Command-line API

pairtools

Flexible tools for Hi-C data processing.

All pairtools have a few common options, which should be typed _before_ the command name.
pairtools [OPTIONS] COMMAND [ARGS]...

Options

--post-mortem

Post mortem debugging

--output-profile <output_profile>

Profile performance with Python cProfile and dump the statistics into a binary file

-v, --verbose

Verbose logging.

-d, --debug

On error, drop into the post-mortem debugger shell.

--version

Show the version and exit.

dedup

Find and remove PCR/optical duplicates.

Find PCR/optical duplicates in an upper-triangular flipped sorted pairs/pairsam file. Allow for a +/-N bp mismatch at each side of duplicated molecules.

PAIRS_PATH : input triu-flipped sorted .pairs or .pairsam file. If the path ends with .gz/.lz4, the input is decompressed by bgzip/lz4c. By default, the input is read from stdin.

pairtools dedup [OPTIONS] [PAIRS_PATH]

Options

-o, --output <output>

output file for pairs after duplicate removal. If the path ends with .gz or .lz4, the output is bgzip-/lz4c-compressed. By default, the output is printed into stdout.

--output-dups <output_dups>

output file for duplicated pairs. If the path ends with .gz or .lz4, the output is bgzip-/lz4c-compressed. If the path is the same as in –output or -, output duplicates together with deduped pairs. By default, duplicates are dropped.

--output-unmapped <output_unmapped>

output file for unmapped pairs. If the path ends with .gz or .lz4, the output is bgzip-/lz4c-compressed. If the path is the same as in –output or -, output unmapped pairs together with deduped pairs. If the path is the same as –output-dups, output unmapped reads together with dups. By default, unmapped pairs are dropped.

--output-stats <output_stats>

output file for duplicate statistics. If file exists, it will be open in the append mode. If the path ends with .gz or .lz4, the output is bgzip-/lz4c-compressed. By default, statistics are not printed.

--output-bytile-stats <output_bytile_stats>

output file for duplicate statistics. Note that the readID should be provided and contain tile information for this option. This analysis is possible when pairtools is run on a dataset with original Illumina-generated read IDs, because SRA does not store original read IDs from the sequencer. By default, by-tile duplicate statistics are not printed. If file exists, it will be open in the append mode. If the path ends with .gz or .lz4, the output is bgzip-/lz4c-compressed.

--max-mismatch <max_mismatch>

Pairs with both sides mapped within this distance (bp) from each other are considered duplicates. [dedup option] [default: 3]

--method <method>

define the mismatch as either the max or the sum of the mismatches ofthe genomic locations of the both sides of the two compared molecules. [dedup option] [default: max]

--backend <backend>

What backend to use: scipy and sklearn are based on KD-trees, cython is online indexed list-based algorithm. With cython backend, duplication is not transitive with non-zero max mismatch (e.g. pairs A and B are duplicates, and B and C are duplicates, then A and C are not necessary duplicates of each other), while with scipy and sklearn it’s transitive (i.e. A and C are necessarily duplicates). Cython is the original version used in pairtools since its beginning. It is available for backwards compatibility and to allow specification of the column order. Now the default scipy backend is generally the fastest, and with chunksize below 1 mln has the lowest memory requirements. [dedup option]

--chunksize <chunksize>

Number of pairs in each chunk. Reduce for lower memory footprint. Below 10,000 performance starts suffering significantly and the algorithm might miss a few duplicates with non-zero –max-mismatch. Only works with ‘–backend scipy or sklearn’. [dedup option] [default: 100000]

--carryover <carryover>

Number of deduped pairs to carry over from previous chunk to the new chunk to avoid breaking duplicate clusters. Only works with ‘–backend scipy or sklearn’. [dedup option] [default: 100]

-p, --n-proc <n_proc>

Number of cores to use. Only applies with sklearn backend.Still needs testing whether it is ever useful. [dedup option]

--mark-dups

If specified, duplicate pairs are marked as DD in “pair_type” and as a duplicate in the sam entries. [output format option]

--keep-parent-id

If specified, duplicate pairs are marked with the readID of the retained deduped read in the ‘parent_readID’ field. [output format option]

--extra-col-pair <extra_col_pair>

Extra columns that also must match for two pairs to be marked as duplicates. Can be either provided as 0-based column indices or as column names (requires the “#columns” header field). The option can be provided multiple times if multiple column pairs must match. Example: –extra-col-pair “phase1” “phase2”. [output format option]

--sep <sep>

Separator (t, v, etc. characters are supported, pass them in quotes). [input format option]

--comment-char <comment_char>

The first character of comment lines. [input format option]

--send-header-to <send_header_to>

Which of the outputs should receive header and comment lines. [input format option]

--c1 <c1>

Chrom 1 column; default 1 Only works with ‘–backend cython’. [input format option]

--c2 <c2>

Chrom 2 column; default 3 Only works with ‘–backend cython’. [input format option]

--p1 <p1>

Position 1 column; default 2 Only works with ‘–backend cython’. [input format option]

--p2 <p2>

Position 2 column; default 4 Only works with ‘–backend cython’. [input format option]

--s1 <s1>

Strand 1 column; default 5 Only works with ‘–backend cython’. [input format option]

--s2 <s2>

Strand 2 column; default 6 Only works with ‘–backend cython’. [input format option]

--unmapped-chrom <unmapped_chrom>

Placeholder for a chromosome on an unmapped side; default !

--yaml, --no-yaml

Output stats in yaml format instead of table. [output stats format option]

--filter <filter>

Filter stats with condition to apply to the data (similar to pairtools select or pairtools stats). For non-YAML output only the first filter will be reported. [output stats filtering option] Note that this will not change the deduplicated output pairs. Example: pairtools dedup –yaml –filter ‘unique:(pair_type==”UU”)’ –filter ‘close:(pair_type==”UU”) and (abs(pos1-pos2)<10)’ –output-stats - test.pairs

--engine <engine>

Engine for regular expression parsing for stats filtering. Python will provide you regex functionality, while pandas does not accept custom funtctions and works faster. [output stats filtering option]

--chrom-subset <chrom_subset>

A path to a chromosomes file (tab-separated, 1st column contains chromosome names) containing a chromosome subset of interest for stats filter. If provided, additionally filter pairs with both sides originating from the provided subset of chromosomes. This operation modifies the #chromosomes: and #chromsize: header fields accordingly. Note that this will not change the deduplicated output pairs. [output stats filtering option]

--startup-code <startup_code>

An auxiliary code to execute before filteringfor stats. Use to define functions that can be evaluated in the CONDITION statement. [output stats filtering option]

-t, --type-cast <type_cast>

Cast a given column to a given type for stats filtering. By default, only pos and mapq are cast to int, other columns are kept as str. Provide as -t <column_name> <type>, e.g. -t read_len1 int. Multiple entries are allowed. [output stats filtering option]

--nproc-in <nproc_in>

Number of processes used by the auto-guessed input decompressing command. [default: 3]

--nproc-out <nproc_out>

Number of processes used by the auto-guessed output compressing command. [default: 8]

--cmd-in <cmd_in>

A command to decompress the input file. If provided, fully overrides the auto-guessed command. Does not work with stdin and pairtools parse. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -dc -n 3

--cmd-out <cmd_out>

A command to compress the output file. If provided, fully overrides the auto-guessed command. Does not work with stdout. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -c -n 8

Arguments

PAIRS_PATH

Optional argument

filterbycov

Remove pairs from regions of high coverage.

Find and remove pairs with >(MAX_COV-1) neighbouring pairs within a +/- MAX_DIST bp window around either side. Useful for single-cell Hi-C experiments, where coverage is naturally limited by the chromosome copy number.

PAIRS_PATH : input triu-flipped sorted .pairs or .pairsam file. If the path ends with .gz/.lz4, the input is decompressed by bgzip/lz4c. By default, the input is read from stdin.

pairtools filterbycov [OPTIONS] [PAIRS_PATH]

Options

-o, --output <output>

output file for pairs from low coverage regions. If the path ends with .gz or .lz4, the output is bgzip-/lz4c-compressed. By default, the output is printed into stdout.

--output-highcov <output_highcov>

output file for pairs from high coverage regions. If the path ends with .gz or .lz4, the output is bgzip-/lz4c-compressed. If the path is the same as in –output or -, output duplicates together with deduped pairs. By default, duplicates are dropped.

--output-unmapped <output_unmapped>

output file for unmapped pairs. If the path ends with .gz or .lz4, the output is bgzip-/lz4c-compressed. If the path is the same as in –output or -, output unmapped pairs together with deduped pairs. If the path is the same as –output-highcov, output unmapped reads together. By default, unmapped pairs are dropped.

--output-stats <output_stats>

output file for statistics of multiple interactors. If file exists, it will be open in the append mode. If the path ends with .gz or .lz4, the output is bgzip-/lz4c-compressed. By default, statistics are not printed.

--max-cov <max_cov>

The maximum allowed coverage per region.

--max-dist <max_dist>

The resolution for calculating coverage. For each pair, the local coverage around each end is calculated as (1 + the number of neighbouring pairs within +/- max_dist bp)

--method <method>

calculate the number of neighbouring pairs as either the sum or the max of the number of neighbours on the two sides [default: max]

--sep <sep>

Separator (t, v, etc. characters are supported, pass them in quotes)

--comment-char <comment_char>

The first character of comment lines

--send-header-to <send_header_to>

Which of the outputs should receive header and comment lines

--c1 <c1>

Chrom 1 column; default 1

--c2 <c2>

Chrom 2 column; default 3

--p1 <p1>

Position 1 column; default 2

--p2 <p2>

Position 2 column; default 4

--s1 <s1>

Strand 1 column; default 5

--s2 <s2>

Strand 2 column; default 6

--unmapped-chrom <unmapped_chrom>

Placeholder for a chromosome on an unmapped side; default !

--mark-multi

If specified, duplicate pairs are marked as FF in “pair_type” and as a duplicate in the sam entries.

--nproc-in <nproc_in>

Number of processes used by the auto-guessed input decompressing command. [default: 3]

--nproc-out <nproc_out>

Number of processes used by the auto-guessed output compressing command. [default: 8]

--cmd-in <cmd_in>

A command to decompress the input file. If provided, fully overrides the auto-guessed command. Does not work with stdin and pairtools parse. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -dc -n 3

--cmd-out <cmd_out>

A command to compress the output file. If provided, fully overrides the auto-guessed command. Does not work with stdout. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -c -n 8

Arguments

PAIRS_PATH

Optional argument

flip

Flip pairs to get an upper-triangular matrix.

Change the order of side1 and side2 in pairs, such that (order(chrom1) < order(chrom2)

or (order(chrom1) == order(chrom2)) and (pos1 <=pos2))

Equivalent to reflecting the lower triangle of a Hi-C matrix onto its upper triangle, resulting in an upper triangular matrix. The order of chromosomes must be provided via a .chromsizes file.

PAIRS_PATH : input .pairs/.pairsam file. If the path ends with .gz or .lz4, the input is decompressed by bgzip/lz4c. By default, the input is read from stdin.

pairtools flip [OPTIONS] [PAIRS_PATH]

Options

-c, --chroms-path <chroms_path>

Chromosome order used to flip interchromosomal mates: path to a chromosomes file (e.g. UCSC chrom.sizes or similar) whose first column lists scaffold names. Any scaffolds not listed will be ordered lexicographically following the names provided. [required]

-o, --output <output>

output file. If the path ends with .gz or .lz4, the output is bgzip-/lz4c-compressed. By default, the output is printed into stdout.

--nproc-in <nproc_in>

Number of processes used by the auto-guessed input decompressing command. [default: 3]

--nproc-out <nproc_out>

Number of processes used by the auto-guessed output compressing command. [default: 8]

--cmd-in <cmd_in>

A command to decompress the input file. If provided, fully overrides the auto-guessed command. Does not work with stdin and pairtools parse. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -dc -n 3

--cmd-out <cmd_out>

A command to compress the output file. If provided, fully overrides the auto-guessed command. Does not work with stdout. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -c -n 8

Arguments

PAIRS_PATH

Optional argument

header

Manipulate the .pairs/.pairsam header
pairtools header [OPTIONS] COMMAND [ARGS]...

generate

Generate the header
pairtools header generate [OPTIONS] [PAIRS_PATH]

Options

-o, --output <output>

output file. If the path ends with .gz or .lz4, the output is bgzip-/lz4c-compressed. By default, the output is printed into stdout.

--nproc-in <nproc_in>

Number of processes used by the auto-guessed input decompressing command. [default: 1]

--nproc-out <nproc_out>

Number of processes used by the auto-guessed output compressing command. [default: 8]

--cmd-in <cmd_in>

A command to decompress the input. If provided, fully overrides the auto-guessed command. Does not work with stdin. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -dc -n 3

--cmd-out <cmd_out>

A command to compress the output. If provided, fully overrides the auto-guessed command. Does not work with stdout. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -c -n 8

--chroms-path <chroms_path>

Chromosome order used to flip interchromosomal mates: path to a chromosomes file (e.g. UCSC chrom.sizes or similar) whose first column lists scaffold names. Any scaffolds not listed will be ordered lexicographically following the names provided.

--sam-path <sam_path>

Input sam file to inherit the header. Either –sam or –chroms-path should be provided to store the chromosome sizes in the header.

--columns <columns>

Report columns describing alignments Can take multiple values as a comma-separated list.By default, assign standard .pairs columns: readID,chrom1,pos1,chrom2,pos2,strand1,strand2,pair_type,sam1,sam2,walk_pair_index,walk_pair_type

--extra-columns <extra_columns>

Report extra columns describing alignments Can take multiple values as a comma-separated list.

--assembly <assembly>

Name of genome assembly (e.g. hg19, mm10) to store in the pairs header.

--no-flip

If specified, assume that the pairs are not filpped in genomic order and instead preserve the order in which they were sequenced.

--pairs, --pairsam

If pairs, then the defult columns will be set to: readID,chrom1,pos1,chrom2,pos2,strand1,strand2,pair_type if pairsam, then to: readID,chrom1,pos1,chrom2,pos2,strand1,strand2,pair_type,sam1,sam2

Arguments

PAIRS_PATH

Optional argument

set-columns

Add the columns to the .pairs/pairsam file
pairtools header set-columns [OPTIONS] [PAIRS_PATH]

Options

-o, --output <output>

output file. If the path ends with .gz or .lz4, the output is bgzip-/lz4c-compressed. By default, the output is printed into stdout.

--nproc-in <nproc_in>

Number of processes used by the auto-guessed input decompressing command. [default: 1]

--nproc-out <nproc_out>

Number of processes used by the auto-guessed output compressing command. [default: 8]

--cmd-in <cmd_in>

A command to decompress the input. If provided, fully overrides the auto-guessed command. Does not work with stdin. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -dc -n 3

--cmd-out <cmd_out>

A command to compress the output. If provided, fully overrides the auto-guessed command. Does not work with stdout. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -c -n 8

-c, --columns <columns>

Comma-separated list of columns to be added, e.g.: readID,chrom1,pos1,chrom2,pos2,strand1,strand2,pair_type,sam1,sam2,walk_pair_index,walk_pair_type [required]

Arguments

PAIRS_PATH

Optional argument

transfer

Transfer the header from one pairs file to another
pairtools header transfer [OPTIONS] [PAIRS_PATH]

Options

-o, --output <output>

output file. If the path ends with .gz or .lz4, the output is bgzip-/lz4c-compressed. By default, the output is printed into stdout.

--nproc-in <nproc_in>

Number of processes used by the auto-guessed input decompressing command. [default: 1]

--nproc-out <nproc_out>

Number of processes used by the auto-guessed output compressing command. [default: 8]

--cmd-in <cmd_in>

A command to decompress the input. If provided, fully overrides the auto-guessed command. Does not work with stdin. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -dc -n 3

--cmd-out <cmd_out>

A command to compress the output. If provided, fully overrides the auto-guessed command. Does not work with stdout. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -c -n 8

-r, --reference-file <reference_file>

Header file for transfer [required]

Arguments

PAIRS_PATH

Optional argument

validate-columns

Validate the columns of the .pairs/pairsam file against reference or within file. If the checks pass, then returns full pairs file. Otherwise throws an exception.

If reference_file is provided, check:
  1. columns are the same between pairs and reference_file
  2. number of columns in the pairs body is the same as the number of columns
If reference_columns are provided, check:
  1. pairs columns are the same as provided
  2. number of columns in the pairs body is the same as the number of columns

If no reference_file or columns, then check only the number of columns in the pairs body. Checks only the first line in the pairs stream!

pairtools header validate-columns [OPTIONS] [PAIRS_PATH]

Options

-o, --output <output>

output file. If the path ends with .gz or .lz4, the output is bgzip-/lz4c-compressed. By default, the output is printed into stdout.

--nproc-in <nproc_in>

Number of processes used by the auto-guessed input decompressing command. [default: 1]

--nproc-out <nproc_out>

Number of processes used by the auto-guessed output compressing command. [default: 8]

--cmd-in <cmd_in>

A command to decompress the input. If provided, fully overrides the auto-guessed command. Does not work with stdin. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -dc -n 3

--cmd-out <cmd_out>

A command to compress the output. If provided, fully overrides the auto-guessed command. Does not work with stdout. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -c -n 8

-r, --reference-file <reference_file>

Header file for comparison (optional)

-c, --reference-columns <reference_columns>

Comma-separated list of columns fro check (optional), e.g.: readID,chrom1,pos1,chrom2,pos2,strand1,strand2,pair_type,sam1,sam2,walk_pair_index,walk_pair_type

Arguments

PAIRS_PATH

Optional argument

markasdup

Tag all pairs in the input file as duplicates.

Change the type of all pairs inside a .pairs/.pairsam file to DD. If sam entries are present, change the pair type in the Yt SAM tag to ‘Yt:Z:DD’.

PAIRSAM_PATH : input .pairs/.pairsam file. If the path ends with .gz, the input is gzip-decompressed. By default, the input is read from stdin.

pairtools markasdup [OPTIONS] [PAIRSAM_PATH]

Options

-o, --output <output>

output .pairsam file. If the path ends with .gz or .lz4, the output is bgzip-/lz4c-compressed. By default, the output is printed into stdout.

--nproc-in <nproc_in>

Number of processes used by the auto-guessed input decompressing command. [default: 3]

--nproc-out <nproc_out>

Number of processes used by the auto-guessed output compressing command. [default: 8]

--cmd-in <cmd_in>

A command to decompress the input file. If provided, fully overrides the auto-guessed command. Does not work with stdin and pairtools parse. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -dc -n 3

--cmd-out <cmd_out>

A command to compress the output file. If provided, fully overrides the auto-guessed command. Does not work with stdout. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -c -n 8

Arguments

PAIRSAM_PATH

Optional argument

merge

Merge .pairs/.pairsam files.

By default, assumes that the files are sorted and maintains the sorting.

Merge triu-flipped sorted pairs/pairsam files. If present, the @SQ records of the SAM header must be identical; the sorting order of these lines is taken from the first file in the list. The ID fields of the @PG records of the SAM header are modified with a numeric suffix to produce unique records. The other unique SAM and non-SAM header lines are copied into the output header.

PAIRS_PATH : upper-triangular flipped sorted .pairs/.pairsam files to merge or a group/groups of .pairs/.pairsam files specified by a wildcard. For paths ending in .gz/.lz4, the files are decompressed by bgzip/lz4c.

pairtools merge [OPTIONS] [PAIRS_PATH]...

Options

-o, --output <output>

output file. If the path ends with .gz/.lz4, the output is compressed by bgzip/lz4c. By default, the output is printed into stdout.

--max-nmerge <max_nmerge>

The maximal number of inputs merged at once. For more, store merged intermediates in temporary files. [default: 8]

--tmpdir <tmpdir>

Custom temporary folder for merged intermediates.

--memory <memory>

The amount of memory used by default. [default: 2G]

--compress-program <compress_program>

A binary to compress temporary merged chunks. Must decompress input when the flag -d is provided. Suggested alternatives: lz4c, gzip, lzop, snzip. NOTE: fails silently if the command syntax is wrong. [default: ]

--nproc <nproc>

Number of threads for merging. [default: 8]

--nproc-in <nproc_in>

Number of processes used by the auto-guessed input decompressing command. [default: 1]

--nproc-out <nproc_out>

Number of processes used by the auto-guessed output compressing command. [default: 8]

--cmd-in <cmd_in>

A command to decompress the input. If provided, fully overrides the auto-guessed command. Does not work with stdin. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -dc -n 3

--cmd-out <cmd_out>

A command to compress the output. If provided, fully overrides the auto-guessed command. Does not work with stdout. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -c -n 8

--keep-first-header, --no-keep-first-header

Keep the first header or merge the headers together. Default: merge headers. [default: False]

--concatenate, --no-concatenate

Simple concatenate instead of merging sorted files. [default: False]

Arguments

PAIRS_PATH

Optional argument(s)

parse

Find ligation pairs in .sam data, make .pairs.
SAM_PATH : an input .sam/.bam file with paired-end sequence alignments of Hi-C molecules. If the path ends with .bam, the input is decompressed from bam with samtools. By default, the input is read from stdin.
pairtools parse [OPTIONS] [SAM_PATH]

Options

-c, --chroms-path <chroms_path>

Chromosome order used to flip interchromosomal mates: path to a chromosomes file (e.g. UCSC chrom.sizes or similar) whose first column lists scaffold names. Any scaffolds not listed will be ordered lexicographically following the names provided. [required]

-o, --output <output>

output file. If the path ends with .gz or .lz4, the output is bgzip-/lz4-compressed.By default, the output is printed into stdout.

--assembly <assembly>

Name of genome assembly (e.g. hg19, mm10) to store in the pairs header.

--min-mapq <min_mapq>

The minimal MAPQ score to consider a read as uniquely mapped [default: 1]

--max-molecule-size <max_molecule_size>

The maximal size of a Hi-C molecule; used to rescue single ligations(from molecules with three alignments) and to rescue complex ligations.The default is based on oriented P(s) at short ranges of multiple Hi-C.Not used with walks-policy all. [default: 750]

--drop-readid

If specified, do not add read ids to the output

--drop-seq

If specified, remove sequences and PHREDs from the sam fields

--drop-sam

If specified, do not add sams to the output

--add-pair-index

If specified, each pair will have pair index in the molecule

--add-columns <add_columns>

Report extra columns describing alignments Possible values (can take multiple values as a comma-separated list): a SAM tag (any pair of uppercase letters) or mapq, pos5, pos3, cigar, read_len, matched_bp, algn_ref_span, algn_read_span, dist_to_5, dist_to_3, seq, mismatches.

--output-parsed-alignments <output_parsed_alignments>

output file for all parsed alignments, including walks. Useful for debugging and rnalysis of walks. If file exists, it will be open in the append mode. If the path ends with .gz or .lz4, the output is bgzip-/lz4-compressed. By default, not used.

--output-stats <output_stats>

output file for various statistics of pairs file. By default, statistics is not generated.

--report-alignment-end <report_alignment_end>

specifies whether the 5’ or 3’ end of the alignment is reported as the position of the Hi-C read.

--max-inter-align-gap <max_inter_align_gap>

read segments that are not covered by any alignment and longer than the specified value are treated as “null” alignments. These null alignments convert otherwise linear alignments into walks, and affect how they get reported as a Hi-C pair (see –walks-policy). [default: 20]

--walks-policy <walks_policy>

the policy for reporting unrescuable walks (reads containing more than one alignment on one or both sides, that can not be explained by a single ligation between two mappable DNA fragments). “mask” - mask walks (chrom=”!”, pos=0, strand=”-“); “5any” - report the 5’-most alignment on each side; “5unique” - report the 5’-most unique alignment on each side, if present; “3any” - report the 3’-most alignment on each side; “3unique” - report the 3’-most unique alignment on each side, if present; “all” - report all available unique alignments on each side. [default: mask]

--readid-transform <readid_transform>

A Python expression to modify read IDs. Useful when read IDs differ between the two reads of a pair. Must be a valid Python expression that uses variables called readID and/or i (the 0-based index of the read pair in the bam file) and returns a new value, e.g. “readID[:-2]+’_’+str(i)”. Make sure that transformed readIDs remain unique!

--flip, --no-flip

If specified, do not flip pairs in genomic order and instead preserve the order in which they were sequenced.

--nproc-in <nproc_in>

Number of processes used by the auto-guessed input decompressing command. [default: 3]

--nproc-out <nproc_out>

Number of processes used by the auto-guessed output compressing command. [default: 8]

--cmd-in <cmd_in>

A command to decompress the input file. If provided, fully overrides the auto-guessed command. Does not work with stdin and pairtools parse. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -dc -n 3

--cmd-out <cmd_out>

A command to compress the output file. If provided, fully overrides the auto-guessed command. Does not work with stdout. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -c -n 8

Arguments

SAM_PATH

Optional argument

parse2

Extracts pairs from .sam/.bam data with complex walks, make .pairs.
SAM_PATH : an input .sam/.bam file with paired-end or single-end sequence alignments of Hi-C (or Hi-C-like) molecules. If the path ends with .bam, the input is decompressed from bam with samtools. By default, the input is read from stdin.
pairtools parse2 [OPTIONS] [SAM_PATH]

Options

-c, --chroms-path <chroms_path>

Chromosome order used to flip interchromosomal mates: path to a chromosomes file (e.g. UCSC chrom.sizes or similar) whose first column lists scaffold names. Any scaffolds not listed will be ordered lexicographically following the names provided. [required]

-o, --output <output>

output file with pairs. If the path ends with .gz or .lz4, the output is bgzip-/lz4-compressed.By default, the output is printed into stdout.

--report-position <report_position>

Reported position of alignments in pairs of complex walks (pos columns). Each alignment in .bam/.sam Hi-C-like data has two ends, and you can report one or another depending of the position of alignment on a read or in a pair.

“junction” - inner ends of sequential alignments in each pair, aka ligation junctions (complex walks default), “read” - 5’-end of alignments relative to R1 or R2 read coordinate system (as in traditional Hi-C), “walk” - 5’-end of alignments relative to the whole walk coordinate system, “outer” - outer ends of sequential alignments in each pair.

--report-orientation <report_orientation>

Reported orientataion of pairs in complex walk (strand columns). Each alignment in .bam/.sam Hi-C-like data has orientation, and you can report it relative to the read, pair or whole walk coordinate system.

“pair” - orientation as if each pair in complex walk was sequenced independently from the outer ends or molecule (as in traditional Hi-C, also complex walks default), “read” - orientation defined by the read (R1 or R2 read coordinate system), “walk” - orientation defined by the walk coordinate system, “junction” - reversed “pair” orientation, as if pair was sequenced in both directions starting from the junction

--assembly <assembly>

Name of genome assembly (e.g. hg19, mm10) to store in the pairs header.

--min-mapq <min_mapq>

The minimal MAPQ score to consider a read as uniquely mapped. [default: 1]

--max-inter-align-gap <max_inter_align_gap>

Read segments that are not covered by any alignment and longer than the specified value are treated as “null” alignments. These null alignments convert otherwise linear alignments into walks, and affect how they get reported as a Hi-C pair. [default: 20]

--max-insert-size <max_insert_size>

When searching for overlapping ends of left and right read (R1 and R2), this sets the minimal distance when two alignments on the same strand and chromosome are considered part of the same fragment (and thus reported as the same alignment and not a pair). For traditional Hi-C with long restriction fragments and shorter molecules after ligation+sonication, this can be the expected molecule size. For complex walks with short restriction fragments, this can be the expected restriction fragment size. Note that unsequenced insert is terra incognita and might contain unsequenced DNA (including ligations) in it. This parameter is ignored in –single-end mode. [default: 500]

--dedup-max-mismatch <dedup_max_mismatch>

Allowed mismatch between intramolecular alignments to detect readthrough duplicates. Pairs with both sides mapped within this distance (bp) from each other are considered duplicates. [default: 3]

--single-end

If specified, the input is single-end. Never use this for paired-end data, because R1 read will be omitted. If single-end data is provided, but parameter is unset, the pairs will be generated, but may contain artificial UN pairs.

--expand, --no-expand

If specified, perform combinatorial expansion on the pairs. Combinatorial expansion is a way to increase the number of contacts in you data, assuming that all DNA fragments in the same molecule (read) are in contact. Expanded pairs have modified pair type, ‘E{separation}_{pair type}’

--max-expansion-depth <max_expansion_depth>

Works in combination with –expand. Maximum number of segments separating pair. By default, expanding all possible pairs.Setting the number will limit the expansion depth and enforce contacts from the same side of the read.

--add-pair-index

If specified, parse2 will report pair index in the walk as additional columns (R1, R2, R1&R2 or R1-R2). See documentation: https://pairtools.readthedocs.io/en/latest/parsing.html#rescuing-complex-walks For combinatorial expanded pairs, two numbers will be reported: original pair index of the left and right segments.

--flip, --no-flip

If specified, flip pairs in genomic order and instead preserve the order in which they were sequenced. Note that no flip is recommended for analysis of walks because it will override the order of alignments in pairs. Flip is required for appropriate deduplication of sorted pairs. Flip is not required for cooler cload, which runs flipping internally.

--add-columns <add_columns>

Report extra columns describing alignments Possible values (can take multiple values as a comma-separated list): a SAM tag (any pair of uppercase letters) or mapq, pos5, pos3, cigar, read_len, matched_bp, algn_ref_span, algn_read_span, dist_to_5, dist_to_3, seq, mismatches.

--drop-readid, --keep-readid

If specified, do not add read ids to the output. By default, keep read ids. Useful for long walks analysis.

--readid-transform <readid_transform>

A Python expression to modify read IDs. Useful when read IDs differ between the two reads of a pair. Must be a valid Python expression that uses variables called readID and/or i (the 0-based index of the read pair in the bam file) and returns a new value, e.g. “readID[:-2]+’_’+str(i)”. Make sure that transformed readIDs remain unique!

--drop-seq, --keep-seq

Remove sequences and PHREDs from the sam fields by default. Kept otherwise.

--drop-sam, --keep-sam

Do not add sams to the output by default. Kept otherwise.

--output-parsed-alignments <output_parsed_alignments>

output file with all parsed alignments (one alignment per line). Useful for debugging and analysis of walks. If file exists, it will be open in the append mode. If the path ends with .gz or .lz4, the output is bgzip-/lz4-compressed. By default, not used.

--output-stats <output_stats>

output file for various statistics of pairs file. By default, statistics is not generated.

--nproc-in <nproc_in>

Number of processes used by the auto-guessed input decompressing command. [default: 3]

--nproc-out <nproc_out>

Number of processes used by the auto-guessed output compressing command. [default: 8]

--cmd-in <cmd_in>

A command to decompress the input file. If provided, fully overrides the auto-guessed command. Does not work with stdin and pairtools parse. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -dc -n 3

--cmd-out <cmd_out>

A command to compress the output file. If provided, fully overrides the auto-guessed command. Does not work with stdout. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -c -n 8

Arguments

SAM_PATH

Optional argument

phase

Phase pairs mapped to a diploid genome.

Diploid genome is the genome with two set of the chromosome variants, where each chromosome has one of two suffixes (phase-suffixes) corresponding to the genome version (phase-suffixes).

By default, phasing adds two additional columns with phase 0, 1 or “.” (unpahsed).

Phasing is based on detection of chromosome origin of each mapped fragment. Three scores are considered: best alignment score (S1), suboptimal alignment (S2) and second suboptimal alignment (S3) scores. Each fragment can be: 1) uniquely mapped and phased (S1>S2>S3, first alignment is the best hit), 2) uniquely mapped but unphased (S1=S2>S3, cannot distinguish between chromosome variants), 3) multiply mapped (S1=S2=S3) or unmapped.

PAIRS_PATH : input .pairs/.pairsam file. If the path ends with .gz or .lz4, the input is decompressed by bgzip/lz4c. By default, the input is read from stdin.

pairtools phase [OPTIONS] [PAIRS_PATH]

Options

-o, --output <output>

output file. If the path ends with .gz or .lz4, the output is bgzip-/lz4c-compressed. By default, the output is printed into stdout.

--phase-suffixes <phase_suffixes>

Phase suffixes (of the chrom names), always a pair.

--clean-output

Drop all columns besides the standard ones and phase1/2

--tag-mode <tag_mode>

Specifies the mode of bwa reporting. XA will parse ‘XA’, the input should be generated with: –add-columns XA,NM,AS,XS –min-mapq 0 XB will parse ‘XB’ tag, the input should be generated with: –add-columns XB,AS,XS –min-mapq 0 Note that XB tag is added by running bwa with -u tag, present in github version. Both modes report similar results: XB reports 0.002% contacts more for phased data, while XA can report ~1-2% more unphased contacts because its definition multiple mappers is more premissive.

--report-scores, --no-report-scores

Report scores of optional, suboptimal and second suboptimal alignments. NM (edit distance) with –tag-mode XA and AS (alfn score) with –tag-mode XB

--nproc-in <nproc_in>

Number of processes used by the auto-guessed input decompressing command. [default: 3]

--nproc-out <nproc_out>

Number of processes used by the auto-guessed output compressing command. [default: 8]

--cmd-in <cmd_in>

A command to decompress the input file. If provided, fully overrides the auto-guessed command. Does not work with stdin and pairtools parse. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -dc -n 3

--cmd-out <cmd_out>

A command to compress the output file. If provided, fully overrides the auto-guessed command. Does not work with stdout. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -c -n 8

Arguments

PAIRS_PATH

Optional argument

restrict

Assign restriction fragments to pairs.

Identify the restriction fragments that got ligated into a Hi-C molecule.

Note: rfrags are 0-indexed

PAIRS_PATH : input .pairs/.pairsam file. If the path ends with .gz/.lz4, the input is decompressed by bgzip/lz4c. By default, the input is read from stdin.

pairtools restrict [OPTIONS] [PAIRS_PATH]

Options

-f, --frags <frags>

a tab-separated BED file with the positions of restriction fragments (chrom, start, end). Can be generated using cooler digest. [required]

-o, --output <output>

output .pairs/.pairsam file. If the path ends with .gz/.lz4, the output is compressed by bgzip/lz4c. By default, the output is printed into stdout.

--nproc-in <nproc_in>

Number of processes used by the auto-guessed input decompressing command. [default: 3]

--nproc-out <nproc_out>

Number of processes used by the auto-guessed output compressing command. [default: 8]

--cmd-in <cmd_in>

A command to decompress the input file. If provided, fully overrides the auto-guessed command. Does not work with stdin and pairtools parse. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -dc -n 3

--cmd-out <cmd_out>

A command to compress the output file. If provided, fully overrides the auto-guessed command. Does not work with stdout. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -c -n 8

Arguments

PAIRS_PATH

Optional argument

sample

Select a random subset of pairs in a pairs file.

FRACTION: the fraction of the randomly selected pairs subset

PAIRS_PATH : input .pairs/.pairsam file. If the path ends with .gz or .lz4, the input is decompressed by bgzip/lz4c. By default, the input is read from stdin.

pairtools sample [OPTIONS] FRACTION [PAIRS_PATH]

Options

-o, --output <output>

output file. If the path ends with .gz or .lz4, the output is bgzip-/lz4c-compressed. By default, the output is printed into stdout.

-s, --seed <seed>

the seed of the random number generator.

--nproc-in <nproc_in>

Number of processes used by the auto-guessed input decompressing command. [default: 3]

--nproc-out <nproc_out>

Number of processes used by the auto-guessed output compressing command. [default: 8]

--cmd-in <cmd_in>

A command to decompress the input file. If provided, fully overrides the auto-guessed command. Does not work with stdin and pairtools parse. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -dc -n 3

--cmd-out <cmd_out>

A command to compress the output file. If provided, fully overrides the auto-guessed command. Does not work with stdout. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -c -n 8

Arguments

FRACTION

Required argument

PAIRS_PATH

Optional argument

scaling

Calculate pairs scalings.

INPUT_PATH : by default, a .pairs/.pairsam file to calculate statistics. If not provided, the input is read from stdin.

The files with paths ending with .gz/.lz4 are decompressed by bgzip/lz4c.

Output is .tsv file with scaling stats (both cis scalings and trans levels).

pairtools scaling [OPTIONS] [INPUT_PATH]...

Options

-o, --output <output>

output .tsv file with summary.

--view, --regions <view>

Path to a BED file which defines which regions (viewframe) of the chromosomes to use. By default, this is parsed from .pairs header.

--chunksize <chunksize>

Number of pairs in each chunk. Reduce for lower memory footprint. [default: 100000]

--dist-range <dist_range>

Distance range. [default: 10, 1000000000]

--n-dist-bins <n_dist_bins>

Number of distance bins to split the distance range. [default: 128]

--nproc-in <nproc_in>

Number of processes used by the auto-guessed input decompressing command. [default: 3]

--nproc-out <nproc_out>

Number of processes used by the auto-guessed output compressing command. [default: 8]

--cmd-in <cmd_in>

A command to decompress the input file. If provided, fully overrides the auto-guessed command. Does not work with stdin and pairtools parse. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -dc -n 3

--cmd-out <cmd_out>

A command to compress the output file. If provided, fully overrides the auto-guessed command. Does not work with stdout. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -c -n 8

Arguments

INPUT_PATH

Optional argument(s)

select

Select pairs according to some condition.

CONDITION : A Python expression; if it returns True, select the read pair. Any column declared in the #columns line of the pairs header can be accessed by its name. If the header lacks the #columns line, the columns are assumed to follow the .pairs/.pairsam standard (readID, chrom1, chrom2, pos1, pos2, strand1, strand2, pair_type). Finally, CONDITION has access to COLS list which contains the string values of columns. In Bash, quote CONDITION with single quotes, and use double quotes for string variables inside CONDITION.

PAIRS_PATH : input .pairs/.pairsam file. If the path ends with .gz or .lz4, the input is decompressed by bgzip/lz4c. By default, the input is read from stdin.

The following functions can be used in CONDITION besides the standard Python functions:

  • csv_match(x, csv) - True if variable x is contained in a list of

comma-separated values, e.g. csv_match(chrom1, ‘chr1,chr2’)

  • wildcard_match(x, wildcard) - True if variable x matches a wildcard,

e.g. wildcard_match(pair_type, ‘C*’)

  • regex_match(x, regex) - True if variable x matches a Python-flavor regex,

e.g. regex_match(chrom1, ‘chrd’)

 Examples: pairtools select ‘(pair_type==”UU”) or (pair_type==”UR”) or (pair_type==”RU”)’ pairtools select ‘chrom1==chrom2’ pairtools select ‘COLS[1]==COLS[3]’ pairtools select ‘(chrom1==chrom2) and (abs(pos1 - pos2) < 1e6)’ pairtools select ‘(chrom1==”!”) and (chrom2!=”!”)’ pairtools select ‘regex_match(chrom1, “chrd+”) and regex_match(chrom2, “chrd+”)’

pairtools select ‘True’ –chrom-subset mm9.reduced.chromsizes

pairtools select [OPTIONS] CONDITION [PAIRS_PATH]

Options

-o, --output <output>

output file. If the path ends with .gz or .lz4, the output is bgzip-/lz4c-compressed. By default, the output is printed into stdout.

--output-rest <output_rest>

output file for pairs of other types. If the path ends with .gz or .lz4, the output is bgzip-/lz4c-compressed. By default, such pairs are dropped.

--chrom-subset <chrom_subset>

A path to a chromosomes file (tab-separated, 1st column contains chromosome names) containing a chromosome subset of interest. If provided, additionally filter pairs with both sides originating from the provided subset of chromosomes. This operation modifies the #chromosomes: and #chromsize: header fields accordingly.

--startup-code <startup_code>

An auxiliary code to execute before filtering. Use to define functions that can be evaluated in the CONDITION statement

-t, --type-cast <type_cast>

Cast a given column to a given type. By default, only pos and mapq are cast to int, other columns are kept as str. Provide as -t <column_name> <type>, e.g. -t read_len1 int. Multiple entries are allowed.

-r, --remove-columns <remove_columns>

Comma-separated list of columns to be removed, e.g.: readID,chrom1,pos1,chrom2,pos2,strand1,strand2,pair_type,sam1,sam2,walk_pair_index,walk_pair_type

--nproc-in <nproc_in>

Number of processes used by the auto-guessed input decompressing command. [default: 3]

--nproc-out <nproc_out>

Number of processes used by the auto-guessed output compressing command. [default: 8]

--cmd-in <cmd_in>

A command to decompress the input file. If provided, fully overrides the auto-guessed command. Does not work with stdin and pairtools parse. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -dc -n 3

--cmd-out <cmd_out>

A command to compress the output file. If provided, fully overrides the auto-guessed command. Does not work with stdout. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -c -n 8

Arguments

CONDITION

Required argument

PAIRS_PATH

Optional argument

sort

Sort a .pairs/.pairsam file.

Sort pairs in the lexicographic order along chrom1 and chrom2, in the numeric order along pos1 and pos2 and in the lexicographic order along pair_type.

PAIRS_PATH : input .pairs/.pairsam file. If the path ends with .gz or .lz4, the input is decompressed by bgzip or lz4c, correspondingly. By default, the input is read as text from stdin.

pairtools sort [OPTIONS] [PAIRS_PATH]

Options

-o, --output <output>

output pairs file. If the path ends with .gz or .lz4, the output is compressed by bgzip or lz4, correspondingly. By default, the output is printed into stdout.

--nproc <nproc>

Number of processes to split the sorting work between. [default: 8]

--tmpdir <tmpdir>

Custom temporary folder for sorting intermediates.

--memory <memory>

The amount of memory used by default. [default: 2G]

--compress-program <compress_program>

A binary to compress temporary sorted chunks. Must decompress input when the flag -d is provided. Suggested alternatives: gzip, lzop, lz4c, snzip. If “auto”, then use lz4c if available, and gzip otherwise. [default: auto]

--nproc-in <nproc_in>

Number of processes used by the auto-guessed input decompressing command. [default: 3]

--nproc-out <nproc_out>

Number of processes used by the auto-guessed output compressing command. [default: 8]

--cmd-in <cmd_in>

A command to decompress the input file. If provided, fully overrides the auto-guessed command. Does not work with stdin and pairtools parse. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -dc -n 3

--cmd-out <cmd_out>

A command to compress the output file. If provided, fully overrides the auto-guessed command. Does not work with stdout. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -c -n 8

Arguments

PAIRS_PATH

Optional argument

split

Split a .pairsam file into .pairs and .sam.

Restore a .sam file from sam1 and sam2 fields of a .pairsam file. Create a .pairs file without sam1/sam2 fields.

PAIRSAM_PATH : input .pairsam file. If the path ends with .gz or .lz4, the input is decompressed by bgzip or lz4c. By default, the input is read from stdin.

pairtools split [OPTIONS] [PAIRSAM_PATH]

Options

--output-pairs <output_pairs>

output pairs file. If the path ends with .gz or .lz4, the output is bgzip-/lz4c-compressed. If -, pairs are printed to stdout. If not specified, pairs are dropped.

--output-sam <output_sam>

output sam file. If the path ends with .bam, the output is compressed into a bam file. If -, sam entries are printed to stdout. If not specified, sam entries are dropped.

--nproc-in <nproc_in>

Number of processes used by the auto-guessed input decompressing command. [default: 3]

--nproc-out <nproc_out>

Number of processes used by the auto-guessed output compressing command. [default: 8]

--cmd-in <cmd_in>

A command to decompress the input file. If provided, fully overrides the auto-guessed command. Does not work with stdin and pairtools parse. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -dc -n 3

--cmd-out <cmd_out>

A command to compress the output file. If provided, fully overrides the auto-guessed command. Does not work with stdout. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -c -n 8

Arguments

PAIRSAM_PATH

Optional argument

stats

Calculate pairs statistics.

INPUT_PATH : by default, a .pairs/.pairsam file to calculate statistics. If not provided, the input is read from stdin. If –merge is specified, then INPUT_PATH is interpreted as an arbitrary number of stats files to merge.

The files with paths ending with .gz/.lz4 are decompressed by bgzip/lz4c.

pairtools stats [OPTIONS] [INPUT_PATH]...

Options

-o, --output <output>

output stats tsv file.

--merge

If specified, merge multiple input stats files instead of calculating statistics of a .pairs/.pairsam file. Merging is performed via summation of all overlapping statistics. Non-overlapping statistics are appended to the end of the file. Supported for tsv stats with single filter.

--with-chromsizes, --no-chromsizes

If enabled, will store sizes of chromosomes from the header of the pairs file in the stats file.

--yaml, --no-yaml

Output stats in yaml format instead of table.

--bytile-dups, --no-bytile-dups

If enabled, will analyse by-tile duplication statistics to estimate library complexity more accurately. Requires parent_readID column to be saved by dedup (will be ignored otherwise) Saves by-tile stats into –output_bytile-stats stream, or regular output if –output_bytile-stats is not provided.

--output-bytile-stats <output_bytile_stats>

output file for tile duplicate statistics. If file exists, it will be open in the append mode. If the path ends with .gz or .lz4, the output is bgzip-/lz4c-compressed. By default, by-tile duplicate statistics are not printed. Note that the readID and parent_readID should be provided and contain tile information for this option.

--filter <filter>

Filters with conditions to apply to the data (similar to pairtools select). For non-YAML output only the first filter will be reported. Example: pairtools stats –yaml –filter ‘unique:(pair_type==”UU”)’ –filter ‘close:(pair_type==”UU”) and (abs(pos1-pos2)<10)’ test.pairs

--engine <engine>

Engine for regular expression parsing. Python will provide you regex functionality, while pandas does not accept custom funtctions and works faster.

--chrom-subset <chrom_subset>

A path to a chromosomes file (tab-separated, 1st column contains chromosome names) containing a chromosome subset of interest. If provided, additionally filter pairs with both sides originating from the provided subset of chromosomes. This operation modifies the #chromosomes: and #chromsize: header fields accordingly.

--startup-code <startup_code>

An auxiliary code to execute before filtering. Use to define functions that can be evaluated in the CONDITION statement

-t, --type-cast <type_cast>

Cast a given column to a given type. By default, only pos and mapq are cast to int, other columns are kept as str. Provide as -t <column_name> <type>, e.g. -t read_len1 int. Multiple entries are allowed.

--nproc-in <nproc_in>

Number of processes used by the auto-guessed input decompressing command. [default: 3]

--nproc-out <nproc_out>

Number of processes used by the auto-guessed output compressing command. [default: 8]

--cmd-in <cmd_in>

A command to decompress the input file. If provided, fully overrides the auto-guessed command. Does not work with stdin and pairtools parse. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -dc -n 3

--cmd-out <cmd_out>

A command to compress the output file. If provided, fully overrides the auto-guessed command. Does not work with stdout. Must read input from stdin and print output into stdout. EXAMPLE: pbgzip -c -n 8

Arguments

INPUT_PATH

Optional argument(s)