def do_count(args, alignment_parser):
"""Count the number and density covering each merged gene in an annotation made made using the `generate` subcommand).
Parameters
----------
args : :py:class:`argparse.Namespace`
command-line arguments for ``count`` subprogram
"""
# we expect many zero-lenght segmentchains, so turn these off for now
warnings.filterwarnings(
"ignore",
".*zero-length SegmentChain.*",
)
keys = ("exon", "utr5", "cds", "utr3")
column_order = ["region"]
gene_positions = read_pl_table(args.position_file)
# read count files
ga = alignment_parser.get_genome_array_from_args(args, printer=printer)
total_counts = ga.sum()
normconst = 1000.0 * 1e6 / total_counts
printer.write("Dataset has %s counts in it." % total_counts)
printer.write("Tallying genes ...")
dtmp = {"region": []}
for x in keys:
for y in ("reads", "length", "rpkm"):
label = "%s_%s" % (x, y)
dtmp[label] = []
column_order.append(label)
for i, name in enumerate(gene_positions["region"]):
dtmp["region"].append(name)
if i % 500 == 0:
printer.write("Processed %s genes ..." % i)
for k in keys:
ivc = SegmentChain.from_str(gene_positions[k][i])
total = sum(ivc.get_counts(ga))
length = ivc.length
rpkm = (normconst * total / length) if length > 0 else numpy.nan
dtmp["%s_reads" % k].append(total)
dtmp["%s_length" % k].append(length)
dtmp["%s_rpkm" % k].append(rpkm)
fout = argsopener("%s.txt" % args.outbase, args, "w")
dtmp = pd.DataFrame(dtmp)
dtmp.to_csv(fout,
sep="\t",
header=True,
index=False,
columns=column_order,
na_rep="nan",
float_format="%.8f")
fout.close()
printer.write("Done.")
def roi_row_to_cds(row):
"""Helper function to extract coding portions from maximal spanning windows
flanking CDS starts that are created by |metagene| ``generate`` subprogram.
Parameters
----------
row : (int, Series)
Row from a :class:`pandas.DataFrame` of an ROI file made by the |metagene|
``generate`` subprogram
Returns
-------
|SegmentChain|
Coding portion of maximal spanning window
"""
chainstr, alignment_offset, zero_point = row[1][["region","alignment_offset","zero_point"]]
chain = SegmentChain.from_str(chainstr)
cds_start = zero_point - alignment_offset
subchain = chain.get_subchain(cds_start,chain.length)
return subchain
def roi_row_to_cds(row):
"""Helper function to extract coding portions from maximal spanning windows
flanking CDS starts that are created by |metagene| ``generate`` subprogram.
Parameters
----------
row : (int, Series)
Row from a :class:`pandas.DataFrame` of an ROI file made by the |metagene|
``generate`` subprogram
Returns
-------
|SegmentChain|
Coding portion of maximal spanning window
"""
chainstr, alignment_offset, zero_point = row[1][[
"region", "alignment_offset", "zero_point"
]]
chain = SegmentChain.from_str(chainstr)
cds_start = zero_point - alignment_offset
subchain = chain.get_subchain(cds_start, chain.length)
return subchain
],
"YPL249C-A": [
"YPL249C-A:0-53^291-334(-)",
],
'YBR215W_mRNA_0': ['YBR215W_mRNA_0:0-108^192-2175(+)'],
'YHL001W_mRNA_0': ['YHL001W_mRNA_0:0-146^544-961(+)'],
'YIL018W_mRNA_0': ['YIL018W_mRNA_0:0-30^430-1280(+)'],
'YIL133C_mRNA_0': ['YIL133C_mRNA_0:0-648^938-1007(-)'],
'YIL156W_B_mRNA_0': ['YIL156W_B_mRNA_0:0-41^103-408(+)'],
'YKL006W_mRNA_0': ['YKL006W_mRNA_0:0-157^555-954(+)'],
'YMR194C_B_mRNA_0': ['YMR194C_B_mRNA_0:0-325^397-729(-)'],
'YNL130C_mRNA_0': ['YNL130C_mRNA_0:0-1204^1296-1382(-)'],
'YPL249C_A_mRNA_0': ['YPL249C_A_mRNA_0:0-415^653-697(-)'],
}
known_juncs = {
K: [SegmentChain.from_str(X) for X in V]
for K, V in known_juncs.items()
}
"""Annotated splice junctions"""
all_known_juncs = []
for v in known_juncs.values():
all_known_juncs.extend(v)
known_juncs_as_tuples = {
"YNL130C": [
("YNL130C", 53, 145, "-"),
],
"YPL249C-A": [
("YPL249C-A", 53, 291, "-"),
],
def do_count(roi_table,ga,norm_start,norm_end,min_counts,min_len,max_len,aggregate=False,printer=NullWriter()):
"""Calculate a :term:`metagene profile` for each read length in the dataset
Parameters
----------
roi_table : :class:`pandas.DataFrame`
Table specifying regions of interest, generated
by :py:func:`plastid.bin.metagene.do_generate`
ga : |BAMGenomeArray|
Count data
norm_start : int
Coordinate in window specifying normalization region start
norm_end : int
Coordinate in window specifying normalization region end
min_counts : float
Minimum number of counts in `window[norm_start:norm_end]`
required for inclusion in metagene profile
min_len : int
Minimum read length to include
max_len : int
Maximum read length to include
aggregate : bool, optional
Estimate P-site from aggregate reads at each position, instead of median
normalized read density. Potentially noisier, but helpful for lower-count
data or read lengths with few counts. (Default: False)
printer : file-like, optional
filehandle to write logging info to (Default: :func:`~plastid.util.io.openers.NullWriter`)
Returns
-------
dict
Dictionary of :class:`numpy.ndarray` s of raw counts at each position (column)
for each window (row)
dict
Dictionary of :class:`numpy.ndarray` s of normalized counts at each position (column)
for each window (row), normalized by the total number of counts in that row
from `norm_start` to `norm_end`
:class:`pandas.DataFrame`
Metagene profile of median normalized counts at each position across
all windows, and the number of windows included in the calculation of each
median, stratified by read length
"""
window_size = roi_table["window_size"][0]
upstream_flank = roi_table["zero_point"][0]
raw_count_dict = OrderedDict()
norm_count_dict = OrderedDict()
shape = (len(roi_table),window_size)
for i in range(min_len,max_len+1):
# mask all by default
raw_count_dict[i] = numpy.ma.MaskedArray(numpy.tile(numpy.nan,shape),
mask=numpy.tile(True,shape),
dtype=float)
for i,row in roi_table.iterrows():
if i % 1000 == 0:
printer.write("Counted %s ROIs ..." % (i+1))
roi = SegmentChain.from_str(row["region"])
mask = SegmentChain.from_str(row["masked"])
roi.add_masks(*mask)
valid_mask = roi.get_masked_counts(ga).mask
offset = int(round((row["alignment_offset"])))
assert offset + roi.length <= window_size
count_vectors = {}
for k in raw_count_dict:
count_vectors[k] = []
for seg in roi:
reads = ga.get_reads(seg)
read_dict = {}
for k in raw_count_dict:
read_dict[k] = []
for read in filter(lambda x: len(x.positions) in read_dict,reads):
read_dict[len(read.positions)].append(read)
for k in read_dict:
count_vector = ga.map_fn(read_dict[k],seg)[1]
count_vectors[k].extend(count_vector)
for k in raw_count_dict:
if roi.strand == "-":
count_vectors[k] = count_vectors[k][::-1]
raw_count_dict[k].data[i,offset:offset+roi.length] = numpy.array(count_vectors[k])
raw_count_dict[k].mask[i,offset:offset+roi.length] = valid_mask
profile_table = { "x" : numpy.arange(-upstream_flank,window_size-upstream_flank) }
printer.write("Counted %s ROIs total." % (i+1))
for k in raw_count_dict:
k_raw = raw_count_dict[k]
denominator = numpy.nansum(k_raw[:,norm_start:norm_end],axis=1)
norm_count_dict[k] = (k_raw.T.astype(float) / denominator).T
# copy mask from raw counts, then add nans and infs
norm_counts = numpy.ma.MaskedArray(norm_count_dict[k],
mask=k_raw.mask)
norm_counts.mask[numpy.isnan(norm_counts)] = True
norm_counts.mask[numpy.isinf(norm_counts)] = True
with warnings.catch_warnings():
# ignore numpy mean of empty slice warning, given by numpy in Python 2.7-3.4
warnings.filterwarnings("ignore",".*mean of empty.*",RuntimeWarning)
try:
if aggregate == False:
profile = numpy.ma.median(norm_counts[denominator >= min_counts],axis=0)
else:
profile = numpy.nansum(k_raw[denominator >= min_counts],axis=0)
# in numpy under Python3.5, this is an IndexError instead of a warning
except IndexError:
profile = numpy.zeros_like(profile_table["x"],dtype=float)
# in new versions of numpy, this is a ValueEror instead of an IndexError
except ValueError:
profile = numpy.zeros_like(profile_table["x"],dtype=float)
num_genes = ((~norm_counts.mask)[denominator >= min_counts]).sum(0)
profile_table["%s-mers" % k] = profile
profile_table["%s_regions_counted" % k] = num_genes
profile_table = pd.DataFrame(profile_table)
return raw_count_dict, norm_count_dict, profile_table
known_juncs = {
"YNL130C" : ["YNL130C:0-53^145-180(-)",],
"YPL249C-A" : ["YPL249C-A:0-53^291-334(-)",],
'YBR215W_mRNA_0' : ['YBR215W_mRNA_0:0-108^192-2175(+)'],
'YHL001W_mRNA_0' : ['YHL001W_mRNA_0:0-146^544-961(+)'],
'YIL018W_mRNA_0' : ['YIL018W_mRNA_0:0-30^430-1280(+)'],
'YIL133C_mRNA_0' : ['YIL133C_mRNA_0:0-648^938-1007(-)'],
'YIL156W_B_mRNA_0': ['YIL156W_B_mRNA_0:0-41^103-408(+)'],
'YKL006W_mRNA_0' : ['YKL006W_mRNA_0:0-157^555-954(+)'],
'YMR194C_B_mRNA_0': ['YMR194C_B_mRNA_0:0-325^397-729(-)'],
'YNL130C_mRNA_0' : ['YNL130C_mRNA_0:0-1204^1296-1382(-)'],
'YPL249C_A_mRNA_0': ['YPL249C_A_mRNA_0:0-415^653-697(-)'],
}
known_juncs = { K : [SegmentChain.from_str(X) for X in V] for K,V in known_juncs.items() }
"""Annotated splice junctions"""
all_known_juncs = []
for v in known_juncs.values():
all_known_juncs.extend(v)
known_juncs_as_tuples = {
"YNL130C" : [("YNL130C",53,145,"-"),],
"YPL249C-A" : [("YPL249C-A",53,291,"-"),],
'YBR215W_mRNA_0' : [('YBR215W_mRNA_0',108,192,'+'),],
'YHL001W_mRNA_0' : [('YHL001W_mRNA_0',146,544,'+'),],
'YIL018W_mRNA_0' : [('YIL018W_mRNA_0',30,430,'+'),],
'YIL133C_mRNA_0' : [('YIL133C_mRNA_0',648,938,'-'),],
'YIL156W_B_mRNA_0': [('YIL156W_B_mRNA_0',41,103,'+'),],
def check_window(tx_ivc,
known_roi,
known_offset,
known_ref_point,
flank_up,
flank_down,
test_method,
test_name,
ref_delta=0):
"""Helper function to test output of window landmark functions
Parameters
----------
tx_ivc : |SegmentChain|
Test Transcript from which window will be derived
known_roi : |SegmentChain|
Reference output for ROI
known_offset : int
Known offset to start of ROI
known_ref_point : (str,int,str) or numpy.nan
Known offset to landmark in ROI as ("chromosome_name",position,"strand")
flank_up : int
Flank upstream of landmark to include in ROI
flank_down : int
Flank downstream of landmark to include in ROI
test_method : function
Function to test (e.g. :py:func:`window_cds_start`, py:func:`window_cds_stop`)
test_name : str
Name of test (for generating rich error output)
ref_delta : int, optional
Distance from reference landmark at which to center windows
"""
err_str = ("Failed %s on %s (strand: '%s', up: %s, down: %s). " %
(test_name, str(tx_ivc), tx_ivc.spanning_segment.strand,
flank_up, flank_down)) + "%s unequal (%s vs %s)"
test_roi, test_offset, test_ref_point = test_method(tx_ivc,
flank_up,
flank_down,
ref_delta=ref_delta)
check_equality(SegmentChain.from_str(known_roi), test_roi)
# if no landmark
if numpy.isnan(known_offset) or isinstance(
known_ref_point, float) and numpy.isnan(known_ref_point):
assert_true(numpy.isnan(test_offset),
msg=err_str % ("offset", known_offset, test_offset))
assert_true(numpy.isnan(test_ref_point),
msg=err_str %
("ref_point", known_ref_point, test_ref_point))
# if landmark
else:
assert_equal(known_offset,
test_offset,
msg=err_str % ("offset", known_offset, test_offset))
assert_equal(known_ref_point,
test_ref_point,
msg=err_str %
("ref_point", known_ref_point, test_ref_point))
def check_maximal_window(test_name, genome_hash, test_group, result_groups,
flank_up, flank_down):
"""
test_name : str
Descriptive name of test
genome_hash : GenomeHash
Mask hash
test_group : list
List of transcript IDs, referring to transcripts in the GFF text above
result_groups : list
list of tuples of (region_str, aligment_offset, window_length) expected from
maximal spanning window output
flank_up : int
Bases to include upstream of landmark in window
flank_down : int
bases to include downstream of landmark in window
"""
# table keys:
# gene_id
# window_size
# roi
# masked
# alignment_offset
# zero_point
err_str = ("Failed %s (up: %s, down: %s). " %
(test_name, flank_up, flank_down)) + "%s unequal (%s vs %s)"
tx_ivcs = (_TRANSCRIPTS[X] for X in test_group)
roi_table = group_regions_make_windows(tx_ivcs, genome_hash, flank_up,
flank_down, window_cds_start)
roi_table.sort(columns=["region"], inplace=True)
trows = [X[1] for X in roi_table.iterrows()]
result_groups = sorted(result_groups, key=lambda x: x[0])
REGION = 0
c = 0
for n, result_group in enumerate(result_groups):
# if no landmark
if numpy.isnan(result_group[1]) or numpy.isnan(result_group[2]):
c += 1 # increment counter for input that will have no output
# if landmark
else:
check_equality(SegmentChain.from_str(result_group[0]),
SegmentChain.from_str(trows[n - c]["region"]),
test_name)
assert_equal(
result_group[1],
trows[n - c]["alignment_offset"],
msg=err_str %
("offset", result_group[1], trows[n - c]["alignment_offset"]))
assert_equal(
result_group[2],
trows[n - c]["zero_point"],
msg=err_str %
("ref_point", result_group[1], trows[n - c]["zero_point"]))
if len(result_group) == 4:
assert_equal(result_group[3],
trows[n - c]["masked"],
msg=err_str %
("mask", result_group[3], trows[n - c]["masked"]))
assert_equal(n + 1 - c, len(roi_table))
crossmap = GenomeHash(_MASKS)
for flank_up, flank_down in _FLANKS:
for test_name, test_group in _DO_GENERATE_MAX_WINDOW.items():
result_group = _DO_GENERATE_MAX_WINDOW_RESULTS_MASKED[
"%s_%s_%s" % (test_name, flank_up, flank_down)]
yield check_maximal_window, test_name, crossmap, test_group, [
result_group
], flank_up, flank_down
#===============================================================================
# INDEX: test data
#===============================================================================
_MASKS = [
SegmentChain.from_str("2L:7985694-7985744(+)"),
SegmentChain.from_str("3R:4519879-4519891(-)"),
SegmentChain.from_str("4:50-50000(+)"),
]
_TRANSCRIPTS_GFF = """##gff-version 3
3R FlyBase mRNA 4517211 4523544 . - . ID=FBtr0081950;Name=hb-RB;Parent=FBgn0001180;Alias=FBtr0002097,FBtr0002098,CG9786-RB,hb[+]R2.8;Dbxref=FlyBase_Annotation_IDs:CG9786-RB,REFSEQ:NM_169234;score_text=Strongly Supported;score=11
3R FlyBase exon 4517211 4519894 . - . Name=hb:2;Parent=FBtr0081950;parent_type=mRNA
3R FlyBase CDS 4517600 4519876 . - 0 Name=hb-cds;Parent=FBtr0081950;parent_type=mRNA
3R FlyBase exon 4523048 4523544 . - . Name=hb:4;Parent=FBtr0081950;parent_type=mRNA
3R FlyBase mRNA 4516702 4520322 . - . ID=FBtr0081951;Name=hb-RA;Parent=FBgn0001180;Alias=FBtr0002096,FBtr0002097,CG9786-RA,hb[+]R3.2;Dbxref=FlyBase_Annotation_IDs:CG9786-RA,REFSEQ:NM_169233;score_text=Strongly Supported;score=11
3R FlyBase exon 4516702 4519894 . - . Name=hb:1;Parent=FBtr0081951;parent_type=mRNA
3R FlyBase CDS 4517600 4519876 . - 0 Name=hb-cds;Parent=FBtr0081951;parent_type=mRNA
3R FlyBase exon 4520178 4520322 . - . Name=hb:3;Parent=FBtr0081951;parent_type=mRNA
],
"YPL249C-A": [
"YPL249C-A:0-53^291-334(-)",
],
'YBR215W_mRNA_0': ['YBR215W_mRNA_0:0-108^192-2175(+)'],
'YHL001W_mRNA_0': ['YHL001W_mRNA_0:0-146^544-961(+)'],
'YIL018W_mRNA_0': ['YIL018W_mRNA_0:0-30^430-1280(+)'],
'YIL133C_mRNA_0': ['YIL133C_mRNA_0:0-648^938-1007(-)'],
'YIL156W_B_mRNA_0': ['YIL156W_B_mRNA_0:0-41^103-408(+)'],
'YKL006W_mRNA_0': ['YKL006W_mRNA_0:0-157^555-954(+)'],
'YMR194C_B_mRNA_0': ['YMR194C_B_mRNA_0:0-325^397-729(-)'],
'YNL130C_mRNA_0': ['YNL130C_mRNA_0:0-1204^1296-1382(-)'],
'YPL249C_A_mRNA_0': ['YPL249C_A_mRNA_0:0-415^653-697(-)'],
}
known_juncs = {
K: [SegmentChain.from_str(X) for X in V]
for K, V in known_juncs.items()
}
"""Annotated splice junctions"""
known_juncs_tuples = {
"YNL130C": [
("YNL130C", 53, 145, "-"),
],
"YPL249C-A": [
("YPL249C-A", 53, 291, "-"),
],
'YBR215W_mRNA_0': [
('YBR215W_mRNA_0', 108, 192, '+'),
],
'YHL001W_mRNA_0': [
known_juncs = {
"YNL130C" : ["YNL130C:0-53^145-180(-)",],
"YPL249C-A" : ["YPL249C-A:0-53^291-334(-)",],
'YBR215W_mRNA_0' : ['YBR215W_mRNA_0:0-108^192-2175(+)'],
'YHL001W_mRNA_0' : ['YHL001W_mRNA_0:0-146^544-961(+)'],
'YIL018W_mRNA_0' : ['YIL018W_mRNA_0:0-30^430-1280(+)'],
'YIL133C_mRNA_0' : ['YIL133C_mRNA_0:0-648^938-1007(-)'],
'YIL156W_B_mRNA_0': ['YIL156W_B_mRNA_0:0-41^103-408(+)'],
'YKL006W_mRNA_0' : ['YKL006W_mRNA_0:0-157^555-954(+)'],
'YMR194C_B_mRNA_0': ['YMR194C_B_mRNA_0:0-325^397-729(-)'],
'YNL130C_mRNA_0' : ['YNL130C_mRNA_0:0-1204^1296-1382(-)'],
'YPL249C_A_mRNA_0': ['YPL249C_A_mRNA_0:0-415^653-697(-)'],
}
known_juncs = { K : [SegmentChain.from_str(X) for X in V] for K,V in known_juncs.items() }
"""Annotated splice junctions"""
known_juncs_tuples = {
"YNL130C" : [("YNL130C",53,145,"-"),],
"YPL249C-A" : [("YPL249C-A",53,291,"-"),],
'YBR215W_mRNA_0' : [('YBR215W_mRNA_0',108,192,'+'),],
'YHL001W_mRNA_0' : [('YHL001W_mRNA_0',146,544,'+'),],
'YIL018W_mRNA_0' : [('YIL018W_mRNA_0',30,430,'+'),],
'YIL133C_mRNA_0' : [('YIL133C_mRNA_0',648,938,'-'),],
'YIL156W_B_mRNA_0': [('YIL156W_B_mRNA_0',41,103,'+'),],
'YKL006W_mRNA_0' : [('YKL006W_mRNA_0',157,555,'+'),],
'YMR194C_B_mRNA_0': [('YMR194C_B_mRNA_0',325,397,'-'),],
'YNL130C_mRNA_0' : [('YNL130C_mRNA_0',1204,1296,'-'),],
'YPL249C_A_mRNA_0': [('YPL249C_A_mRNA_0',415,653,'-'),],
