Merge pull request #29 from VukManojlovic/CTX-4247

CTX-4247: Created a bioinformatics folder, moved the qiime2 folder th…

coretex/qiime2/__init__.py → coretex/bioinformatics/qiime2/__init__.py

@@ -15,52 +15,14 @@
 #     You should have received a copy of the GNU Affero General Public License
 #     along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
-from typing import List, Optional
-from pathlib import Path
+from typing import Optional
 
-import subprocess
-import logging
+from .utils import compressGzip, createSample, getDemuxSamples, getDenoisedSamples, \
+    getFastqDPSamples, getFastqMPSamples, getMetadataSample, getPhylogeneticTreeSamples, \
+    isDemultiplexedSample, isDenoisedSample, isFastqDPSample, isFastqMPSample, \
+    isMetadataSample, isPhylogeneticTreeSample, sampleNumber
 
-
-class QiimeCommandException(Exception):
-    pass
-
-
-def logProcessOutput(output: bytes, severity: int) -> None:
-    decoded = output.decode("UTF-8")
-
-    for line in decoded.split("\n"):
-        # skip empty lines
-        if line.strip() == "":
-            continue
-
-        # ignoring type for now, has to be fixed in coretexpylib
-        logging.getLogger("coretexpylib").log(severity, line)
-
-
-def QiimeCommand(args: List[str]) -> None:
-    process = subprocess.Popen(
-        args,
-        shell = False,
-        cwd = Path(__file__).parent,
-        stdout = subprocess.PIPE,
-        stderr = subprocess.PIPE
-    )
-
-    stdout, stderr = process.communicate()
-
-    if len(stdout) > 0:
-        logProcessOutput(stdout, logging.INFO)
-
-    if len(stderr) > 0:
-        severity = logging.CRITICAL
-        if process.returncode == 0:
-            severity = logging.WARNING
-
-        logProcessOutput(stderr, severity)
-
-    if process.returncode != 0:
-        raise QiimeCommandException
+from ..utils import command
 
 
 def toolsImport(
@@ -82,7 +44,7 @@ def toolsImport(
             "--input-format" , inputFormat
         ])
 
-    QiimeCommand(args)
+    command(args)
 
 
 def demuxEmpSingle(
@@ -93,7 +55,7 @@ def demuxEmpSingle(
     errorCorretctionDetailsPath: str
 ) -> None:
 
-    QiimeCommand([
+    command([
         "qiime", "demux", "emp-single",
         "--i-seqs", sequencesPath,
         "--m-barcodes-file", barcodesPath,
@@ -105,7 +67,7 @@ def demuxEmpSingle(
 
 
 def demuxSummarize(dataPath: str, visualizationPath: str) -> None:
-    QiimeCommand([
+    command([
         "qiime", "demux", "summarize",
         "--i-data", dataPath,
         "--o-visualization", visualizationPath
@@ -121,7 +83,7 @@ def dada2DenoiseSingle(
     denoisingStatsPath: str
 ) -> None:
 
-    QiimeCommand([
+    command([
         "qiime", "dada2", "denoise-single",
         "--i-demultiplexed-seqs", inputPath,
         "--p-trim-left", str(trimLeft),
@@ -133,15 +95,15 @@ def dada2DenoiseSingle(
 
 
 def metadataTabulate(inputFile: str, visualizationPath: str) -> None:
-    QiimeCommand([
+    command([
         "qiime", "metadata", "tabulate",
         "--m-input-file", inputFile,
         "--o-visualization", visualizationPath
     ])
 
 
 def featureTableSummarize(inputPath: str, visualizationPath: str, metadataPath: str) -> None:
-    QiimeCommand([
+    command([
         "qiime", "feature-table", "summarize",
         "--i-table", inputPath,
         "--o-visualization", visualizationPath,
@@ -150,7 +112,7 @@ def featureTableSummarize(inputPath: str, visualizationPath: str, metadataPath:
 
 
 def featureTableTabulateSeqs(inputPath: str, visualizationPath: str) -> None:
-    QiimeCommand([
+    command([
         "qiime", "feature-table", "tabulate-seqs",
         "--i-data", inputPath,
         "--o-visualization", visualizationPath
@@ -165,7 +127,7 @@ def phylogenyAlignToTreeMafftFasttree(
     rootedTreePath: str
 ) -> None:
 
-    QiimeCommand([
+    command([
         "qiime", "phylogeny", "align-to-tree-mafft-fasttree",
         "--i-sequences", sequencesPath,
         "--o-alignment", aligmentPath,
@@ -183,7 +145,7 @@ def diversityCoreMetricsPhylogenetic(
     outputDir: str
 ) -> None:
 
-    QiimeCommand([
+    command([
         "qiime", "diversity", "core-metrics-phylogenetic",
         "--i-phylogeny", phlogenyPath,
         "--i-table", tablePath,
@@ -199,7 +161,7 @@ def diversityAlphaGroupSignificance(
     visualizationPath: str
 ) -> None:
 
-    QiimeCommand([
+    command([
         "qiime", "diversity", "alpha-group-significance",
         "--i-alpha-diversity", alphaDiversityPath,
         "--m-metadata-file", metadataPath,
@@ -215,7 +177,7 @@ def diversityBetaGroupSignificance(
     pairwise: bool
 ) -> None:
 
-    QiimeCommand([
+    command([
         "qiime", "diversity", "beta-group-significance",
         "--i-distance-matrix", distanceMatrixPath,
         "--m-metadata-file", metadataPath,
@@ -232,7 +194,7 @@ def emperorPlot(
     visualizationPath: str
 ) -> None:
 
-    QiimeCommand([
+    command([
         "qiime", "emperor", "plot",
         "--i-pcoa", pcoaPath,
         "--m-metadata-file", metadataPath,
@@ -249,7 +211,7 @@ def diversityAlphaRarefaction(
     visualizationPath: str
 ) -> None:
 
-    QiimeCommand([
+    command([
         "qiime", "diversity", "alpha-rarefaction",
         "--i-table", tablePath,
         "--i-phylogeny", phylogenyPath,
@@ -265,7 +227,7 @@ def featureClassifierClassifySklearn(
     classificationPath: str
 ) -> None:
 
-    QiimeCommand([
+    command([
         "qiime", "feature-classifier", "classify-sklearn",
         "--i-classifier", classifierPath,
         "--i-reads", readsPath,
@@ -280,7 +242,7 @@ def taxaBarplot(
     visualizationPath: str
 ) -> None:
 
-    QiimeCommand([
+    command([
         "qiime", "taxa", "barplot",
         "--i-table", tablePath,
         "--i-taxonomy", taxonomyPath,
@@ -296,7 +258,7 @@ def featureTableFilterSamples(
     filteredTablePath: str
 ) -> None:
 
-    QiimeCommand([
+    command([
         "qiime", "feature-table", "filter-samples",
         "--i-table", tablePath,
         "--m-metadata-file", metadataPath,
@@ -306,7 +268,7 @@ def featureTableFilterSamples(
 
 
 def compositionAddPseudocount(tablePath: str, compositionTablePath: str) -> None:
-    QiimeCommand([
+    command([
         "qiime", "composition", "add-pseudocount",
         "--i-table", tablePath,
         "--o-composition-table", compositionTablePath
@@ -320,7 +282,7 @@ def compositionAncom(
     visualizationPath: str
 ) -> None:
 
-    QiimeCommand([
+    command([
         "qiime", "composition", "ancom",
         "--i-table", tablePath,
         "--m-metadata-file", metadataPath,
@@ -336,7 +298,7 @@ def taxaCollapse(
     collapsedTablePath: str
 ) -> None:
 
-    QiimeCommand([
+    command([
         "qiime", "taxa", "collapse",
         "--i-table", tablePath,
         "--i-taxonomy", taxonomyPath,

coretex/qiime2/utils.py → coretex/bioinformatics/qiime2/utils.py

@@ -21,7 +21,7 @@
 import logging
 import gzip
 
-from ..coretex import Experiment, CustomSample, CustomDataset
+from ...coretex import Experiment, CustomSample, CustomDataset
 
 
 def createSample(name: str, datasetId: int, path: Path, experiment: Experiment, stepName: str, retryCount: int = 0) -> CustomSample: