v0.3

sigven · Apr 12, 2017 · 8d70d8d · 8d70d8d
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diff --git a/README.md b/README.md
@@ -15,7 +15,7 @@ The Personal Cancer Genome Reporter (PCGR) is a stand-alone software package int
 [![Documentation Status](https://readthedocs.org/projects/pcgr/badge/?version=latest)](http://pcgr.readthedocs.io/en/latest/?badge=latest)
 
 
-### Annotation resources included in PCGR (v0.2)
+### Annotation resources included in PCGR (v0.3)
 
 * [VEP v85](http://www.ensembl.org/info/docs/tools/vep/index.html) - Variant Effect Predictor release 85 (GENCODE v19 as the gene reference dataset)
 * [COSMIC v80](http://cancer.sanger.ac.uk/cosmic/) - Catalogue of somatic mutations in cancer (February 2017)
@@ -53,14 +53,15 @@ A local installation of Python (it has been tested with [version 2.7.13](https:/
 
 #### STEP 2: Download PCGR
 
-1. Download and unpack the [latest release](https://github.com/sigven/pcgr/releases/latest)
+<font color="red"><b>April 12th 2017</b>: New release (v0.3)</font>
+1. Download and unpack the [latest release (v0.3)](https://github.com/sigven/pcgr/releases/latest)
 2. Download and unpack the data bundle (approx. 17Gb) in the PCGR directory
-   * Download [the latest data bundle](https://drive.google.com/file/d/0B8aYD2TJ472mQjZOMmg4djZfT1k/) from Google Drive to `~/pcgr-X.X` (replace _X.X_ with the version number)
+   * Download [the latest data bundle](https://drive.google.com/file/d/0B8aYD2TJ472mQjZOMmg4djZfT1k/) from Google Drive to `~/pcgr-X.X` (replace _X.X_ with the version number, e.g `~/pcgr-0.3`)
    * Unpack the data bundle, e.g. through the following Unix command: `gzip -dc pcgr.databundle.GRCh37.YYYYMMDD.tgz | tar xvf -`
 
     A _data/_ folder within the _pcgr-X.X_ software folder should now have been produced
-3. Pull the [PCGR Docker image](https://hub.docker.com/r/sigven/pcgr/) from DockerHub:
-   * `docker pull sigven/pcgr` (PCGR annotation engine)
+3. Pull the [PCGR Docker image (v0.3)](https://hub.docker.com/r/sigven/pcgr/) from DockerHub (3.1Gb):
+   * `docker pull sigven/pcgr:0.3` (PCGR annotation engine)
 
 #### STEP 3: Input preprocessing
 
@@ -94,55 +95,57 @@ Here, _Chromosome_, _Start_, and _End_ denote the chromosomal segment (GRCh37),
 
 #### STEP 4: Run example
 
-A tumor sample report is generated by calling the Python script __run_pcgr.py__ in the PCGR software folder, which takes the following arguments and options:
-
-    usage: run_pcgr.py [-h] [--input_vcf INPUT_VCF]
-                   [--input_cna_segments INPUT_CNA_SEGMENTS]
-                   [--logR_threshold_amplification LOGR_THRESHOLD_AMPLIFICATION]
-                   [--logR_threshold_homozygous_deletion LOGR_THRESHOLD_HOMOZYGOUS_DELETION]
-                   [--num_vcfanno_processes NUM_VCFANNO_PROCESSES]
-                   [--num_vep_forks NUM_VEP_FORKS] [--force_overwrite]
-                   pcgr_directory working_directory sample_id
-
-    Personal Cancer Genome Reporter (PCGR) workflow for clinical interpretation of
-    somatic nucleotide variants and copy number aberration segments
-
-    positional arguments:
-    pcgr_directory        PCGR base directory
-    working_directory     Working directory - directory with input/output files
-    sample_id             Tumor sample/cancer genome identifier - prefix for
-                        output files
-
-    optional arguments:
-    -h, --help            show this help message and exit
-    --input_vcf INPUT_VCF
-                        VCF input file with somatic query variants
-                        (SNVs/InDels) (default: None)
-    --input_cna_segments INPUT_CNA_SEGMENTS
-                        Somatic copy number alteration segments (tab-separated
-                        values) (default: None)
-    --logR_threshold_amplification LOGR_THRESHOLD_AMPLIFICATION
-                        Log(2) ratio treshold for calling copy number
-                        amplifications in HTML report (default: 0.8)
-    --logR_threshold_homozygous_deletion LOGR_THRESHOLD_HOMOZYGOUS_DELETION
-                        Log(2) ratio treshold for calling homozygous deletions
-                        in HTML report (default: -0.8)
-    --num_vcfanno_processes NUM_VCFANNO_PROCESSES
-                        Number of processes used during vcfanno annotation
-                        (default: 4)
-    --num_vep_forks NUM_VEP_FORKS
-                        Number of forks (--forks option in VEP) used during
-                        VEP annotation (default: 4)
-    --force_overwrite     By default, the script will fail with an error if any
-                        output file already exists. You can force the
-                        overwrite of existing result files by using this flag
-                        (default: False)
-
+A tumor sample report is generated by calling the Python script __pcgr.py__ in the PCGR software folder, which takes the following arguments and options:
+
+      usage: pcgr.py [-h] [--input_vcf INPUT_VCF]
+                     [--input_cna_segments INPUT_CNA_SEGMENTS]
+                     [--logR_threshold_amplification LOGR_THRESHOLD_AMPLIFICATION]
+                     [--logR_threshold_homozygous_deletion LOGR_THRESHOLD_HOMOZYGOUS_DELETION]
+                     [--num_vcfanno_processes NUM_VCFANNO_PROCESSES]
+                     [--num_vep_forks NUM_VEP_FORKS] [--force_overwrite]
+                     [--version]
+                     pcgr_dir output_dir sample_id
+
+      Personal Cancer Genome Reporter (PCGR) workflow for clinical interpretation of
+      somatic nucleotide variants and copy number aberration segments
+
+      positional arguments:
+      pcgr_dir              PCGR base directory with accompanying data directory,
+                          e.g. ~/pcgr-0.3
+      output_dir            Output directory
+      sample_id             Tumor sample/cancer genome identifier - prefix for
+                          output files
+
+      optional arguments:
+      -h, --help            show this help message and exit
+      --input_vcf INPUT_VCF
+                          VCF input file with somatic query variants
+                          (SNVs/InDels) (default: None)
+      --input_cna_segments INPUT_CNA_SEGMENTS
+                          Somatic copy number alteration segments (tab-separated
+                          values) (default: None)
+      --logR_threshold_amplification LOGR_THRESHOLD_AMPLIFICATION
+                          Log(2) ratio treshold for calling copy number
+                          amplifications in HTML report (default: 0.8)
+      --logR_threshold_homozygous_deletion LOGR_THRESHOLD_HOMOZYGOUS_DELETION
+                          Log(2) ratio treshold for calling homozygous deletions
+                          in HTML report (default: -0.8)
+      --num_vcfanno_processes NUM_VCFANNO_PROCESSES
+                          Number of processes used during vcfanno annotation
+                          (default: 4)
+      --num_vep_forks NUM_VEP_FORKS
+                          Number of forks (--forks option in VEP) used during
+                          VEP annotation (default: 4)
+      --force_overwrite     By default, the script will fail with an error if any
+                          output file already exists. You can force the
+                          overwrite of existing result files by using this flag
+                          (default: False)
+      --version             show program's version number and exit
 
 
 The _examples_ folder contain sample files from TCGA. A report for a colorectal tumor case can be generated through the following command:
 
-`python run_pcgr.py --input_vcf tumor_sample.COAD.vcf.gz --input_cna_segments tumor_sample.COAD.cna.tsv ~/pcgr-X.X ~/pcgr-X.X/examples tumor_sample.COAD`
+`python pcgr.py --input_vcf tumor_sample.COAD.vcf.gz --input_cna_segments tumor_sample.COAD.cna.tsv ~/pcgr-0.3 ~/pcgr-0.3/examples tumor_sample.COAD`
 
 This command will run the Docker-based PCGR workflow and produce the following output files in the _examples_ folder:
 

diff --git a/docs/_build/doctrees/annotation_resources.doctree b/docs/_build/doctrees/annotation_resources.doctree
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/getting_started.doctree b/docs/_build/doctrees/getting_started.doctree
diff --git a/docs/_build/html/_sources/annotation_resources.rst.txt b/docs/_build/html/_sources/annotation_resources.rst.txt
@@ -92,19 +92,24 @@ corresponds to variants reported with other HGVS nomenclature (e.g.
 Other data quality concerns
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-**Clinical biomarkers** Clinical biomarkers included in PCGR is limited
-to the following: \* Markers reported at the variant level (e.g. **BRAF
-p.V600E**) \* Markers reported at the codon level (e.g. **KRAS p.G12**)
-\* Markers reported at the exon level (e.g. **KIT exon 11 mutation**) \*
-Within CBMDB, only markers collected from FDA/NCCN guidelines,
-scientific literature and clinical trials are included (markers
-collected from conference abstracts are not included)
-
-**COSMIC variants** The COSMIC dataset that is part of the PCGR
-annotation bundle is the subset of variants that satisfy the following
-criteria: \* **Mutation somatic status** is either
-'*confirmed\_somatic*' or
-'*reported\_in\_another\_cancer\_sample\_as\_somatic*'. \*
-**Site/histology** must be known and the sample must come from a
-malignant tumor (i.e. not polyps/adenomas, which are also found in
-COSMIC)
+**Clinical biomarkers**
+
+Clinical biomarkers included in PCGR is limited to the following:
+
+-  Markers reported at the variant level (e.g. **BRAF p.V600E**)
+-  Markers reported at the codon level (e.g. **KRAS p.G12**)
+-  Markers reported at the exon level (e.g. **KIT exon 11 mutation**)
+-  Within CBMDB, only markers collected from FDA/NCCN guidelines,
+   scientific literature and clinical trials are included (markers
+   collected from conference abstracts are not included)
+
+**COSMIC variants**
+
+The COSMIC dataset that is part of the PCGR annotation bundle is the
+subset of variants that satisfy the following criteria:
+
+-  **Mutation somatic status** is either '*confirmed\_somatic*' or
+   '*reported\_in\_another\_cancer\_sample\_as\_somatic*'.
+-  **Site/histology** must be known and the sample must come from a
+   malignant tumor (i.e. not polyps/adenomas, which are also found in
+   COSMIC)
diff --git a/docs/_build/html/_sources/getting_started.rst.txt b/docs/_build/html/_sources/getting_started.rst.txt
@@ -42,51 +42,53 @@ terminal window.
 Download PCGR
 ^^^^^^^^^^^^^
 
--  Download and unpack the `latest
-   release <https://github.com/sigven/pcgr/releases/latest>`__
+April 12th 2017: New release (v0.3) \* Download and unpack the `latest
+release (v0.3) <https://github.com/sigven/pcgr/releases/latest>`__
 
 -  Download and unpack the data bundle (approx. 17Gb) in the PCGR
    directory
 
    -  Download `the latest data
       bundle <https://drive.google.com/file/d/0B8aYD2TJ472mQjZOMmg4djZfT1k/>`__
       from Google Drive to ``~/pcgr-X.X`` (replace *X.X* with the
-      version number)
+      version number, e.g. ``~/pcgr-0.3``)
    -  Decompress and untar the bundle, e.g. through the following Unix
       command:
       ``gzip -dc pcgr.databundle.GRCh37.YYYYMMDD.tgz | tar xvf -``
 
    A *data/* folder within the *pcgr-X.X* software folder should now
    have been produced
 
--  Pull the `PCGR Docker
-   image <https://hub.docker.com/r/sigven/pcgr/>`__ (3.5Gb) from
-   DockerHub):
+-  Pull the `PCGR Docker image -
+   v0.3 <https://hub.docker.com/r/sigven/pcgr/>`__ from DockerHub
+   (3.1Gb) :
 
-   -  ``docker pull sigven/pcgr`` (PCGR annotation engine)
+   -  ``docker pull sigven/pcgr:0.3`` (PCGR annotation engine)
 
 Run test - generation of clinical report for a cancer genome
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 A tumor sample report is generated by calling the Python script
-**run\_pcgr.py**, which takes the following arguments and options:
+**pcgr.py**, which takes the following arguments and options:
 
 ::
 
-    usage: run_pcgr.py [-h] [--input_vcf INPUT_VCF]
+    usage: pcgr.py [-h] [--input_vcf INPUT_VCF]
                    [--input_cna_segments INPUT_CNA_SEGMENTS]
                    [--logR_threshold_amplification LOGR_THRESHOLD_AMPLIFICATION]
                    [--logR_threshold_homozygous_deletion LOGR_THRESHOLD_HOMOZYGOUS_DELETION]
                    [--num_vcfanno_processes NUM_VCFANNO_PROCESSES]
                    [--num_vep_forks NUM_VEP_FORKS] [--force_overwrite]
-                   pcgr_directory working_directory sample_id
+                   [--version]
+                   pcgr_dir output_dir sample_id
 
     Personal Cancer Genome Reporter (PCGR) workflow for clinical interpretation of
     somatic nucleotide variants and copy number aberration segments
 
     positional arguments:
-    pcgr_directory        PCGR base directory
-    working_directory     Working directory - directory with input/output files
+    pcgr_dir              PCGR base directory with accompanying data directory,
+                        e.g. ~/pcgr-0.3
+    output_dir            Output directory
     sample_id             Tumor sample/cancer genome identifier - prefix for
                         output files
 
@@ -114,13 +116,14 @@ A tumor sample report is generated by calling the Python script
                         output file already exists. You can force the
                         overwrite of existing result files by using this flag
                         (default: False)
+    --version             show program's version number and exit
 
 The *examples* folder contain input files from two tumor samples
 sequenced within TCGA. A report for a colorectal tumor case can be
 generated by running the following command in your terminal window:
 
-``python run_pcgr.py --input_vcf tumor_sample.COAD.vcf.gz --input_cna_segments``
-``tumor_sample.COAD.cna.tsv ~/pcgr-X.X ~/pcgr-X.X/examples tumor_sample.COAD``
+``python pcgr.py --input_vcf examples/tumor_sample.COAD.vcf.gz --input_cna_segments``
+``examples/tumor_sample.COAD.cna.tsv ~/pcgr-0.3 ~/pcgr-0.3/examples tumor_sample.COAD``
 
 This command will run the Docker-based PCGR workflow and produce the
 following output files in the *examples* folder:

diff --git a/docs/_build/html/annotation_resources.html b/docs/_build/html/annotation_resources.html
@@ -246,21 +246,26 @@ <h2>Genome mapping<a class="headerlink" href="#genome-mapping" title="Permalink
 </div>
 <div class="section" id="other-data-quality-concerns">
 <h2>Other data quality concerns<a class="headerlink" href="#other-data-quality-concerns" title="Permalink to this headline">¶</a></h2>
-<p><strong>Clinical biomarkers</strong> Clinical biomarkers included in PCGR is limited
-to the following: * Markers reported at the variant level (e.g. <strong>BRAF
-p.V600E</strong>) * Markers reported at the codon level (e.g. <strong>KRAS p.G12</strong>)
-* Markers reported at the exon level (e.g. <strong>KIT exon 11 mutation</strong>) *
-Within CBMDB, only markers collected from FDA/NCCN guidelines,
+<p><strong>Clinical biomarkers</strong></p>
+<p>Clinical biomarkers included in PCGR is limited to the following:</p>
+<ul class="simple">
+<li>Markers reported at the variant level (e.g. <strong>BRAF p.V600E</strong>)</li>
+<li>Markers reported at the codon level (e.g. <strong>KRAS p.G12</strong>)</li>
+<li>Markers reported at the exon level (e.g. <strong>KIT exon 11 mutation</strong>)</li>
+<li>Within CBMDB, only markers collected from FDA/NCCN guidelines,
 scientific literature and clinical trials are included (markers
-collected from conference abstracts are not included)</p>
-<p><strong>COSMIC variants</strong> The COSMIC dataset that is part of the PCGR
-annotation bundle is the subset of variants that satisfy the following
-criteria: * <strong>Mutation somatic status</strong> is either
-&#8216;<em>confirmed_somatic</em>&#8216; or
-&#8216;<em>reported_in_another_cancer_sample_as_somatic</em>&#8216;. *
-<strong>Site/histology</strong> must be known and the sample must come from a
+collected from conference abstracts are not included)</li>
+</ul>
+<p><strong>COSMIC variants</strong></p>
+<p>The COSMIC dataset that is part of the PCGR annotation bundle is the
+subset of variants that satisfy the following criteria:</p>
+<ul class="simple">
+<li><strong>Mutation somatic status</strong> is either &#8216;<em>confirmed_somatic</em>&#8216; or
+&#8216;<em>reported_in_another_cancer_sample_as_somatic</em>&#8216;.</li>
+<li><strong>Site/histology</strong> must be known and the sample must come from a
 malignant tumor (i.e. not polyps/adenomas, which are also found in
-COSMIC)</p>
+COSMIC)</li>
+</ul>
 </div>
 </div>