segment-liftover 0.950

Convert segments between genomic assemblies in whole.

segment_liftover
================

Converting genome coordinates between different genome assemblies is a
common task in bioinformatics. Services and tools such as UCSC Liftover,
NCBI Remap and CrossMap are available to perform such conversion.

When converting a genomic segment, those conversion tools will break the
segment into smaller parts if the segment is not continuous in the new
assembly. However, in some circumstances such as copy number analyses,
where the quantitative representation of a genomic range takes
precedence over base-specific representation, the integrity of a single
segment needs to be kept.

Moreover, all those tools are designed for single file processing, and
offer nothing to facilitate batch processing. But in Bioinformatic
studies, it is very often that people need to deal with hundreds and
even thousands of files at a time.

*segment_liftover* is a Python program that can convert segments between
genome assemblies, without breaking them apart. Part of its
functionality is based on re-conversion by locus approximation, in
instances where a precise conversion of genomic positions fails.

Key features: - converts continuous segments - performs approximate
conversion when direct conversion fails - batch processing of any number
of files - automatic folder traversal and file discovery - detailed logs
- resuming from interruption - accept both segment (i.e. start => end)
and probe (i.e., single position) data

Program dependency
~~~~~~~~~~~~~~~~~~

*segment_liftover* depends on the *UCSC Liftover program*, which can be
found `here <https://genome-store.ucsc.edu/>`__. Please note that the
UCSC Liftover is only free for non-commercial use. Despite the
inconvenience of licensing, Liftover offers some very convenient
features: - it is a stand-alone command-line tool - it can convert
assemblies of any species, even between species - it runs locally and
does not require network access

How to install
--------------

The easiest way is to install through pip:

::

pip install segment_liftover
segment_liftover --help

Another option is to copy ``segment_liftover/segmentLiftover.py`` and
``segment_liftover/chains/*`` from
`github <https://github.com/baudisgroup/segment-liftover>`__.
Dependencies need to be installed manually.

::

python3 segmentLiftover.py --help

**Important: Add the UCSC ``liftOver`` program to your working
directory, or use -l to specify its location.**

How to use
----------

See the
`manual <https://github.com/baudisgroup/segment-liftover/blob/master/manual.md>`__
for details.

Quick start
~~~~~~~~~~~

::

segment_liftover -l ./liftOver -i /Volumes/data/hg18/ -o /Volumes/data/hg19/ -c hg18ToHg19 -si segments.tsv -so seg.tsv

Demo mode
~~~~~~~~~

::

segment_liftover -l .liftOver --demo .

This will copy a few example files to the current directory and run a
quick conversion with default settings.

General Usage
~~~~~~~~~~~~~

::

Usage: segment_liftover [OPTIONS]

Options:
-i, --input_dir TEXT The directory to start processing.
-o, --output_dir TEXT The directory to write new files.
-c, --chain_file TEXT Specify the chain file name.
-si, --segment_input_file TEXT Specify the segment input file name.
-so, --segment_output_file TEXT
Specify the segment output file name.
-pi, --probe_input_file TEXT Specify the probe input file name.
-po, --probe_output_file TEXT Specify the probe output file name.
-l, --liftover TEXT Specify the location of the UCSC liftover
program.
-t, --test_mode INTEGER Only process a limited number of files.
-f, --file_indexing Only generate the index file.
-x, --index_file FILENAME Specify an index file containing file paths.
-m, --mapping_file FILENAME Specify a pre-defined file of position
mappings.
--step_size INTEGER The step size of approximate conversion (in
bases, default:400).
--range INTEGER The searching range of approximate
conversion (in kilo bases, default:10).
--beta FLOAT Parameter in quality control.
--no_approximate_conversion Do not perform approximate conversion.
--new_segment_header TEXT... Specify 4 new column names for new segment
files.
--new_probe_header TEXT... Specify 3 new column names for new probe
files.
--resume TEXT... Specify a index file and a progress file to
resume an interrupted job.
--demo TEXT Copy example files to a user defined
directory and run a demonstration.
--log_path TEXT Specify the directory to write logging
files.
--help Show this message and exit.

Required options are:

- ``-i, --input_dir TEXT``
- ``-o, --output_dir TEXT``
- ``-c, --chain_file TEXT``
- either of both of ``-si, --segment_input_file TEXT`` and
``-pi, --probe_input_file TEXT``

The liftOver program
~~~~~~~~~~~~~~~~~~~~

By default, *segment_liftover* looks system path for the *UCSC liftOver*
program. It can also be manually specified with the ``-l`` option.

Start with your input file
~~~~~~~~~~~~~~~~~~~~~~~~~~

*segment_liftover* is designed to process a large number of files in one
run.

- It requires ***an input directory***, and will traverse through all
sub-directories to index all files matching ***the input file
name***.
- It requires ***an output directory***, and will keep the original
directory structure in the output directory.
- Segment and probe files are treated differently - therefore, you need
to use different options to pass the input file name.
- You can also create a list of input files to start. Please see
`manual <https://github.com/baudisgroup/segment-liftover/blob/master/manual.md>`__
for more details.
- Regular expressions are supported for input names.

Input file format
~~~~~~~~~~~~~~~~~

Use ``-si filename`` for segment file names. All files should:

- be **tab separated**, without quoted values
- have at least **4** columns as id, chromosome, start and end (names
do not matter, order does).

Extra columns will be copied over.

An example:

::

id chro start stop value_1 value_2
GSM378022 1 775852 143752373 0.025 9992
GSM378022 1 143782024 214220966 0.1607 6381
GSM378022 2 88585000 144628991 0.0131 4256
GSM378022 2 144635510 146290468 0.1432 146
GSM378022 3 48603 8994748 0.0544 1469

Use ``-pi filename`` for probe file names. All files should:

- be **tab separated**, without quoted values
- have at least **3** columns as id, chromosome and position (names do
not matter, order does).

Extra columns will be copied over.

An example:

::

PROBEID CHRO BASEPOS VALUE
ID_2_1 1 51599 -0.6846
ID_3_2 1 51672 -0.2546
ID_4_3 1 51687 0.0833
ID_5_4 1 52016 -0.5201
ID_6_5 1 52784 0.1997
ID_7_6 1 52801 -0.3800
ID_8_7 1 62568 -0.2435
ID_9_8 1 62640 0.3516
ID_10_9 1 72034 -0.5687

Chromosome names
~~~~~~~~~~~~~~~~

Two formats are supported: chr10 or 10.

Chain files
~~~~~~~~~~~

A chain file is required by the *UCSC liftOver* program to convert from
one assembly to another, therefore it’s also **required** by
*segment_liftover*.

Common chain files for human genome editions (from UCSC) are provider as
part of *segment_liftover*. Please check the
`manual <https://github.com/baudisgroup/segment-liftover/blob/master/manual.md>`__
for details.

Other chain files can be accessed `at the UCSC download
area <http://hgdownload.cse.ucsc.edu/downloads.html>`__

Output files
~~~~~~~~~~~~

- The file structure of the input directory will be kept in output
directory.
- Output files can be renamed with ``-so, --segment_output_file TEXT``
or ``-po, --probe_output_file TEXT``

Log files
~~~~~~~~~

By default, a ``log/`` directory is created in the output directory
after the conversion.

::

./logs/parameters.log The command history and parameter settings.
./logs/fileList.log The indexing file from traversing input_dir.
./logs/general.log The main log file, keeps records for all the works done and errors encountered.
./logs/progress.log A list of successfully processed files.
./logs/unconverted.log A list of all positions that could not be lifted and re-converted.
./logs/approximate_conversion.log A list of all the approximately converted positions (when LiftOver fails).
./logs/failed_files.log A list of files failed to be converted.

If *segment_liftover* does not work as expected, you can check
**general.log** for execution details.

If you are interested in unique re-converted or unconverted results, you
can check **approximate_conversion.log**.

If you want to get information of rejection or conversion result of a
specific file, you can check **unconverted.log**.

Overwriting behavior
~~~~~~~~~~~~~~~~~~~~

The script **WILL overwrite ``output_dir``**

Python dependencies
~~~~~~~~~~~~~~~~~~~

The script is developed in python3.6

Packages: click6.7, pandas0.20.1

Advanced use
------------

Start from a file
~~~~~~~~~~~~~~~~~

With the **index_file** option, you can provide a file containing files
you want to process. One file name per line, using the file’s full path.

After each run, a **fileList.log** file can be found in **./logs/**,
which can be used as quick start for next time. You can also generate a
*file list* using the following command:

::

>segment_liftover -i /Volumes/data/hg18/ -o /Volumes/data/hg19/ -c hg18ToHg19 -si segments.tsv -x ./myfilelist.txt

Reuse approximate conversion results
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

With the **–mapping_file** option, you can reuse a previously generated
log file to speed up processing.

After each run, a **approximate_conversion.log** file can be found in
**./logs/**.

Specify parameters of approximate conversion
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

With ``--step_size`` and ``--range``, you can control the resolution and
scope of searching for the closest liftable position when a position can
not be lifted. The default values are *500* (bases) and *10*
(kilo-bases).

.. raw:: html

<!--### Choose good parameters
-->

Resume from interruption
~~~~~~~~~~~~~~~~~~~~~~~~

If the execution of the script is interrupted, it can be resumed using
**–resume** as following:

::

>segment_liftover --resume ./logs/fileList.log ./logs/progress.log -i /Volumes/data/hg18/ -o /Volumes/data/hg19/ -c hg18ToHg19 -si segments.tsv

Parallel processing
~~~~~~~~~~~~~~~~~~~

*segment_liftover* does not support multiprocessing directly, but very
tasks can be divided into smaller tasks and run parallel with ease.

- First, generate a **fileList** as instructed in *Start from a file*
section.
- Then (optional), shuffle the lines in the **fileList**.
- Next, split **fileList** into smaller files and put them in separated
folders.
- Finally, run *lift_over* with option **–index_file** in each folder.