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Prepend chromosomes with chr to match the SAM/BAM files. #132

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Prepend chromosomes with chr to match the SAM/BAM files. #132

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2 changes: 1 addition & 1 deletion chanjo/annotator/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
from __future__ import absolute_import

from .cli import annotate
from .core import annotate_bed_stream
from .core import annotate_bed_stream, apply_bed_stream
from .stages import (
assign_relative_positions,
calculate_metrics,
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50 changes: 37 additions & 13 deletions chanjo/annotator/core.py
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Expand Up @@ -22,17 +22,15 @@
)
from ..utils import bed_to_interval, split, validate_bed_format


def annotate_bed_stream(bed_stream, bam_path, cutoff=10, extension=0,
contig_prefix='', bp_threshold=17000):
"""Annotate all intervals from a BED-file stream.

Yields tuple data for each interval with calculated coverage and
completeness.

def apply_bed_stream(bed_stream, bam_path, fn, extension=0,
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This is a nice addition!

contig_prefix='', bp_threshold=17000):
"""Maps a function to all intervals of a BED stream
Args:
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Would be awesome with a simple description of the fn argument here!

bed_stream (sequence): usually a BED-file handle to read from
bam_path (str): path to BAM-file
fn: function that takes a list of intervals and read depths
and computes a summary statistic over them. See
annotator.stages.calculate_metrics for an example.
cutoff (int, optional): threshold for completeness calculation,
defaults to 10
extension (int, optional): number of bases to extend each interval
Expand All @@ -41,10 +39,6 @@ def annotate_bed_stream(bed_stream, bam_path, cutoff=10, extension=0,
defaults to empty string
bp_threshold (int, optional): optimization threshold for reading
BAM-file in chunks, default to 17000

Yields:
tuple: :class:`chanjo.BaseInterval`, coverage (float), and
completeness (float)
"""
# setup: connect to BAM-file
bam = BamFile(bam_path)
Expand All @@ -62,5 +56,35 @@ def annotate_bed_stream(bed_stream, bam_path, cutoff=10, extension=0,
group_intervals(bp_threshold=bp_threshold), # group by threshold
map(process_interval_group(bam)), # read coverage
concat, # flatten list of lists
map(calculate_metrics(threshold=cutoff)) # calculate cov./compl.
map(fn) # map provided function
)


def annotate_bed_stream(bed_stream, bam_path, cutoff=10, extension=0,
contig_prefix='', bp_threshold=17000):
"""Annotate all intervals from a BED-file stream.

Yields tuple data for each interval with calculated coverage and
completeness.

Args:
bed_stream (sequence): usually a BED-file handle to read from
bam_path (str): path to BAM-file
cutoff (int, optional): threshold for completeness calculation,
defaults to 10
extension (int, optional): number of bases to extend each interval
with (+/-), defaults to 0
contig_prefix (str, optional): rename contigs by prefixing,
defaults to empty string
bp_threshold (int, optional): optimization threshold for reading
BAM-file in chunks, default to 17000

Yields:
tuple: :class:`chanjo.BaseInterval`, coverage (float), and
completeness (float)
"""
# setup: connect to BAM-file
fn = calculate_metrics(threshold=cutoff)

return apply_bed_stream(bed_stream, bam_path, fn, extension,
contig_prefix, bp_threshold)
12 changes: 6 additions & 6 deletions chanjo/demo/files/CCDS.mini.txt
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@@ -1,7 +1,7 @@
#chromosome nc_accession gene gene_id ccds_id ccds_status cds_strand cds_from cds_to cds_locations match_type
1 NC_000001.8 LINC00115 79854 CCDS1.1 Withdrawn - 801942 802433 [801942-802433] Identical
1 NC_000001.10 SAMD11 148398 CCDS2.2 Public + 11 35 [11-18, 25-30, 32-35] Identical
22 NC_000022.10 RFPL2 10739 CCDS54521.1 Public - 32586758 32589173 [32586758-32587338, 32588888-32589173] Identical
22 NC_000022.10 RFPL2 10739 CCDS46694.1 Public - 32586758 32589260 [32586758-32587338, 32588888-32589260] Identical
X NC_000023.10 TRO 7216 CCDS59529.1 Public + 54951423 54957452 [54951423-54951500, 54952024-54952115, 54952842-54952921, 54953015-54953057, 54953475-54953537, 54954099-54954213, 54955035-54957452] Identical
Y NC_000024.9 TSPY8 728403 CCDS59533.1 Public + 9195451 9198013 [9195451-9195936, 9196544-9196621, 9196750-9196861, 9196963-9197108, 9197215-9197296, 9197991-9198013] Identical
chr1 NC_000001.8 LINC00115 79854 CCDS1.1 Withdrawn - 801942 802433 [801942-802433] Identical
chr1 NC_000001.10 SAMD11 148398 CCDS2.2 Public + 11 35 [11-18, 25-30, 32-35] Identical
chr22 NC_000022.10 RFPL2 10739 CCDS54521.1 Public - 32586758 32589173 [32586758-32587338, 32588888-32589173] Identical
chr22 NC_000022.10 RFPL2 10739 CCDS46694.1 Public - 32586758 32589260 [32586758-32587338, 32588888-32589260] Identical
chrX NC_000023.10 TRO 7216 CCDS59529.1 Public + 54951423 54957452 [54951423-54951500, 54952024-54952115, 54952842-54952921, 54953015-54953057, 54953475-54953537, 54954099-54954213, 54955035-54957452] Identical
chrY NC_000024.9 TSPY8 728403 CCDS59533.1 Public + 9195451 9198013 [9195451-9195936, 9196544-9196621, 9196750-9196861, 9196963-9197108, 9197215-9197296, 9197991-9198013] Identical
38 changes: 19 additions & 19 deletions tests/fixtures/CCDS.mini.bed
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@@ -1,19 +1,19 @@
1 11 18 1-11-18 0 + CCDS2.2 SAMD11
1 25 30 1-25-30 0 + CCDS2.2 SAMD11
1 32 35 1-32-35 0 + CCDS2.2 SAMD11
22 32586758 32587338 22-32586758-32587338 0 - CCDS54521.1,CCDS46694.1 RFPL2,RFPL2
22 32588888 32589260 22-32588888-32589260 0 - CCDS46694.1 RFPL2
22 32588888 32589173 22-32588888-32589173 0 - CCDS54521.1 RFPL2
X 54951423 54951500 X-54951423-54951500 0 + X-CCDS59529.1 X-TRO
X 54952024 54952115 X-54952024-54952115 0 + X-CCDS59529.1 X-TRO
X 54952842 54952921 X-54952842-54952921 0 + X-CCDS59529.1 X-TRO
X 54953015 54953057 X-54953015-54953057 0 + X-CCDS59529.1 X-TRO
X 54953475 54953537 X-54953475-54953537 0 + X-CCDS59529.1 X-TRO
X 54954099 54954213 X-54954099-54954213 0 + X-CCDS59529.1 X-TRO
X 54955035 54957452 X-54955035-54957452 0 + X-CCDS59529.1 X-TRO
Y 9195451 9195936 Y-9195451-9195936 0 + Y-CCDS59533.1 Y-TSPY8
Y 9196544 9196621 Y-9196544-9196621 0 + Y-CCDS59533.1 Y-TSPY8
Y 9196750 9196861 Y-9196750-9196861 0 + Y-CCDS59533.1 Y-TSPY8
Y 9196963 9197108 Y-9196963-9197108 0 + Y-CCDS59533.1 Y-TSPY8
Y 9197215 9197296 Y-9197215-9197296 0 + Y-CCDS59533.1 Y-TSPY8
Y 9197991 9198013 Y-9197991-9198013 0 + Y-CCDS59533.1 Y-TSPY8
chr1 11 18 1-11-18 0 + CCDS2.2 SAMD11
chr1 25 30 1-25-30 0 + CCDS2.2 SAMD11
chr1 32 35 1-32-35 0 + CCDS2.2 SAMD11
chr22 32586758 32587338 22-32586758-32587338 0 - CCDS54521.1,CCDS46694.1 RFPL2,RFPL2
chr22 32588888 32589260 22-32588888-32589260 0 - CCDS46694.1 RFPL2
chr22 32588888 32589173 22-32588888-32589173 0 - CCDS54521.1 RFPL2
chrX 54951423 54951500 X-54951423-54951500 0 + X-CCDS59529.1 X-TRO
chrX 54952024 54952115 X-54952024-54952115 0 + X-CCDS59529.1 X-TRO
chrX 54952842 54952921 X-54952842-54952921 0 + X-CCDS59529.1 X-TRO
chrX 54953015 54953057 X-54953015-54953057 0 + X-CCDS59529.1 X-TRO
chrX 54953475 54953537 X-54953475-54953537 0 + X-CCDS59529.1 X-TRO
chrX 54954099 54954213 X-54954099-54954213 0 + X-CCDS59529.1 X-TRO
chrX 54955035 54957452 X-54955035-54957452 0 + X-CCDS59529.1 X-TRO
chrY 9195451 9195936 Y-9195451-9195936 0 + Y-CCDS59533.1 Y-TSPY8
chrY 9196544 9196621 Y-9196544-9196621 0 + Y-CCDS59533.1 Y-TSPY8
chrY 9196750 9196861 Y-9196750-9196861 0 + Y-CCDS59533.1 Y-TSPY8
chrY 9196963 9197108 Y-9196963-9197108 0 + Y-CCDS59533.1 Y-TSPY8
chrY 9197215 9197296 Y-9197215-9197296 0 + Y-CCDS59533.1 Y-TSPY8
chrY 9197991 9198013 Y-9197991-9198013 0 + Y-CCDS59533.1 Y-TSPY8
38 changes: 19 additions & 19 deletions tests/fixtures/CCDS.mini.coverage.bed
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@@ -1,20 +1,20 @@
#{"group_id": null, "sample_id": "tiriwiro", "coverage_source": "/Users/robinandeer/Projects/clinical-genomics/qxt/bam/Sample_E2-QXT-prep2/sorted.bam", "cutoff": 10, "extension": 0}
1 12 18 1-11-18 0 + CCDS2.2 SAMD11 0.0 0.0
1 26 30 1-25-30 0 + CCDS2.2 SAMD11 0.0 0.0
1 33 35 1-32-35 0 + CCDS2.2 SAMD11 0.0 0.0
22 32586759 32587338 22-32586758-32587338 0 - CCDS54521.1,CCDS46694.1 RFPL2,RFPL2 139.862068966 1.0
22 32588889 32589260 22-32588888-32589260 0 - CCDS46694.1 RFPL2 146.86827957 1.0
22 32588889 32589173 22-32588888-32589173 0 - CCDS54521.1 RFPL2 140.631578947 1.0
X 54951424 54951500 X-54951423-54951500 0 + X-CCDS59529.1 X-TRO 13.8961038961 1.0
X 54952025 54952115 X-54952024-54952115 0 + X-CCDS59529.1 X-TRO 81.5714285714 1.0
X 54952843 54952921 X-54952842-54952921 0 + X-CCDS59529.1 X-TRO 37.7974683544 1.0
X 54953016 54953057 X-54953015-54953057 0 + X-CCDS59529.1 X-TRO 13.0714285714 0.9523809523809523
X 54953476 54953537 X-54953475-54953537 0 + X-CCDS59529.1 X-TRO 19.5 1.0
X 54954100 54954213 X-54954099-54954213 0 + X-CCDS59529.1 X-TRO 23.5350877193 1.0
X 54955036 54957452 X-54955035-54957452 0 + X-CCDS59529.1 X-TRO 43.4224244932 1.0
Y 9195452 9195936 Y-9195451-9195936 0 + Y-CCDS59533.1 Y-TSPY8 0.0 0.0
Y 9196545 9196621 Y-9196544-9196621 0 + Y-CCDS59533.1 Y-TSPY8 0.0 0.0
Y 9196751 9196861 Y-9196750-9196861 0 + Y-CCDS59533.1 Y-TSPY8 0.0 0.0
Y 9196964 9197108 Y-9196963-9197108 0 + Y-CCDS59533.1 Y-TSPY8 0.0 0.0
Y 9197216 9197296 Y-9197215-9197296 0 + Y-CCDS59533.1 Y-TSPY8 0.0 0.0
Y 9197992 9198013 Y-9197991-9198013 0 + Y-CCDS59533.1 Y-TSPY8 0.0 0.0
chr1 12 18 1-11-18 0 + CCDS2.2 SAMD11 0.0 0.0
chr1 26 30 1-25-30 0 + CCDS2.2 SAMD11 0.0 0.0
chr1 33 35 1-32-35 0 + CCDS2.2 SAMD11 0.0 0.0
chr22 32586759 32587338 22-32586758-32587338 0 - CCDS54521.1,CCDS46694.1 RFPL2,RFPL2 139.862068966 1.0
chr22 32588889 32589260 22-32588888-32589260 0 - CCDS46694.1 RFPL2 146.86827957 1.0
chr22 32588889 32589173 22-32588888-32589173 0 - CCDS54521.1 RFPL2 140.631578947 1.0
chrX 54951424 54951500 X-54951423-54951500 0 + X-CCDS59529.1 X-TRO 13.8961038961 1.0
chrX 54952025 54952115 X-54952024-54952115 0 + X-CCDS59529.1 X-TRO 81.5714285714 1.0
chrX 54952843 54952921 X-54952842-54952921 0 + X-CCDS59529.1 X-TRO 37.7974683544 1.0
chrX 54953016 54953057 X-54953015-54953057 0 + X-CCDS59529.1 X-TRO 13.0714285714 0.9523809523809523
chrX 54953476 54953537 X-54953475-54953537 0 + X-CCDS59529.1 X-TRO 19.5 1.0
chrX 54954100 54954213 X-54954099-54954213 0 + X-CCDS59529.1 X-TRO 23.5350877193 1.0
chrX 54955036 54957452 X-54955035-54957452 0 + X-CCDS59529.1 X-TRO 43.4224244932 1.0
chrY 9195452 9195936 Y-9195451-9195936 0 + Y-CCDS59533.1 Y-TSPY8 0.0 0.0
chrY 9196545 9196621 Y-9196544-9196621 0 + Y-CCDS59533.1 Y-TSPY8 0.0 0.0
chrY 9196751 9196861 Y-9196750-9196861 0 + Y-CCDS59533.1 Y-TSPY8 0.0 0.0
chrY 9196964 9197108 Y-9196963-9197108 0 + Y-CCDS59533.1 Y-TSPY8 0.0 0.0
chrY 9197216 9197296 Y-9197215-9197296 0 + Y-CCDS59533.1 Y-TSPY8 0.0 0.0
chrY 9197992 9198013 Y-9197991-9198013 0 + Y-CCDS59533.1 Y-TSPY8 0.0 0.0