCGTCTTAATCTAGCGGAATGTGCCGACGCCAAGTTTCGGT +CATAGTAAGGTGTGGTGCTAGGGGCTCCTATACGCTCAGTGTGGGCGACTGATTTGCGTA +CGGAGCGACTTAATGCGTTCCAGGTCTCTAACCGCGAAGCTTGCCTTCAATGTCGGGGCA +AAAACCGCACCTCTTATCGCACTTAGGGCCGACGTGCACTATCTTCTCCGCCCCAGACAT +CGATTGGAACTGATGATCGCGAGAAACTCTGCTGTACTTGGAGATAGGCTATTCATCACC +CGCTACACGATCGGTCATCGAGGGGCGGGAGGGATAGCCTGGGTCACAGAAGCTGCAGGG +GGTCGTCCATGACATGGATGGACTAGCTAGATACATGCAACGGTCATATGCTACCCTATC +TGCGCCCTCAGGAGACCCCACGTAAATTAATACAGTGAATATTTCTCACAAATATAGCAC +ATTTTTTTAACTAAATCTCAGCGAATGGCGACGAGTGATGCTTAAACAATGGTTACGTGT +GCTCTAAGCTACTCCCTACGAGAGTGCCCCCCATGGTCAAAGGATCGCCACCAATTTAAA +ATGGCTTCCACGCCTGCTATAGCGGCCCAAACATCTTCGGTCCGTTAAAGCCTGCGGCCC +CCATCCTAGCGTTGCCTGTAATAGTATCAATCGCGCTAGTACGGTCGGTTGGCGCTTATA +CCTTGCACCATGACTTCAGTCCTGAGCCGATTGATTGAGCGAGCGCTGCCAGCGCTCATA +TGATTAGCAATCTCCGGCTGAGAGATGAGCAGTACACGCGTGGTTACCTATTCAATGCTG +GCTACGCTAGTGGTAACAAGAAACTCAGTTAGTGGCCACTTGCTGGGAGTAATCGTCTCG +GAATCCATGCGCGGAGTACCTGGCTGCAAGCGGCATACTGATCCGTGTTGTTCCCTAGAC +GCTGGGTGTCTCGTCGGACGATAATTTACGTTGCTGGTTCCTATAGTCTCCTGTCACAGG +ATCACGGCAGAAAGGAGGGG