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Convert segments between genomic assemblies in whole.

Project description

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. 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/ and segment_liftover/chains/* from github. Dependencies need to be installed manually.

python3 --help

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

How to use

See the manual 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]

  -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
  -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
  --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
  --new_probe_header TEXT...      Specify 3 new column names for new probe
  --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
  --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 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:

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 for details.

Other chain files can be accessed at the UCSC download area

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).

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.

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