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0.16.0 dev
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sbslee authored Jul 2, 2021
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23 changes: 23 additions & 0 deletions CHANGELOG.rst
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Changelog
*********

0.16.0 (2021-07-02)
-------------------

* Rename the commands (e.g. :command:`vcf_merge` to :command:`vcf-merge`).
* Add ``flip`` argument to :meth:`pymaf.MafFrame.plot_vaf` method.
* Update :meth:`pymaf.MafFrame.plot_vaf` method to support creation of a grouped bar plot.
* Factor out ``count`` mode of :meth:`pymaf.MafFrame.plot_snvcls` method to new method :meth:`pymaf.MafFrame.plot_snvclsc`.
* Factor out ``proportion`` mode of :meth:`pymaf.MafFrame.plot_snvcls` method to new method :meth:`pymaf.MafFrame.plot_snvclsp`.
* Factor out ``samples`` mode of :meth:`pymaf.MafFrame.plot_snvcls` method to new method :meth:`pymaf.MafFrame.plot_snvclss`.
* Factor out ``titv`` mode of :meth:`pymaf.MafFrame.plot_snvcls` method to new method :meth:`pymaf.MafFrame.plot_titv`.
* Deprecate :meth:`pymaf.MafFrame.plot_snvcls` method.
* Add ``hue_order`` argument to :meth:`pyvcf.VcfFrame.plot_hist` method.
* Update aesthetic aspect of :meth:`pymaf.MafFrame.plot_oncoplot` method.
* Add ``width`` argument to :meth:`pymaf.MafFrame.plot_tmb` method.
* Add ``palette`` and ``flip`` arguments to :meth:`pymaf.MafFrame.plot_vartype` method.
* Update :meth:`pymaf.MafFrame.plot_snvclsc` method to support creation of a grouped bar plot.
* Update :meth:`pymaf.MafFrame.plot_snvclsp` method to support creation of a grouped box plot.
* Add :meth:`pyvcf.VcfFrame.plot_snvclsc` method (simply wraps :meth:`pymaf.MafFrame.plot_snvclsc` method).
* Add :meth:`pyvcf.VcfFrame.plot_snvclsp` method (simply wraps :meth:`pymaf.MafFrame.plot_snvclsp` method).
* Add :meth:`pyvcf.VcfFrame.plot_snvclss` method (simply wraps :meth:`pymaf.MafFrame.plot_snvclss` method).
* Add :meth:`pyvcf.VcfFrame.plot_titv` method (simply wraps :meth:`pymaf.MafFrame.plot_titv` method).
* Update :meth:`pymaf.MafFrame.from_vcf` method to handle unannotated VCF data.

0.15.0 (2021-06-24)
-------------------

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82 changes: 41 additions & 41 deletions README.rst
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Expand Up @@ -72,13 +72,13 @@ The following packages are required to run fuc:
scipy
seaborn
There are various ways you can install fuc. The recommended way is via conda:
There are various ways you can install fuc. The recommended way is via conda (`Anaconda <https://www.anaconda.com/>`__):

.. code-block:: text
$ conda install -c bioconda fuc
Above will automatically download and install all the dependencies as well. Alternatively, you can use pip to install fuc and all of its dependencies:
Above will automatically download and install all the dependencies as well. Alternatively, you can use pip (`PyPI <https://pypi.org/>`__) to install fuc and all of its dependencies:

.. code-block:: text
Expand Down Expand Up @@ -108,40 +108,40 @@ For getting help on the fuc CLI:
positional arguments:
COMMAND
bam_head [BAM] Print the header of a SAM/BAM/CRAM file.
bam_index [BAM] Index a SAM/BAM/CRAM file.
bam_rename [BAM] Rename the samples in a SAM/BAM/CRAM file.
bam_slice [BAM] Slice a SAM/BAM/CRAM file.
bed_intxn [BED] Find the intersection of two or more BED files.
bed_sum [BED] Summarize a BED file.
fq_count [FASTQ] Count sequence reads in FASTQ files.
fq_sum [FASTQ] Summarize a FASTQ file.
fuc_compf [FUC] Compare the contents of two files.
fuc_demux [FUC] Parse the Reports directory from bcl2fastq.
fuc_exist [FUC] Check whether certain files exist.
fuc_find [FUC] Find all files with a certain extension recursively.
maf_maf2vcf [MAF] Convert a MAF file to a VCF file.
maf_oncoplt [MAF] Create an oncoplot with a MAF file.
maf_sumplt [MAF] Create a summary plot with a MAF file.
maf_vcf2maf [MAF] Convert a 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.
vcf_vcf2bed [VCF] Convert a VCF file to a BED file.
vcf_vep [VCF] Filter a VCF file annotated by Ensemble VEP.
bam-head [BAM] Print the header of a SAM/BAM/CRAM file.
bam-index [BAM] Index a SAM/BAM/CRAM file.
bam-rename [BAM] Rename the samples in a SAM/BAM/CRAM file.
bam-slice [BAM] Slice a SAM/BAM/CRAM file.
bed-intxn [BED] Find the intersection of two or more BED files.
bed-sum [BED] Summarize a BED file.
fq-count [FASTQ] Count sequence reads in FASTQ files.
fq-sum [FASTQ] Summarize a FASTQ file.
fuc-compf [FUC] Compare the contents of two files.
fuc-demux [FUC] Parse the Reports directory from bcl2fastq.
fuc-exist [FUC] Check whether certain files exist.
fuc-find [FUC] Find all files with a certain extension recursively.
maf-maf2vcf [MAF] Convert a MAF file to a VCF file.
maf-oncoplt [MAF] Create an oncoplot with a MAF file.
maf-sumplt [MAF] Create a summary plot with a MAF file.
maf-vcf2maf [MAF] Convert a 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.
vcf-vcf2bed [VCF] Convert a VCF file to a BED file.
vcf-vep [VCF] Filter a VCF file annotated by Ensemble VEP.
optional arguments:
-h, --help Show this help message and exit.
-v, --version Show the version number and exit.
For getting help on a specific command (e.g. vcf_merge):
For getting help on a specific command (e.g. vcf-merge):

.. code-block:: text
$ fuc vcf_merge -h
$ fuc vcf-merge -h
Below is the list of submodules available in the fuc API:

Expand Down Expand Up @@ -171,77 +171,77 @@ To print the header of a SAM file:

.. code-block:: text
$ fuc bam_head in.sam
$ fuc bam-head in.sam
To index a CRAM file:

.. code-block:: text
$ fuc bam_index in.cram
$ fuc bam-index in.cram
To rename the samples in a SAM file:

.. code-block:: text
$ fuc bam_rename in.sam NA12878 > out.sam
$ fuc bam-rename in.sam NA12878 > out.sam
To slice a BAM file:

.. code-block:: text
$ fuc bam_slice in.bam chr1:100-200 > out.bam
$ fuc bam-slice in.bam chr1:100-200 > out.bam
**BED**

To find intersection between BED files:

.. code-block:: text
$ fuc bed_intxn 1.bed 2.bed 3.bed > intersect.bed
$ fuc bed-intxn 1.bed 2.bed 3.bed > intersect.bed
**FASTQ**

To count sequence reads in a FASTQ file:

.. code-block:: text
$ fuc fq_count example.fastq
$ fuc fq-count example.fastq
**FUC**

To check whether a file exists in the operating system:

.. code-block:: text
$ fuc fuc_exist example.txt
$ fuc fuc-exist example.txt
To find all VCF files within the current directory recursively:

.. code-block:: text
$ fuc fuc_find .vcf.gz
$ fuc fuc-find .vcf.gz
**TABLE**

To merge two tab-delimited files:

.. code-block:: text
$ fuc tbl_merge left.tsv right.tsv > merged.tsv
$ fuc tbl-merge left.tsv right.tsv > merged.tsv
**VCF**

To merge VCF files:

.. code-block:: text
$ fuc vcf_merge 1.vcf 2.vcf 3.vcf > merged.vcf
$ fuc vcf-merge 1.vcf 2.vcf 3.vcf > merged.vcf
To filter a VCF file annotated by Ensemble VEP:

.. code-block:: text
$ fuc vcf_vep in.vcf 'SYMBOL == "TP53"' > out.vcf
$ fuc vcf-vep in.vcf 'SYMBOL == "TP53"' > out.vcf
API Examples
============
Expand Down Expand Up @@ -328,7 +328,7 @@ To create an oncoplot with a MAF file:
.. image:: https://raw.githubusercontent.com/sbslee/fuc-data/main/images/oncoplot.png

To create a customized oncoplot with a MAF file, see the 'Create customized oncoplot' tutorial:
To create a customized oncoplot with a MAF file, see the `Create customized oncoplot <https://sbslee-fuc.readthedocs.io/en/latest/tutorials.html#create-customized-oncoplots>`__ tutorial:

.. image:: https://raw.githubusercontent.com/sbslee/fuc-data/main/images/customized_oncoplot.png

Expand All @@ -342,5 +342,5 @@ To create a summary figure for a MAF file:
>>> mf = pymaf.MafFrame.from_file(f)
>>> mf.plot_summary()
.. image:: https://raw.githubusercontent.com/sbslee/fuc-data/main/images/maf_summary.png
.. image:: https://raw.githubusercontent.com/sbslee/fuc-data/main/images/maf_summary-2.png

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