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Merge branch 'develop'. Version update to 1.0.1. Close #28
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44 changes: 44 additions & 0 deletions
44
src/main/groovy/com/antigenomics/vdjtools/profile/BasicAminoAcidProperties.groovy
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| /* | ||
| * Copyright 2013-2015 Mikhail Shugay (mikhail.shugay@gmail.com) | ||
| * | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); | ||
| * you may not use this file except in compliance with the License. | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| */ | ||
|
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| package com.antigenomics.vdjtools.profile | ||
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| import com.antigenomics.vdjtools.util.CommonUtil | ||
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| class BasicAminoAcidProperties { | ||
| static final BasicAminoAcidProperties INSTANCE = new BasicAminoAcidProperties() | ||
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| private final AminoAcidProperty[] aminoAcidProperties | ||
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| private BasicAminoAcidProperties() { | ||
| aminoAcidProperties = AminoAcidProperty.fromInput(CommonUtil.resourceStream("profile/aa_property_table.txt")) | ||
| } | ||
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| List<String> getPropertyNames() { | ||
| aminoAcidProperties.collect { it.name } | ||
| } | ||
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| AminoAcidProperty[] getProperties(List<String> propertyNames) { | ||
| if (propertyNames.isEmpty()) | ||
| return getProperties() | ||
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| aminoAcidProperties.findAll { propertyNames.contains(it.name) } as AminoAcidProperty[] | ||
| } | ||
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| AminoAcidProperty[] getProperties() { | ||
| Arrays.copyOf(aminoAcidProperties, aminoAcidProperties.length) | ||
| } | ||
| } |
152 changes: 152 additions & 0 deletions
152
src/main/groovy/com/antigenomics/vdjtools/profile/CalcCdrAAProfile.groovy
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| /* | ||
| * Copyright 2013-2015 Mikhail Shugay (mikhail.shugay@gmail.com) | ||
| * | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); | ||
| * you may not use this file except in compliance with the License. | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| */ | ||
|
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| package com.antigenomics.vdjtools.profile | ||
|
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| import com.antigenomics.vdjtools.sample.Sample | ||
| import com.antigenomics.vdjtools.sample.SampleCollection | ||
| import com.antigenomics.vdjtools.sample.metadata.MetadataTable | ||
| import com.antigenomics.vdjtools.util.RUtil | ||
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| import static com.antigenomics.vdjtools.util.ExecUtil.formOutputPath | ||
| import static com.antigenomics.vdjtools.util.ExecUtil.toPlotPath | ||
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| def DEFAULT_AA_PROPERTIES = BasicAminoAcidProperties.INSTANCE.propertyNames.join(","), | ||
| DEFAULT_BINNING = "V-germ:5,VJ-junc:3,J-germ:5" | ||
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| def cli = new CliBuilder(usage: "CalcCdrAAProfile [options] " + | ||
| "[sample1 sample2 sample3 ... if -m is not specified] output_prefix") | ||
| cli.h("display help message") | ||
| cli.m(longOpt: "metadata", argName: "filename", args: 1, | ||
| "Metadata file. First and second columns should contain file name and sample id. " + | ||
| "Header is mandatory and will be used to assign column names for metadata.") | ||
| cli.u(longOpt: "unweighted", "Will count each clonotype only once, apart from conventional frequency-weighted histogram.") | ||
| cli.o(longOpt: "property-list", argName: "group1,...", args: 1, | ||
| "Comma-separated list of amino-acid properties to analyze. " + | ||
| "Allowed values: $DEFAULT_AA_PROPERTIES. " + | ||
| "[default = use all]") | ||
| cli.r(longOpt: "region-list", argName: "segment1:nbins1,...", args: 1, | ||
| "List of segments to analyze and corresponding bin counts. " + | ||
| "Allowed segments: ${KnownCdr3Regions.INSTANCE.regionNames.join(",")}. " + | ||
| "[default = $DEFAULT_BINNING]") | ||
| cli.p(longOpt: "plot", "Plot amino acid property distributions for a specified list of segments.") | ||
| cli.f(longOpt: "factor", argName: "string", args: 1, "Metadata entry used to group samples in plot.") | ||
| cli._(longOpt: "plot-type", argName: "<pdf|png>", args: 1, "Plot output format [default=pdf]") | ||
| cli._(longOpt: "include-cfw", "Consider first and last AAs of CDR3, which are normally conserved C and F/W") | ||
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| def opt = cli.parse(args) | ||
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| if (opt == null) | ||
| System.exit(-1) | ||
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| if (opt.h || opt.arguments().size() == 0) { | ||
| cli.usage() | ||
| System.exit(-1) | ||
| } | ||
|
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| // Check if metadata is provided | ||
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| def metadataFileName = opt.m | ||
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| if (metadataFileName ? opt.arguments().size() != 1 : opt.arguments().size() < 2) { | ||
| if (metadataFileName) | ||
| println "Only output prefix should be provided in case of -m" | ||
| else | ||
| println "At least 1 sample files should be provided if not using -m" | ||
| cli.usage() | ||
| System.exit(-1) | ||
| } | ||
|
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| // Remaining arguments | ||
|
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| def outputFilePrefix = opt.arguments()[-1], | ||
| unweighted = (boolean) opt.u, | ||
| binning = (opt.r ?: DEFAULT_BINNING).split(",").collectEntries { | ||
| def split2 = it.split(":") | ||
| [(KnownCdr3Regions.INSTANCE.getByName(split2[0])): split2[1].toInteger()] | ||
| }, | ||
| properties = (opt.o ?: DEFAULT_AA_PROPERTIES).split(","), | ||
| plot = (boolean) opt.p, | ||
| plotType = (opt.'plot-type' ?: "pdf").toString(), | ||
| includeCFW = (boolean) opt.'include-cfw' | ||
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| def badProperties = properties.findAll { !BasicAminoAcidProperties.INSTANCE.propertyNames.contains(it) } | ||
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| if (badProperties.size() > 0) { | ||
| println "[ERROR] Unknown amino acid properties: ${badProperties.join(",")}. " + | ||
| "Allowed values are $DEFAULT_AA_PROPERTIES" | ||
| System.exit(-1) | ||
| } | ||
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| def scriptName = getClass().canonicalName.split("\\.")[-1] | ||
|
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| // | ||
| // Batch load all samples (lazy) | ||
| // | ||
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| println "[${new Date()} $scriptName] Reading sample(s)" | ||
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| def sampleCollection = metadataFileName ? | ||
| new SampleCollection((String) metadataFileName) : | ||
| new SampleCollection(opt.arguments()[0..-2]) | ||
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| println "[${new Date()} $scriptName] ${sampleCollection.size()} sample(s) prepared" | ||
|
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| // | ||
| // Compute and output diversity measures, spectratype, etc | ||
| // | ||
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| def profileBuilder = new Cdr3AAProfileBuilder(binning, !unweighted, !includeCFW, properties) | ||
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| def outputFileName = formOutputPath(outputFilePrefix, "cdr3aa", "profile", (unweighted ? "unwt" : "wt")) | ||
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| new File(outputFileName).withPrintWriter { pw -> | ||
| def header = "#$MetadataTable.SAMPLE_ID_COLUMN\t" + | ||
| sampleCollection.metadataTable.columnHeader + "\t" + | ||
| "cdr3.segment\tbin\tproperty\tvalue\ttotal" | ||
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| pw.println(header) | ||
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| def sampleCounter = 0 | ||
|
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| sampleCollection.each { Sample sample -> | ||
| def profiles = profileBuilder.create(sample) | ||
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| println "[${new Date()} $scriptName] ${++sampleCounter} sample(s) processed" | ||
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| profiles.each { profileEntry -> | ||
| def segmentName = profileEntry.key.name | ||
| profileEntry.value.bins.each { bin -> | ||
| bin.summary.each { | ||
| pw.println([sample.sampleMetadata.sampleId, sample.sampleMetadata, | ||
| segmentName, bin.index, it.key, | ||
| it.value, bin.total].join("\t")) | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| if (plot) { | ||
| RUtil.execute("cdr3aa_profile.r", | ||
| outputFileName, | ||
| toPlotPath(outputFileName, plotType), | ||
| opt.f ? (sampleCollection.metadataTable.getColumnIndex(opt.f) + 2).toString() : "0", | ||
| ) | ||
| } | ||
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| println "[${new Date()} $scriptName] Finished" |
56 changes: 56 additions & 0 deletions
56
src/main/groovy/com/antigenomics/vdjtools/profile/Cdr3AAProfileBuilder.groovy
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,56 @@ | ||
| /* | ||
| * Copyright 2013-2015 Mikhail Shugay (mikhail.shugay@gmail.com) | ||
| * | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); | ||
| * you may not use this file except in compliance with the License. | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| */ | ||
|
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| package com.antigenomics.vdjtools.profile | ||
|
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| import com.antigenomics.vdjtools.sample.Clonotype | ||
|
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| class Cdr3AAProfileBuilder { | ||
| private final Map<Cdr3Region, Integer> binning | ||
| private final boolean weighted, excludeCysPhe | ||
| private final List<String> groups | ||
|
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| Cdr3AAProfileBuilder(Map<Cdr3Region, Integer> binning, boolean weighted, | ||
| boolean excludeCysPhe, | ||
| String... groups) { | ||
| this.binning = binning | ||
| this.weighted = weighted | ||
| this.excludeCysPhe = excludeCysPhe | ||
| this.groups = groups | ||
| } | ||
|
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| Map<Cdr3Region, AminoAcidProfile> create(Iterable<Clonotype> clonotypes) { | ||
| def profiles = new HashMap<Cdr3Region, AminoAcidProfile>() | ||
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| binning.each { | ||
| profiles.put(it.key, new AminoAcidProfile(it.value, | ||
| BasicAminoAcidProperties.INSTANCE.getProperties(groups))) | ||
| } | ||
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| clonotypes.each { clonotype -> | ||
| if (clonotype.isCoding()) { | ||
| profiles.each { | ||
| def aaSeq = it.key.extractAminoAcid(clonotype, excludeCysPhe) | ||
| if (aaSeq.size() > 0) { | ||
| it.value.update(aaSeq, weighted ? clonotype.freq : 1.0d) | ||
| } | ||
| } | ||
| } | ||
| } | ||
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| profiles | ||
| } | ||
| } |
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