Return estimated fragment coverage over intervals specified in intervals. Fragments are read from input_file which may be a BAM, CRAM, or fragment file. Uses an algorithm where the @@ -404,7 +404,7 @@
Return np.ndarray containing lengths of fragments in input_file that are above the quality threshold and are proper-paired reads.
Takes input_file, computes frag lengths of fragments and returns two arrays containing bins and counts by size. Optionally prints data to output as a tab delimited table or histogram.
@@ -566,7 +566,7 @@Cleavage profile calculated over a single interval.
A function that replicates the methodology of Christiano et al (2019).
Reads kmer frequency from a two-column tab-delimited file.
Function that reads fragments from a BAM, CRAM, or tabix indexed file and returns the 5’ k-mer (default is 4-mer) end motif frequencies as a dictionary. Optionally writes data to a tsv. This @@ -605,7 +605,7 @@
Function that reads fragments from a BAM, CRAM, or tabix indexed file and user-specified intervals and returns the 5’ k-mer (default is 4-mer) end motif. Optionally writes data to a tsv.
@@ -752,7 +752,7 @@Accepts the path to a BAM, CRAM, or BED file and creates a filtered version.
+Filter reads/intervals based on exceeding the specified quality threshold, +intersections with a region in the region bed (if provided), and read length.
+For BAM/CRAM files, it also filters reads based on being read1 in a proper pair.
+input_file (str) – Path string to the input BAM, CRAM, or BED file.
whitelist_file (str, optional) – Path to a BED file defining regions to include.
blacklist_file (str, optional) – Path to a BED file defining regions to exclude.
output_file (str, optional) – Path to the output filtered file. If None, a temporary file is created.
min_length (int, optional) – Minimum length for reads/intervals
max_length (int, optional) – Maximum length for reads/intervals
intersect_policy (str, optional) – Specifies how to determine whether fragments are in interval for +whitelisting and blacklisting functionality.’midpoint’ (default) +calculates the central coordinate of each fragment and only +selects the fragment if the midpoint is in the interval. +‘any’ includes fragments with any overlap with the interval.
quality_threshold (int, optional) – Minimum mapping quality score
workers (int, optional) – Number of worker threads for samtools.
verbose (bool, optional) – Default is False
fraction_low (int, optional) – Deprecated alias for min_length
fraction_high (int, optional) – Deprecated alias for max_length
output_file – Path to the filtered output file.
+str
+Reads from BAM, CRAM, or fragment file and returns a three column matrix with fragment start and stop positions and strand.
filter_file()agg_bw()chrom_sizes_to_list()chrom_sizes_to_dict()filter_file()agg_bw()chrom_sizes_to_list()chrom_sizes_to_dict()Return (raw) Windowed Protection Scores as specified in Snyder et al (2016) over a region [start,stop).
Function that aggregates WPS over sites in BED file according to the method described by Snyder et al (2016).
show program’s version number and exit
@@ -368,8 +368,7 @@Calculates fragmentation coverage over intervals defined in a BED file based on alignment data from a BAM/CRAM/Fragment file.
-finaletoolkit coverage [-h] [-o OUTPUT_FILE] [-n] [-s SCALE_FACTOR] [-min MIN_LENGTH] [-max MAX_LENGTH] [-p {midpoint,any}] [-q QUALITY_THRESHOLD]
- [-w WORKERS] [-v]
+finaletoolkit coverage [-h] [-o OUTPUT_FILE] [-n] [-s SCALE_FACTOR] [-min MIN_LENGTH] [-max MAX_LENGTH] [-p {midpoint,any}] [-q QUALITY_THRESHOLD] [-w WORKERS] [-v]
input_file interval_file
@@ -384,24 +383,24 @@ Positional Arguments
-
-Named Arguments#
+
+Named Arguments#
- -o, --output-file
A BED file containing coverage values over the intervals specified in interval file.
-Default: “-”
+Default: '-'
- -n, --normalize
If flag set, multiplies by user inputed scale factor if given and normalizes output by total coverage. May lead to longer execution time for high-throughput data.
-Default: False
+Default: False
- -s, --scale-factor
Scale factor for coverage values. Default is 1.
-Default: 1.0
+Default: 1.0
- -min, --min-length
Minimum length for a fragment to be included in coverage.
-Default: 0
+Default: 0
- -max, --max-length
Maximum length for a fragment to be included in coverage.
@@ -409,19 +408,19 @@ Named Arguments'midpoint'
- -q, --quality-threshold
Minimum mapping quality threshold.
-Default: 30
+Default: 30
- -w, --workers
Number of worker processes.
-Default: 1
+Default: 1
- -v, --verbose
Enable verbose mode to display detailed processing information.
-Default: False
+Default: False
@@ -429,8 +428,8 @@ Named Arguments
frag-length-bins#
Retrieves fragment lengths grouped in bins given a BAM/CRAM/Fragment file.
-finaletoolkit frag-length-bins [-h] [-c CONTIG] [-S START] [-E STOP] [-min MIN_LENGTH] [-max MAX_LENGTH] [-p {midpoint,any}] [--bin-size BIN_SIZE]
- [-o OUTPUT_FILE] [--histogram-path HISTOGRAM_PATH] [-q QUALITY_THRESHOLD] [-v]
+finaletoolkit frag-length-bins [-h] [-c CONTIG] [-S START] [-E STOP] [-min MIN_LENGTH] [-max MAX_LENGTH] [-p {midpoint,any}] [--bin-size BIN_SIZE] [-o OUTPUT_FILE]
+ [--histogram-path HISTOGRAM_PATH] [-q QUALITY_THRESHOLD] [-v]
input_file
@@ -442,8 +441,8 @@ Positional Arguments
-Named Arguments#
+
+Named Arguments#
- -c, --contig
Specify the contig or chromosome to select fragments from. (Required if using –start or –stop.)
@@ -456,7 +455,7 @@ Named Arguments0
- -max, --max-length
Maximum length for a fragment to be included in fragment length.
@@ -464,26 +463,26 @@ Named Arguments'midpoint'
- --bin-size
Specify the size of the bins to group fragment lengths into.
-Default: 1
+Default: 1
- -o, --output-file
A .TSV file containing containing fragment lengths binned according to the specified bin size.
-Default: “-”
+Default: '-'
- --histogram-path
Path to store histogram.
- -q, --quality-threshold
Minimum mapping quality threshold.
-Default: 30
+Default: 30
- -v, --verbose
Enable verbose mode to display detailed processing information.
-Default: 0
+Default: 0
@@ -491,8 +490,7 @@ Named Arguments
frag-length-intervals#
Retrieves fragment length summary statistics over intervals defined in a BED file based on alignment data from a BAM/CRAM/Fragment file.
-finaletoolkit frag-length-intervals [-h] [-min MIN_LENGTH] [-max MAX_LENGTH] [-p {midpoint,any}] [-o OUTPUT_FILE] [-q QUALITY_THRESHOLD] [-w WORKERS] [-v]
- input_file interval_file
+finaletoolkit frag-length-intervals [-h] [-min MIN_LENGTH] [-max MAX_LENGTH] [-p {midpoint,any}] [-o OUTPUT_FILE] [-q QUALITY_THRESHOLD] [-w WORKERS] [-v] input_file interval_file
@@ -506,12 +504,12 @@ Positional Arguments
-Named Arguments#
+
+Named Arguments#
- -min, --min-length
Minimum length for a fragment to be included in fragment length.
-Default: 0
+Default: 0
- -max, --max-length
Maximum length for a fragment to be included in fragment length.
@@ -519,23 +517,23 @@ Named Arguments'midpoint'
- -o, --output-file
A BED file containing fragment length summary statistics (mean, median, st. dev, min, max) over the intervals specified in the interval file.
-Default: “-”
+Default: '-'
- -q, --quality-threshold
Minimum mapping quality threshold.
-Default: 30
+Default: 30
- -w, --workers
Number of worker processes.
-Default: 1
+Default: 1
- -v, --verbose
Enable verbose mode to display detailed processing information.
-Default: 0
+Default: 0
@@ -543,8 +541,8 @@ Named Arguments
cleavage-profile#
Calculates cleavage proportion over intervals defined in a BED file based on alignment data from a BAM/CRAM/Fragment file.
-finaletoolkit cleavage-profile [-h] [-c CHROM_SIZES] [-o OUTPUT_FILE] [-min MIN_LENGTH] [-max MAX_LENGTH] [-lo MIN_LENGTH] [-hi MAX_LENGTH]
- [-q QUALITY_THRESHOLD] [-l LEFT] [-r RIGHT] [-w WORKERS] [-v]
+finaletoolkit cleavage-profile [-h] [-c CHROM_SIZES] [-o OUTPUT_FILE] [-min MIN_LENGTH] [-max MAX_LENGTH] [-lo MIN_LENGTH] [-hi MAX_LENGTH] [-q QUALITY_THRESHOLD] [-l LEFT] [-r RIGHT]
+ [-w WORKERS] [-v]
input_file interval_file
@@ -559,19 +557,19 @@ Positional Arguments
-Named Arguments#
+
+Named Arguments#
- -c, --chrom-sizes
A .chrom.sizes file containing chromosome names and sizes.
- -o, --output-file
A bigWig file containing the cleavage proportion results over the intervals specified in interval file.
-Default: “-”
+Default: '-'
- -min, --min-length
Minimum length for a fragment to be included.
-Default: 0
+Default: 0
- -max, --max-length
Maximum length for a fragment to be included.
@@ -584,23 +582,23 @@ Named Arguments20
- -l, --left
Number of base pairs to subtract from start coordinate to create interval. Useful when dealing with BED files with only CpG coordinates. Default is 0.
-Default: 0
+Default: 0
- -r, --right
Number of base pairs to add to stop coordinate to create interval. Useful when dealing with BED files with only CpG coordinates. Default is 0.
-Default: 0
+Default: 0
- -w, --workers
Number of worker processes.
-Default: 1
+Default: 1
- -v, --verbose
Enable verbose mode to display detailed processing information.
-Default: 0
+Default: 0
@@ -608,8 +606,8 @@ Named Arguments
wps#
Calculates Windowed Protection Score (WPS) over intervals defined in a BED file based on alignment data from a BAM/CRAM/Fragment file.
-finaletoolkit wps [-h] [-c CHROM_SIZES] [-o OUTPUT_FILE] [-i INTERVAL_SIZE] [-W WINDOW_SIZE] [-min MIN_LENGTH] [-max MAX_LENGTH] [-lo MIN_LENGTH]
- [-hi MAX_LENGTH] [-q QUALITY_THRESHOLD] [-w WORKERS] [-v]
+finaletoolkit wps [-h] [-c CHROM_SIZES] [-o OUTPUT_FILE] [-i INTERVAL_SIZE] [-W WINDOW_SIZE] [-min MIN_LENGTH] [-max MAX_LENGTH] [-lo MIN_LENGTH] [-hi MAX_LENGTH] [-q QUALITY_THRESHOLD]
+ [-w WORKERS] [-v]
input_file site_bed
@@ -624,31 +622,31 @@ Positional Arguments
-Named Arguments#
+
+Named Arguments#
- -c, --chrom-sizes
A .chrom.sizes file containing chromosome names and sizes.
- -o, --output-file
A bigWig file containing the WPS results over the intervals specified in interval file.
-Default: “-”
+Default: '-'
- -i, --interval-size
Size in bp of the intervals to calculate WPS over. Thesenew intervals are centered over those specified in the site_bed.Default is 5000
-Default: 5000
+Default: 5000
- -W, --window-size
Size of the sliding window used to calculate WPS scores. Default is 120
-Default: 120
+Default: 120
- -min, --min-length
Minimum length for a fragment to be included. Default is 120, corresponding to L-WPS.
-Default: 120
+Default: 120
- -max, --max-length
Maximum length for a fragment to be included. Default is 180, corresponding to L-WPS.
-Default: 180
+Default: 180
- -lo, --fraction_low
Minimum length for a fragment to be included in WPS calculation. Deprecated. Use –min-length instead.
@@ -658,15 +656,15 @@ Named Arguments30
- -w, --workers
Number of worker processes.
-Default: 1
+Default: 1
- -v, --verbose
Enable verbose mode to display detailed processing information.
-Default: 0
+Default: 0
@@ -674,8 +672,8 @@ Named Arguments
adjust-wps#
Adjusts raw Windowed Protection Score (WPS) by applying a median filter and Savitsky-Golay filter.
-finaletoolkit adjust-wps [-h] [-o OUTPUT_FILE] [-i INTERVAL_SIZE] [-m MEDIAN_WINDOW_SIZE] [-s SAVGOL_WINDOW_SIZE] [-p SAVGOL_POLY_DEG] [-S] [-w WORKERS]
- [--mean] [--subtract-edges] [--edge-size EDGE_SIZE] [-v]
+finaletoolkit adjust-wps [-h] [-o OUTPUT_FILE] [-i INTERVAL_SIZE] [-m MEDIAN_WINDOW_SIZE] [-s SAVGOL_WINDOW_SIZE] [-p SAVGOL_POLY_DEG] [-S] [-w WORKERS] [--mean] [--subtract-edges]
+ [--edge-size EDGE_SIZE] [-v]
input_file interval_file chrom_sizes
@@ -693,48 +691,48 @@ Positional Arguments
-Named Arguments#
+
+Named Arguments#
- -o, --output-file
A bigWig file containing the adjusted WPS results over the intervals specified in interval file.
-Default: “-”
+Default: '-'
- -i, --interval_size
Size in bp of each interval in the interval file.
-Default: 5000
+Default: 5000
- -m, --median-window-size
Size of the median filter or mean filter window used to adjust WPS scores.
-Default: 1000
+Default: 1000
- -s, --savgol-window-size
Size of the Savitsky-Golay filter window used to adjust WPS scores.
-Default: 21
+Default: 21
- -p, --savgol-poly-deg
Degree polynomial for Savitsky-Golay filter.
-Default: 2
+Default: 2
- -S, --exclude-savgol
Do not perform Savitsky-Golay filteringscores.
-Default: True
+Default: True
- -w, --workers
Number of worker processes.
-Default: 1
+Default: 1
- --mean
A mean filter is used instead of median.
-Default: False
+Default: False
- --subtract-edges
Take the median of the first and last 500 bases in a window and subtract from the whole interval.
-Default: False
+Default: False
- --edge-size
size of the edge subtracted from ends of window when –subtract-edges is set. Default is 500.
-Default: 500
+Default: 500
- -v, --verbose
Enable verbose mode to display detailed processing information.
@@ -766,8 +764,8 @@ Positional Arguments
-Named Arguments#
+
+Named Arguments#
- -b, --blacklist-file
BED file containing regions to ignore when calculating DELFI.
@@ -777,35 +775,35 @@ Named Arguments'-'
- -G, --no-gc-correct
Skip GC correction.
-Default: True
+Default: True
- -R, --keep-nocov
Skip removal two regions in hg19 with no coverage. Use this flag when not using hg19 human reference genome.
-Default: True
+Default: True
- -M, --no-merge-bins
Keep 100kb bins and do not merge to 5Mb size.
-Default: True
+Default: True
- -s, --window-size
Specify size of large genomic intervals to merge smaller 100kb intervals (or whatever the user specified in bins_file) into. Defaultis 5000000
-Default: 5000000
+Default: 5000000
- -q, --quality-threshold
Minimum mapping quality threshold.
-Default: 30
+Default: 30
- -w, --workers
Number of worker processes.
-Default: 1
+Default: 1
- -v, --verbose
Enable verbose mode to display detailed processing information.
-Default: 0
+Default: 0
@@ -824,16 +822,16 @@ Positional Arguments
-Named Arguments#
+
+Named Arguments#
- -o, --output-file
BED to print GC-corrected DELFI fractions. If “-”, will write to stdout.
-Default: “-”
+Default: '-'
- --header-lines
Number of header lines in BED.
-Default: 1
+Default: 1
- -v, --verbose
Enable verbose mode to display detailed processing information.
@@ -844,8 +842,7 @@ Named Arguments
end-motifs#
Measures frequency of k-mer 5’ end motifs.
-finaletoolkit end-motifs [-h] [-k K] [-min MIN_LENGTH] [-max MAX_LENGTH] [-B] [-n] [-o OUTPUT_FILE] [-q QUALITY_THRESHOLD] [-w WORKERS] [-v]
- input_file refseq_file
+finaletoolkit end-motifs [-h] [-k K] [-min MIN_LENGTH] [-max MAX_LENGTH] [-B] [-n] [-o OUTPUT_FILE] [-q QUALITY_THRESHOLD] [-w WORKERS] [-v] input_file refseq_file
@@ -859,43 +856,43 @@ Positional Arguments
-Named Arguments#
+
+Named Arguments#
- -k
Length of k-mer.
-Default: 4
+Default: 4
- -min, --min-length
Minimum length for a fragment to be included.
-Default: 0
+Default: 0
- -max, --max-length
Maximum length for a fragment to be included.
- -B, --no-both-strands
Set flag to only consider one strand for end-motifs.
-Default: True
+Default: True
- -n, --negative-strand
Set flag in conjunction with -B to only consider 5’ end motifs on the negative strand.
-Default: False
+Default: False
- -o, --output-file
TSV to print k-mer frequencies. If “-”, will write to stdout.
-Default: “-”
+Default: '-'
- -q, --quality-threshold
Minimum mapping quality threshold.
-Default: 20
+Default: 20
- -w, --workers
Number of worker processes.
-Default: 1
+Default: 1
- -v, --verbose
Enable verbose mode to display detailed processing information.
-Default: 0
+Default: 0
@@ -903,8 +900,7 @@ Named Arguments
interval-end-motifs#
Measures frequency of k-mer 5’ end motifs in each region specified in a BED file and writes data into a table.
-finaletoolkit interval-end-motifs [-h] [-k K] [-min MIN_LENGTH] [-max MAX_LENGTH] [-lo MIN_LENGTH] [-hi MAX_LENGTH] [-B] [-n] [-o OUTPUT_FILE]
- [-q QUALITY_THRESHOLD] [-w WORKERS] [-v]
+finaletoolkit interval-end-motifs [-h] [-k K] [-min MIN_LENGTH] [-max MAX_LENGTH] [-lo MIN_LENGTH] [-hi MAX_LENGTH] [-B] [-n] [-o OUTPUT_FILE] [-q QUALITY_THRESHOLD] [-w WORKERS] [-v]
input_file refseq_file intervals
@@ -922,16 +918,16 @@ Positional Arguments
-Named Arguments#
+
+Named Arguments#
- -k
Length of k-mer.
-Default: 4
+Default: 4
- -min, --min-length
Minimum length for a fragment to be included.
-Default: 0
+Default: 0
- -max, --max-length
Maximum length for a fragment to be included.
@@ -944,27 +940,27 @@ Named Arguments
- -B, --single-strand
Set flag to only consider one strand for end-motifs. By default, the positive strand is calculated, but with the -n flag, the 5’ end motifs of the negative strand are considered instead.
-Default: True
+Default: True
- -n, --negative-strand
Set flag in conjunction with -B to only consider 5’ end motifs on the negative strand.
-Default: False
+Default: False
- -o, --output-file
Path to TSV or CSV file to write end motif frequencies to.
-Default: “-”
+Default: '-'
- -q, --quality-threshold
Minimum mapping quality threshold.
-Default: 20
+Default: 20
- -w, --workers
Number of worker processes.
-Default: 1
+Default: 1
- -v, --verbose
Enable verbose mode to display detailed processing information.
-Default: 0
+Default: 0
@@ -980,20 +976,20 @@ Positional Arguments
- file_path
Tab-delimited or similar file containing one column for all k-mers a one column for frequency. Reads from stdin by default.
-Default: “-”
+Default: '-'
-Named Arguments#
+
+Named Arguments#
- -s, --sep
Separator used in tabular file.
-Default: “ “
+Default: ' '
- --header
Number of header rows to ignore. Default is 0
-Default: 0
+Default: 0
@@ -1009,24 +1005,24 @@ Positional Arguments
- file_path
Tab-delimited or similar file containing one column for all k-mers a one column for frequency. Reads from stdin by default.
-Default: “-”
+Default: '-'
- file_out
Path to the output BED/BEDGraph file containing MDS for each interval.
-Default: “-”
+Default: '-'
-
-Named Arguments#
+
+Named Arguments#
- -s, --sep
Separator used in tabular file.
-Default: “ “
+Default: ' '
- --header
Number of header rows to ignore. Default is 0
-Default: 0
+Default: 0
@@ -1034,8 +1030,8 @@ Named Arguments
filter-file#
Filters a BED/BAM/CRAM file so that all reads/intervals, when applicable,are in mapped pairs, exceed a certain MAPQ, are not flagged for quality, are read1, are not secondary or supplementary alignments, are within/excluding specified intervals, and are on the same reference sequence as the mate.
-finaletoolkit filter-file [-h] [-W WHITELIST_FILE] [-B BLACKLIST_FILE] [-o OUTPUT_FILE] [-q QUALITY_THRESHOLD] [-min MIN_LENGTH] [-max MAX_LENGTH]
- [-lo MIN_LENGTH] [-hi MAX_LENGTH] [-w WORKERS] [-v]
+finaletoolkit filter-file [-h] [-W WHITELIST_FILE] [-B BLACKLIST_FILE] [-o OUTPUT_FILE] [-q QUALITY_THRESHOLD] [-min MIN_LENGTH] [-max MAX_LENGTH] [-p {midpoint,any}] [-lo MIN_LENGTH]
+ [-hi MAX_LENGTH] [-w WORKERS] [-v]
input_file
@@ -1047,8 +1043,8 @@ Positional Arguments
-Named Arguments#
+
+Named Arguments#
- -W, --whitelist-file
Only output alignments overlapping the intervals in this BED file will be included.
@@ -1058,11 +1054,11 @@ Named Arguments
- -o, --output-file
Output BED/BAM/CRAM file path.
-Default: “-”
+Default: '-'
- -q, --quality-threshold
Minimum mapping quality threshold.
-Default: 30
+Default: 30
- -min, --min-length
Minimum length for a fragment to be included.
@@ -1070,6 +1066,11 @@ Named Arguments-max, --max-length
Maximum length for a fragment to be included.
- -p, --intersect-policy
+Possible choices: midpoint, any
+Specifies what policy is used to include/exclude fragments in the given interval. See User Guide for more information.
+Default: 'midpoint'
+- -lo, --fraction-low
Deprecated alias for –min-length
Named Arguments
- -w, --workers
Number of worker processes.
-Default: 1
+Default: 1
- -v, --verbose
Enable verbose mode to display detailed processing information.
@@ -1105,20 +1106,20 @@ Positional Arguments
-Named Arguments#
+
+Named Arguments#
- -o, --output-file
A wiggle file containing the aggregate signal over the intervals specified in interval file.
-Default: “-”
+Default: '-'
- -m, --median-window-size
Size of the median filter window used to aggregate scores. Set to 120 if aggregating WPS signals.
-Default: 1
+Default: 1
- -a, --mean
use mean instead
-Default: False
+Default: False
- -v, --verbose
Enable verbose mode to display detailed processing information.
@@ -1196,76 +1197,76 @@ Positional Arguments