.. _cli-reference: CLI Reference ============= .. toctree:: :maxdepth: 1 Quick reference --------------- .. program:: cooler .. code-block:: shell cooler [OPTIONS] COMMAND [ARGS]... .. list-table:: :widths: 25 100 :align: left :header-rows: 1 * - Data ingest - * - `cooler cload`_ - Create a cooler from genomic point pairs and bins. * - `cooler load`_ - Create a cooler from a pre-binned matrix. .. list-table:: :widths: 25 100 :align: left :header-rows: 1 * - Reduction - * - `cooler merge`_ - Merge multiple coolers with identical axes. * - `cooler coarsen`_ - Coarsen a cooler to a lower resolution. * - `cooler zoomify`_ - Generate a multi-resolution cooler file by coarsening. .. list-table:: :widths: 25 100 :align: left :header-rows: 1 * - Normalization - * - `cooler balance`_ - Out-of-core matrix balancing. .. list-table:: :widths: 25 100 :align: left :header-rows: 1 * - Export/visualization - * - `cooler info`_ - Display a cooler’s info and metadata. * - `cooler dump`_ - Dump a cooler’s data to a text stream. * - `cooler show`_ - Display and browse a cooler with matplotlib. .. list-table:: :widths: 25 100 :align: left :header-rows: 1 * - File manipulation/info - * - `cooler tree`_ - Display a file’s data hierarchy. * - `cooler attrs`_ - Display a file’s attribute hierarchy. * - `cooler ls`_ - List all coolers inside a file. * - `cooler cp`_ - Copy a cooler from one file to another or within the same file. * - `cooler mv`_ - Rename a cooler within the same file. * - `cooler ln`_ - Create a hard, soft or external link to a cooler. .. list-table:: :widths: 25 100 :align: left :header-rows: 1 * - Helper commands - * - `cooler makebins`_ - Generate fixed-width genomic bins. * - `cooler digest`_ - Generate fragment-delimited genomic bins. * - `cooler csort`_ - Sort and index a contact list. .. rubric:: Options .. option:: -v, --verbose Verbose logging. .. option:: -d, --debug On error, drop into the post-mortem debugger shell. .. option:: -V, --version Show the version and exit. See the cooler_cli.ipynb Jupyter Notebook for specific examples on usage: (https://github.com/open2c/cooler-binder). ---- cooler cload ------------ Create a cooler from genomic pairs and bins. Choose a subcommand based on the format of the input contact list. .. program:: cooler cload .. code-block:: shell cooler cload [OPTIONS] COMMAND [ARGS]... .. rubric:: Commands .. hlist:: :columns: 4 * .. object:: hiclib * .. object:: pairix * .. object:: pairs * .. object:: tabix ---- cooler cload pairs ------------------ Bin any text file or stream of pairs. Pairs data need not be sorted. Accepts compressed files. To pipe input from stdin, set PAIRS_PATH to '-'. BINS : One of the following : 1. Path to a chromsizes file, 2. Bin size in bp : Path to BED file defining the genomic bin segmentation. PAIRS_PATH : Path to contacts (i.e. read pairs) file. COOL_PATH : Output COOL file path or URI. .. program:: cooler cload pairs .. code-block:: shell cooler cload pairs [OPTIONS] BINS PAIRS_PATH COOL_PATH .. rubric:: Arguments .. option:: BINS Required argument .. option:: PAIRS_PATH Required argument .. option:: COOL_PATH Required argument .. rubric:: Options .. option:: --metadata Path to JSON file containing user metadata. .. option:: --assembly Name of genome assembly (e.g. hg19, mm10) .. option:: -c1, --chrom1 chrom1 field number (one-based) [required] .. option:: -p1, --pos1 pos1 field number (one-based) [required] .. option:: -c2, --chrom2 chrom2 field number (one-based) [required] .. option:: -p2, --pos2 pos2 field number (one-based) [required] .. option:: --chunksize Number of input lines to load at a time .. option:: -0, --zero-based Positions are zero-based [default: False] .. option:: --comment-char Comment character that indicates lines to ignore. [default: #] .. option:: -N, --no-symmetric-upper Create a complete square matrix without implicit symmetry. This allows for distinct upper- and lower-triangle values .. option:: --input-copy-status Copy status of input data when using symmetric-upper storage. | `unique`: Incoming data comes from a unique half of a symmetric map, regardless of how the coordinates of a pair are ordered. `duplex`: Incoming data contains upper- and lower-triangle duplicates. All input records that map to the lower triangle will be discarded! | If you wish to treat lower- and upper-triangle input data as distinct, use the ``--no-symmetric-upper`` option. [default: unique] .. option:: --field Specify quantitative input fields to aggregate into value columns using the syntax ``--field =``. Optionally, append ``:`` followed by ``dtype=`` to specify the data type (e.g. float), and/or ``agg=`` to specify an aggregation function different from sum (e.g. mean). Field numbers are 1-based. Passing 'count' as the target name will override the default behavior of storing pair counts. Repeat the ``--field`` option for each additional field. .. option:: --temp-dir Create temporary files in a specified directory. Pass ``-`` to use the platform default temp dir. .. option:: --no-delete-temp Do not delete temporary files when finished. .. option:: --max-merge Maximum number of chunks to merge before invoking recursive merging [default: 200] .. option:: --storage-options Options to modify the data filter pipeline. Provide as a comma-separated list of key-value pairs of the form 'k1=v1,k2=v2,...'. See http://docs.h5py.org/en/stable/high/dataset.html#filter-pipeline for more details. .. option:: -a, --append Pass this flag to append the output cooler to an existing file instead of overwriting the file. ---- cooler cload pairix ------------------- Bin a pairix-indexed contact list file. BINS : One of the following : 1. Path to a chromsizes file, 2. Bin size in bp : Path to BED file defining the genomic bin segmentation. PAIRS_PATH : Path to contacts (i.e. read pairs) file. COOL_PATH : Output COOL file path or URI. See also: 'cooler csort' to sort and index a contact list file Pairix on GitHub: . .. program:: cooler cload pairix .. code-block:: shell cooler cload pairix [OPTIONS] BINS PAIRS_PATH COOL_PATH .. rubric:: Arguments .. option:: BINS Required argument .. option:: PAIRS_PATH Required argument .. option:: COOL_PATH Required argument .. rubric:: Options .. option:: --metadata Path to JSON file containing user metadata. .. option:: --assembly Name of genome assembly (e.g. hg19, mm10) .. option:: -p, --nproc Number of processes to split the work between. [default: 8] .. option:: -0, --zero-based Positions are zero-based [default: False] .. option:: -s, --max-split Divide the pairs from each chromosome into at most this many chunks. Smaller chromosomes will be split less frequently or not at all. Increase ths value if large chromosomes dominate the workload on multiple processors. [default: 2] ---- cooler cload tabix ------------------ Bin a tabix-indexed contact list file. BINS : One of the following : 1. Path to a chromsizes file, 2. Bin size in bp : Path to BED file defining the genomic bin segmentation. PAIRS_PATH : Path to contacts (i.e. read pairs) file. COOL_PATH : Output COOL file path or URI. See also: 'cooler csort' to sort and index a contact list file Tabix manpage: . .. program:: cooler cload tabix .. code-block:: shell cooler cload tabix [OPTIONS] BINS PAIRS_PATH COOL_PATH .. rubric:: Arguments .. option:: BINS Required argument .. option:: PAIRS_PATH Required argument .. option:: COOL_PATH Required argument .. rubric:: Options .. option:: --metadata Path to JSON file containing user metadata. .. option:: --assembly Name of genome assembly (e.g. hg19, mm10) .. option:: -p, --nproc Number of processes to split the work between. [default: 8] .. option:: -c2, --chrom2 chrom2 field number (one-based) .. option:: -p2, --pos2 pos2 field number (one-based) .. option:: -0, --zero-based Positions are zero-based [default: False] .. option:: -s, --max-split Divide the pairs from each chromosome into at most this many chunks. Smaller chromosomes will be split less frequently or not at all. Increase ths value if large chromosomes dominate the workload on multiple processors. [default: 2] ---- cooler cload hiclib ------------------- Bin a hiclib HDF5 contact list (frag) file. BINS : One of the following : 1. Path to a chromsizes file, 2. Bin size in bp : Path to BED file defining the genomic bin segmentation. PAIRS_PATH : Path to contacts (i.e. read pairs) file. COOL_PATH : Output COOL file path or URI. hiclib on BitBucket: . .. program:: cooler cload hiclib .. code-block:: shell cooler cload hiclib [OPTIONS] BINS PAIRS_PATH COOL_PATH .. rubric:: Arguments .. option:: BINS Required argument .. option:: PAIRS_PATH Required argument .. option:: COOL_PATH Required argument .. rubric:: Options .. option:: --metadata Path to JSON file containing user metadata. .. option:: --assembly Name of genome assembly (e.g. hg19, mm10) .. option:: -c, --chunksize Control the number of pixels handled by each worker process at a time. [default: 100000000] ---- cooler load ----------- Create a cooler from a pre-binned matrix. BINS_PATH : One of the following : 1. Path to a chromsizes file, 2. Bin size in bp : Path to BED file defining the genomic bin segmentation. PIXELS_PATH : Text file containing nonzero pixel values. May be gzipped. Pass '-' to use stdin. COOL_PATH : Output COOL file path or URI. **Notes** Two input format options (tab-delimited). Input pixel file may be compressed. COO: COO-rdinate sparse matrix format (a.k.a. ijv triple). 3 columns: "bin1_id, bin2_id, count", BG2: 2D version of the bedGraph format. 7 columns: "chrom1, start1, end1, chrom2, start2, end2, count" **Examples** cooler load -f bg2 : in.bg2.gz out.cool .. program:: cooler load .. code-block:: shell cooler load [OPTIONS] BINS_PATH PIXELS_PATH COOL_PATH .. rubric:: Arguments .. option:: BINS_PATH Required argument .. option:: PIXELS_PATH Required argument .. option:: COOL_PATH Required argument .. rubric:: Options .. option:: -f, --format 'coo' refers to a tab-delimited sparse triplet file (bin1, bin2, count). 'bg2' refers to a 2D bedGraph-like file (chrom1, start1, end1, chrom2, start2, end2, count). [required] .. option:: --metadata Path to JSON file containing user metadata. .. option:: --assembly Name of genome assembly (e.g. hg19, mm10) .. option:: --field Add supplemental value fields or override default field numbers for the specified format. Specify quantitative input fields to aggregate into value columns using the syntax ``--field =``. Optionally, append ``:`` followed by ``dtype=`` to specify the data type (e.g. float). Field numbers are 1-based. Repeat the ``--field`` option for each additional field. .. option:: -c, --chunksize Size (in number of lines/records) of data chunks to read and process from the input file at a time. These chunks will be saved as temporary partial Coolers and merged at the end. Also specifies the size of the buffer during the merge step. .. option:: --count-as-float Store the 'count' column as floating point values instead of as integers. Can also be specified using the `--field` option. .. option:: --one-based Pass this flag if the bin IDs listed in a COO file are one-based instead of zero-based. .. option:: --comment-char Comment character that indicates lines to ignore. [default: #] .. option:: -N, --no-symmetric-upper Create a complete square matrix without implicit symmetry. This allows for distinct upper- and lower-triangle values .. option:: --input-copy-status Copy status of input data when using symmetric-upper storage. | `unique`: Incoming data comes from a unique half of a symmetric matrix, regardless of how element coordinates are ordered. Execution will be aborted if duplicates are detected. `duplex`: Incoming data contains upper- and lower-triangle duplicates. All lower-triangle input elements will be discarded! | If you wish to treat lower- and upper-triangle input data as distinct, use the ``--no-symmetric-upper`` option instead. [default: unique] .. option:: --temp-dir Create temporary files in a specified directory. Pass ``-`` to use the platform default temp dir. .. option:: --no-delete-temp Do not delete temporary files when finished. .. option:: --storage-options Options to modify the data filter pipeline. Provide as a comma-separated list of key-value pairs of the form 'k1=v1,k2=v2,...'. See http://docs.h5py.org/en/stable/high/dataset.html#filter-pipeline for more details. .. option:: -a, --append Pass this flag to append the output cooler to an existing file instead of overwriting the file. ---- cooler merge ------------ Merge multiple coolers with identical axes. OUT_PATH : Output file path or URI. IN_PATHS : Input file paths or URIs of coolers to merge. **Notes** Data columns merged: pixels/bin1_id, pixels/bin2_id, pixels/ Data columns preserved: chroms/name, chroms/length bins/chrom, bins/start, bins/end Additional columns in the the input files are not transferred to the output. .. program:: cooler merge .. code-block:: shell cooler merge [OPTIONS] OUT_PATH [IN_PATHS]... .. rubric:: Arguments .. option:: OUT_PATH Required argument .. option:: IN_PATHS Optional argument(s) .. rubric:: Options .. option:: -c, --chunksize Size of the merge buffer in number of pixel table rows. [default: 20000000] .. option:: --field Specify the names of value columns to merge as ''. Repeat the `--field` option for each one. Use ',dtype=' to specify the dtype. Include ',agg=' to specify an aggregation function different from 'sum'. .. option:: -a, --append Pass this flag to append the output cooler to an existing file instead of overwriting the file. ---- cooler coarsen -------------- Coarsen a cooler to a lower resolution. Works by pooling *k*-by-*k* neighborhoods of pixels and aggregating. Each chromosomal block is coarsened individually. COOL_PATH : Path to a COOL file or Cooler URI. .. program:: cooler coarsen .. code-block:: shell cooler coarsen [OPTIONS] COOL_PATH .. rubric:: Arguments .. option:: COOL_PATH Required argument .. rubric:: Options .. option:: -k, --factor Gridding factor. The contact matrix is coarsegrained by grouping each chromosomal contact block into k-by-k element tiles [default: 2] .. option:: -n, -p, --nproc Number of processes to use for batch processing chunks of pixels [default: 1, i.e. no process pool] .. option:: -c, --chunksize Number of pixels allocated to each process [default: 10000000] .. option:: --field Specify the names of value columns to merge as ''. Repeat the `--field` option for each one. Use ',dtype=' to specify the dtype. Include ',agg=' to specify an aggregation function different from 'sum'. .. option:: -o, --out Output file or URI [required] .. option:: -a, --append Pass this flag to append the output cooler to an existing file instead of overwriting the file. ---- cooler zoomify -------------- Generate a multi-resolution cooler file by coarsening. COOL_PATH : Path to a COOL file or Cooler URI. .. program:: cooler zoomify .. code-block:: shell cooler zoomify [OPTIONS] COOL_PATH .. rubric:: Arguments .. option:: COOL_PATH Required argument .. rubric:: Options .. option:: -n, -p, --nproc Number of processes to use for batch processing chunks of pixels [default: 1, i.e. no process pool] .. option:: -c, --chunksize Number of pixels allocated to each process [default: 10000000] .. option:: -r, --resolutions Comma-separated list of target resolutions. Use suffixes B or N to specify a progression: B for binary (geometric steps of factor 2), N for nice (geometric steps of factor 10 interleaved with steps of 2 and 5). Examples: 1000B=1000,2000,4000,8000,... 1000N=1000,2000,5000,10000,... 5000N=5000,10000,25000,50000,... 4DN is an alias for 1000,2000,5000N [default: B] .. option:: --balance Apply balancing to each zoom level. Off by default. .. option:: --balance-args Additional arguments to pass to cooler balance. To deal with space ambiguity, use quotes to pass multiple arguments, e.g. ``--balance-args '--nproc 8 --ignore-diags 3'``. Note that nproc for balancing must be specified independently of zoomify arguments. .. option:: -i, --base-uri One or more additional base coolers to aggregate from, if needed. .. option:: -o, --out Output file or URI .. option:: --field Specify the names of value columns to merge as ''. Repeat the ``--field`` option for each one. Use ':dtype=' to specify the dtype. Include ',agg=' to specify an aggregation function different from 'sum'. .. option:: --legacy Use the legacy layout of integer-labeled zoom levels. ---- cooler balance -------------- Out-of-core matrix balancing. Matrix must be symmetric. See the help for various filtering options to mask out poorly mapped bins. COOL_PATH : Path to a COOL file. .. program:: cooler balance .. code-block:: shell cooler balance [OPTIONS] COOL_PATH .. rubric:: Arguments .. option:: COOL_PATH Required argument .. rubric:: Options .. option:: --cis-only Calculate weights against intra-chromosomal data only instead of genome-wide. .. option:: --trans-only Calculate weights against inter-chromosomal data only instead of genome-wide. .. option:: --ignore-diags Number of diagonals of the contact matrix to ignore, including the main diagonal. Examples: 0 ignores nothing, 1 ignores the main diagonal, 2 ignores diagonals (-1, 0, 1), etc. [default: 2] .. option:: --ignore-dist Distance from the diagonal in bp to ignore. The maximum of the corresponding number of diagonals and `--ignore-diags` will be used. .. option:: --mad-max Ignore bins from the contact matrix using the 'MAD-max' filter: bins whose log marginal sum is less than ``mad-max`` median absolute deviations below the median log marginal sum of all the bins in the same chromosome. [default: 5] .. option:: --min-nnz Ignore bins from the contact matrix whose marginal number of nonzeros is less than this number. [default: 10] .. option:: --min-count Ignore bins from the contact matrix whose marginal count is less than this number. [default: 0] .. option:: --blacklist Path to a 3-column BED file containing genomic regions to mask out during the balancing procedure, e.g. sequence gaps or regions of poor mappability. .. option:: -p, --nproc Number of processes to split the work between. [default: 8] .. option:: -c, --chunksize Control the number of pixels handled by each worker process at a time. [default: 10000000] .. option:: --tol Threshold value of variance of the marginals for the algorithm to converge. [default: 1e-05] .. option:: --max-iters Maximum number of iterations to perform if convergence is not achieved. [default: 200] .. option:: --name Name of column to write to. [default: weight] .. option:: -f, --force Overwrite the target dataset, 'weight', if it already exists. .. option:: --check Check whether a data column 'weight' already exists. .. option:: --stdout Print weight column to stdout instead of saving to file. .. option:: --convergence-policy What to do with weights when balancing doesn't converge in max_iters. 'store_final': Store the final result, regardless of whether the iterations converge to the specified tolerance; 'store_nan': Store a vector of NaN values to indicate that the matrix failed to converge; 'discard': Store nothing and exit gracefully; 'error': Abort with non-zero exit status. [default: store_final] ---- cooler info ----------- Display a cooler's info and metadata. COOL_PATH : Path to a COOL file or cooler URI. .. program:: cooler info .. code-block:: shell cooler info [OPTIONS] COOL_PATH .. rubric:: Arguments .. option:: COOL_PATH Required argument .. rubric:: Options .. option:: -f, --field Print the value of a specific info field. .. option:: -m, --metadata Print the user metadata in JSON format. .. option:: -o, --out Output file (defaults to stdout) ---- cooler dump ----------- Dump a cooler's data to a text stream. COOL_PATH : Path to COOL file or cooler URI. .. program:: cooler dump .. code-block:: shell cooler dump [OPTIONS] COOL_PATH .. rubric:: Arguments .. option:: COOL_PATH Required argument .. rubric:: Options .. option:: -t, --table Which table to dump. Choosing 'chroms' or 'bins' will cause all pixel-related options to be ignored. Note that for coolers stored in symmetric-upper mode, 'pixels' only holds the upper triangle values of the matrix. [default: pixels] .. option:: -c, --columns Restrict output to a subset of columns, provided as a comma-separated list. .. option:: -H, --header Print the header of column names as the first row. [default: False] .. option:: --na-rep Missing data representation. Default is empty ''. .. option:: --float-format Format string for floating point numbers (e.g. '.12g', '03.2f'). [default: g] .. option:: -r, --range The coordinates of a genomic region shown along the row dimension, in UCSC-style notation. (Example: chr1:10,000,000-11,000,000). If omitted, the entire contact matrix is printed. .. option:: -r2, --range2 The coordinates of a genomic region shown along the column dimension. If omitted, the column range is the same as the row range. .. option:: -f, --fill-lower For coolers using 'symmetric-upper' storage, populate implicit areas of the genomic query box by generating lower triangle pixels. If not specified, only upper triangle pixels are reported. This option has no effect on coolers stored in 'square' mode. [default: False] .. option:: -b, --balanced, --no-balance Apply balancing weights to data. This will print an extra column called `balanced` [default: False] .. option:: --join Print the full chromosome bin coordinates instead of bin IDs. This will replace the `bin1_id` column with `chrom1`, `start1`, and `end1`, and the `bin2_id` column with `chrom2`, `start2` and `end2`. [default: False] .. option:: --annotate Join additional columns from the bin table against the pixels. Provide a comma separated list of column names (no spaces). The merged columns will be suffixed by '1' and '2' accordingly. .. option:: --one-based-ids Print bin IDs as one-based rather than zero-based. .. option:: --one-based-starts Print start coordinates as one-based rather than zero-based. .. option:: -k, --chunksize Sets the number of pixel records loaded from disk at one time. Can affect the performance of joins on high resolution datasets. [default: 1000000] .. option:: -o, --out Output text file If .gz extension is detected, file is written using zlib. Default behavior is to stream to stdout. ---- cooler show ----------- Display and browse a cooler in matplotlib. COOL_PATH : Path to a COOL file or Cooler URI. RANGE : The coordinates of the genomic region to display, in UCSC notation. Example: chr1:10,000,000-11,000,000 .. program:: cooler show .. code-block:: shell cooler show [OPTIONS] COOL_PATH RANGE .. rubric:: Arguments .. option:: COOL_PATH Required argument .. option:: RANGE Required argument .. rubric:: Options .. option:: -r2, --range2 The coordinates of a genomic region shown along the column dimension. If omitted, the column range is the same as the row range. Use to display asymmetric matrices or trans interactions. .. option:: -b, --balanced Show the balanced contact matrix. If not provided, display the unbalanced counts. .. option:: -o, --out Save the image of the contact matrix to a file. If not specified, the matrix is displayed in an interactive window. The figure format is deduced from the extension of the file, the supported formats are png, jpg, svg, pdf, ps and eps. .. option:: --dpi The DPI of the figure, if saving to a file .. option:: -s, --scale Scale transformation of the colormap: linear, log2 or log10. Default is log10. .. option:: -f, --force Force display very large matrices (>=10^8 pixels). Use at your own risk as it may cause performance issues. .. option:: --zmin The minimal value of the color scale. Units must match those of the colormap scale. To provide a negative value use a equal sign and quotes, e.g. -zmin='-0.5' .. option:: --zmax The maximal value of the color scale. Units must match those of the colormap scale. To provide a negative value use a equal sign and quotes, e.g. -zmax='-0.5' .. option:: --cmap The colormap used to display the contact matrix. See the full list at http://matplotlib.org/examples/color/colormaps_reference.html .. option:: --field Pixel values to display. [default: count] ---- cooler tree ----------- Display a file's data hierarchy. .. program:: cooler tree .. code-block:: shell cooler tree [OPTIONS] URI .. rubric:: Arguments .. option:: URI Required argument .. rubric:: Options .. option:: -L, --level ---- cooler attrs ------------ Display a file's attribute hierarchy. .. program:: cooler attrs .. code-block:: shell cooler attrs [OPTIONS] URI .. rubric:: Arguments .. option:: URI Required argument .. rubric:: Options .. option:: -L, --level ---- cooler ls --------- List all coolers inside a file. .. program:: cooler ls .. code-block:: shell cooler ls [OPTIONS] COOL_PATH .. rubric:: Arguments .. option:: COOL_PATH Required argument .. rubric:: Options .. option:: -l, --long Long listing format ---- cooler cp --------- Copy a cooler from one file to another or within the same file. See also: h5copy, h5repack tools from HDF5 suite. .. program:: cooler cp .. code-block:: shell cooler cp [OPTIONS] SRC_URI DST_URI .. rubric:: Arguments .. option:: SRC_URI Required argument .. option:: DST_URI Required argument .. rubric:: Options .. option:: -w, --overwrite Truncate and replace destination file if it already exists. ---- cooler mv --------- Rename a cooler within the same file. .. program:: cooler mv .. code-block:: shell cooler mv [OPTIONS] SRC_URI DST_URI .. rubric:: Arguments .. option:: SRC_URI Required argument .. option:: DST_URI Required argument .. rubric:: Options .. option:: -w, --overwrite Truncate and replace destination file if it already exists. ---- cooler ln --------- Create a hard link to a cooler (rather than a true copy) in the same file. Also supports soft links (in the same file) or external links (different files). .. program:: cooler ln .. code-block:: shell cooler ln [OPTIONS] SRC_URI DST_URI .. rubric:: Arguments .. option:: SRC_URI Required argument .. option:: DST_URI Required argument .. rubric:: Options .. option:: -w, --overwrite Truncate and replace destination file if it already exists. .. option:: -s, --soft Creates a soft link rather than a hard link if the source and destination file are the same. Otherwise, creates an external link. This type of link uses a path rather than a pointer. ---- cooler makebins --------------- Generate fixed-width genomic bins. Output a genome segmentation at a fixed resolution as a BED file. CHROMSIZES_PATH : UCSC-like chromsizes file, with chromosomes in desired order. BINSIZE : Resolution (bin size) in base pairs . .. program:: cooler makebins .. code-block:: shell cooler makebins [OPTIONS] CHROMSIZES_PATH BINSIZE .. rubric:: Arguments .. option:: CHROMSIZES_PATH Required argument .. option:: BINSIZE Required argument .. rubric:: Options .. option:: -o, --out Output file (defaults to stdout) .. option:: -H, --header Print the header of column names as the first row. [default: False] .. option:: -i, --rel-ids Include a column of relative bin IDs for each chromosome. Choose whether to report them as 0- or 1-based. ---- cooler digest ------------- Generate fragment-delimited genomic bins. Output a genome segmentation of restriction fragments as a BED file. CHROMSIZES_PATH : UCSC-like chromsizes file, with chromosomes in desired order. FASTA_PATH : Genome assembly FASTA file or folder containing FASTA files (uncompressed). ENZYME : Name of restriction enzyme .. program:: cooler digest .. code-block:: shell cooler digest [OPTIONS] CHROMSIZES_PATH FASTA_PATH ENZYME .. rubric:: Arguments .. option:: CHROMSIZES_PATH Required argument .. option:: FASTA_PATH Required argument .. option:: ENZYME Required argument .. rubric:: Options .. option:: -o, --out Output file (defaults to stdout) .. option:: -H, --header Print the header of column names as the first row. [default: False] .. option:: -i, --rel-ids Include a column of relative bin IDs for each chromosome. Choose whether to report them as 0- or 1-based. ---- cooler csort ------------ Sort and index a contact list. Order the mates of each pair record so that all contacts are upper triangular with respect to the chromosome ordering given by the chromosomes file, sort contacts by genomic location, and index the resulting file. PAIRS_PATH : Contacts (i.e. read pairs) text file, optionally compressed. CHROMOSOMES_PATH : File listing desired chromosomes in the desired order. May be tab-delimited, e.g. a UCSC-style chromsizes file. Contacts mapping to other chromosomes will be discarded. **Notes** - csort can also be used to sort and index a text representation of a contact *matrix* in bedGraph-like format. In this case, substitute `pos1` and `pos2` with `start1` and `start2`, respectively. - Requires Unix tools: sort, bgzip + tabix or pairix. If indexing with Tabix, the output file will have the following properties: - Upper triangular: the read pairs on each row are assigned to side 1 or 2 in such a way that (chrom1, pos1) is always "less than" (chrom2, pos2) - Rows are lexicographically sorted by chrom1, pos1, chrom2, pos2; i.e. "positionally sorted" - Compressed with bgzip [*] - Indexed using Tabix [*] on chrom1 and pos1. If indexing with Pairix, the output file will have the following properties: - Upper triangular: the read pairs on each row are assigned to side 1 or 2 in such a way that (chrom1, pos1) is always "less than" (chrom2, pos2) - Rows are lexicographically sorted by chrom1, chrom2, pos1, pos2; i.e. "block sorted" - Compressed with bgzip [*] - Indexed using Pairix [+] on chrom1, chrom2 and pos1. [*] Tabix manpage: . [+] Pairix on Github: .. program:: cooler csort .. code-block:: shell cooler csort [OPTIONS] PAIRS_PATH CHROMOSOMES_PATH .. rubric:: Arguments .. option:: PAIRS_PATH Required argument .. option:: CHROMOSOMES_PATH Required argument .. rubric:: Options .. option:: -c1, --chrom1 chrom1 field number in the input file (starting from 1) [required] .. option:: -c2, --chrom2 chrom2 field number [required] .. option:: -p1, --pos1 pos1 field number [required] .. option:: -p2, --pos2 pos2 field number [required] .. option:: -i, --index Select the preset sort and indexing options [default: pairix] .. option:: --flip-only Only flip mates; no sorting or indexing. Write to stdout. [default: False] .. option:: -p, --nproc Number of processors [default: 8] .. option:: -0, --zero-based Read positions are zero-based [default: False] .. option:: --sep Data delimiter in the input file [default: \t] .. option:: --comment-char Comment character to skip header [default: #] .. option:: --sort-options Quoted list of additional options to `sort` command .. option:: -o, --out Output gzip file .. option:: -s1, --strand1 strand1 field number (deprecated) .. option:: -s2, --strand2 strand2 field number (deprecated) ----