Convert segments between genomic assemblies in whole.
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
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/segmentLiftover.py and segment_liftover/chains/* from github. 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 for details.
segment_liftover -l ./liftOver -i /Volumes/data/hg18/ -o /Volumes/data/hg19/ -c hg18ToHg19 -si segments.tsv -so seg.tsv
segment_liftover -l .liftOver --demo .
This will copy a few example files to the current directory and run a quick conversion with default settings.
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 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.
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.
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
Two formats are supported: chr10 or 10.
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
- 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
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.
The script WILL overwrite ``output_dir``
The script is developed in python3.6
Packages: click6.7, pandas0.20.1
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
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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