Merge pull request #25 from sbslee/0.14.0-dev

0.14.0 dev

CHANGELOG.rst

@@ -1,6 +1,16 @@
 Changelog
 *********
 
+0.14.0 (2021-06-20)
+-------------------
+
+* :issue:`23`: Deprecate methods :meth:`pyvcf.VcfFrame.markmiss_ad/af/dp` and add new method :meth:`pyvcf.VcfFrame.markmiss`.
+* Add new command :command:`vcf_filter`.
+* Update methods :meth:`pycov.CovFrame.slice/plot_region`.
+* :issue:`24`: Add new method :meth:`pyvcf.VcfFrame.drop_duplicates`.
+* Update :meth:`pymaf.MafFrame.plot_snvcls` method to support various plotting modes.
+* Rename ``horizontal`` argument of :meth:`pymaf.MafFrame.plot_varsum` method to ``flip``.
+
 0.13.0 (2021-06-16)
 -------------------
 

README.rst

@@ -126,6 +126,7 @@ For getting help on the fuc CLI:
        maf_vcf2maf  [MAF] convert an annotated VCF file to a MAF file
        tbl_merge    [TABLE] merge two table files
        tbl_sum      [TABLE] summarize a table file
+       vcf_filter   [VCF] filter a VCF file
        vcf_merge    [VCF] merge two or more VCF files
        vcf_rename   [VCF] rename the samples in a VCF file.
        vcf_slice    [VCF] slice a VCF file
@@ -164,8 +165,7 @@ For getting help on a specific submodule (e.g. pyvcf):
 CLI Examples
 ============
 
-BAM
----
+**BAM**
 
 To print the header of a SAM file:
 
@@ -185,26 +185,23 @@ To slice a BAM file:
 
    $ fuc bam_slice in.bam chr1:100-200 out.bam
 
-BED
----
+**BED**
 
 To find intersection between BED files:
 
 .. code-block:: text
 
    $ fuc bed_intxn 1.bed 2.bed 3.bed > intersect.bed
 
-FASTQ
------
+**FASTQ**
 
 To count sequence reads in a FASTQ file:
 
 .. code-block:: text
 
    $ fuc fq_count example.fastq
 
-FUC
----
+**FUC**
 
 To check whether a file exists in the operating system:
 
@@ -218,17 +215,15 @@ To find all VCF files within the current directory recursively:
 
    $ fuc fuc_find .vcf.gz
 
-TABLE
------
+**TABLE**
 
 To merge two tab-delimited files:
 
 .. code-block:: text
 
    $ fuc tbl_merge left.tsv right.tsv > merged.tsv
 
-VCF
----
+**VCF**
 
 To merge VCF files:
 
@@ -245,8 +240,7 @@ To filter a VCF file annotated by Ensemble VEP:
 API Examples
 ============
 
-BAM
----
+**BAM**
 
 To create read depth profile of a region from a CRAM file:
 
@@ -259,8 +253,7 @@ To create read depth profile of a region from a CRAM file:
 
 .. image:: https://raw.githubusercontent.com/sbslee/fuc-data/main/images/coverage.png
 
-VCF
----
+**VCF**
 
 To filter a VCF file based on a BED file:
 
@@ -315,8 +308,7 @@ To create various figures for normal-tumor analysis:
 
 .. image:: https://raw.githubusercontent.com/sbslee/fuc-data/main/images/normal-tumor.png
 
-MAF
----
+**MAF**
 
 To create an oncoplot with a MAF file:
 

docs/cli.rst

@@ -36,6 +36,7 @@ For getting help on the fuc CLI:
        maf_vcf2maf  [MAF] convert an annotated VCF file to a MAF file
        tbl_merge    [TABLE] merge two table files
        tbl_sum      [TABLE] summarize a table file
+       vcf_filter   [VCF] filter a VCF file
        vcf_merge    [VCF] merge two or more VCF files
        vcf_rename   [VCF] rename the samples in a VCF file.
        vcf_slice    [VCF] slice a VCF file
@@ -551,6 +552,43 @@ tbl_sum
                            columns to be summarized (by default, all columns will
                            be included)
 
+vcf_filter
+==========
+
+.. code-block:: text
+
+   $ fuc vcf_filter -h
+   usage: fuc vcf_filter [-h] [--greedy] [--opposite] [--samples PATH]
+                         [--filter_empty]
+                         vcf expr
+   
+   This command will filter a VCF file (both zipped and unzipped). It essentially
+   wraps the 'pyvcf.VcfFrame.markmiss' method from the fuc API.
+   
+   usage examples:
+     $ fuc vcf_filter in.vcf 'GT == "0/0"' > out.vcf
+     $ fuc vcf_filter in.vcf 'GT != "0/0"' > out.vcf
+     $ fuc vcf_filter in.vcf 'DP < 30' > out.vcf
+     $ fuc vcf_filter in.vcf 'DP < 30' --greedy > out.vcf
+     $ fuc vcf_filter in.vcf 'AD[1] < 10' --greedy > out.vcf
+     $ fuc vcf_filter in.vcf 'AD[1] < 10 and DP < 30' --greedy > out.vcf
+     $ fuc vcf_filter in.vcf 'AD[1] < 10 or DP < 30' --greedy > out.vcf
+     $ fuc vcf_filter in.vcf 'AD[1] < 10 or DP < 30' --opposite > out.vcf
+     $ fuc vcf_filter in.vcf 'np.mean(AD) < 10' --greedy --samples sample.list > out.vcf
+   
+   positional arguments:
+     vcf             VCF file
+     expr            expression to evaluate
+   
+   optional arguments:
+     -h, --help      show this help message and exit
+     --greedy        use this flag to mark even ambiguous genotypes as missing
+     --opposite      use this flag to mark all genotypes that do not satisfy the
+                     query expression as missing and leave those that do intact
+     --samples PATH  file of sample names to apply the marking (one sample per
+                     line)
+     --filter_empty  use this flag to remove rows with no genotype calls at all
+
 vcf_merge
 =========
 

docs/conf.py

@@ -31,6 +31,7 @@
     'sphinx.ext.autodoc',
     'sphinx.ext.napoleon',
     'sphinx.ext.linkcode',
+    'sphinx.ext.autosectionlabel',
     'sphinx_rtd_theme',
     'sphinx_issues',
     'autodocsumm',
@@ -51,6 +52,8 @@
 
 napoleon_use_param = False
 
+autosectionlabel_prefix_document = True
+
 # Include the example source for plots in API docs
 plot_include_source = True
 plot_formats = [('png', 90)]

docs/create.py

@@ -153,8 +153,7 @@
 CLI Examples
 ============
 
-BAM
----
+**BAM**
 
 To print the header of a SAM file:
 
@@ -174,26 +173,23 @@
 
    $ fuc bam_slice in.bam chr1:100-200 out.bam
 
-BED
----
+**BED**
 
 To find intersection between BED files:
 
 .. code-block:: text
 
    $ fuc bed_intxn 1.bed 2.bed 3.bed > intersect.bed
 
-FASTQ
------
+**FASTQ**
 
 To count sequence reads in a FASTQ file:
 
 .. code-block:: text
 
    $ fuc fq_count example.fastq
 
-FUC
----
+**FUC**
 
 To check whether a file exists in the operating system:
 
@@ -207,17 +203,15 @@
 
    $ fuc fuc_find .vcf.gz
 
-TABLE
------
+**TABLE**
 
 To merge two tab-delimited files:
 
 .. code-block:: text
 
    $ fuc tbl_merge left.tsv right.tsv > merged.tsv
 
-VCF
----
+**VCF**
 
 To merge VCF files:
 
@@ -234,8 +228,7 @@
 API Examples
 ============
 
-BAM
----
+**BAM**
 
 To create read depth profile of a region from a CRAM file:
 
@@ -248,8 +241,7 @@
 
 .. image:: https://raw.githubusercontent.com/sbslee/fuc-data/main/images/coverage.png
 
-VCF
----
+**VCF**
 
 To filter a VCF file based on a BED file:
 
@@ -304,8 +296,7 @@
 
 .. image:: https://raw.githubusercontent.com/sbslee/fuc-data/main/images/normal-tumor.png
 
-MAF
----
+**MAF**
 
 To create an oncoplot with a MAF file:
 

docs/glossary.rst

@@ -0,0 +1,4 @@
+Glossary
+********
+
+This section is currently empty.

docs/index.rst

@@ -11,6 +11,7 @@ Welcome to fuc's documentation!
    :caption: Contents:
 
    readme
+   glossary
    cli
    api
    tutorials