def write_matrix(outfile, matrix):
from genomicode import AnnotationMatrix as AM
if isinstance(matrix, AM.AnnotationMatrix):
AM.write(outfile, matrix)
else:
write_express(outfile, matrix)
def make_matrix(samples, callers, annot_header, annot_data, named_data,
call_data):
# annot_header list of headers for annot_data.
# annot_data list of tuples: chrom, pos, ref, alt[, more]
# named_data list of (name, headers, all_annots)
# call_data list of tuples: chrom, pos, ref, alt, sample, caller, call
# chrom string
# pos int
# ref string
# alt string
# sample string
# caller string
# call Call object
from genomicode import AnnotationMatrix
# Make sure there's no duplicates.
assert annot_header[:4] == ["Chrom", "Pos", "Ref", "Alt"]
seen = {}
for x in annot_data:
x = x[:4]
x = tuple(x)
assert x not in seen, "Duplicate"
seen[x] = 1
# Make annotation matrix.
for x in annot_data:
assert len(x) == len(annot_header)
headers = annot_header
all_annots = []
for i in range(len(headers)):
x = [x[i] for x in annot_data]
all_annots.append(x)
annot_matrix = AnnotationMatrix.create_from_annotations(
headers, all_annots)
# Make named matrices.
named_matrices = []
for x in named_data:
name, headers, all_annots = x
matrix = AnnotationMatrix.create_from_annotations(headers, all_annots)
x = name, matrix
named_matrices.append(x)
# Make call matrix.
call_matrix = SparseCallMatrix(call_data)
return SimpleVariantMatrix(samples, callers, annot_matrix, named_matrices,
call_matrix)
def run(self, network, in_data, out_attributes, user_options, num_cores,
out_filename):
import os
import stat
from genomicode import AnnotationMatrix
# If the file is empty, then just create an empty positions file.
if os.stat(in_data.identifier)[stat.ST_SIZE] == 0:
open(out_filename, 'w')
return
M = AnnotationMatrix.read(in_data.identifier, header_char="##")
# Headers are:
# #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT [Samples...]
# Pull out the #CHROM and POS columns.
assert M.num_headers()
assert M.headers[0] == "#CHROM"
assert M.headers[1] == "POS"
chrom_annots = M["#CHROM"]
pos_annots = M["POS"]
lines = []
seen = {}
for chrom, pos in zip(chrom_annots, pos_annots):
chrom, pos = chrom.strip(), pos.strip()
x = chrom, pos
if x in seen:
continue
seen[x] = 1
x = "\t".join(x) + "\n"
lines.append(x)
open(out_filename, 'w').writelines(lines)
def filter_min_gene_expression_in_every_sample(MATRIX, gxp):
# Gene expression >= 1 in all samples.
from genomicode import AnnotationMatrix
assert type(gxp) is type(0.0)
x = MATRIX.headers
x = [x for x in x if x.startswith("Gene Expression")]
sample_h = x
assert sample_h, 'Missing: "Gene Expression" columns'
I_keep = []
for i in range(MATRIX.num_annots()):
keep = True
for h in sample_h:
if not MATRIX[h][i]:
keep = False
break
# 5.3
# 0,0.379
x = MATRIX[h][i]
x = x.split(",")
x = [float(x) for x in x]
x = max(x)
exp = x
if exp < gxp:
keep = False
break
if not keep:
continue
I_keep.append(i)
x = AnnotationMatrix.rowslice(MATRIX, I_keep)
return x
def filter_min_coverage_in_every_sample(MATRIX, coverage):
from genomicode import AnnotationMatrix
assert type(coverage) is type(0)
x = MATRIX.headers
x = [x for x in x if x.startswith("Coverage")]
sample_h = x
assert sample_h, 'Missing: "Coverage" columns'
I_keep = []
for i in range(MATRIX.num_annots()):
keep = True
for h in sample_h:
if not MATRIX[h][i]:
keep = False
break
# Ref/Alt/VAF
x = MATRIX[h][i]
x = x.split("/")
assert len(x) == 3
cov = int(x[0]) + int(x[1])
if cov < coverage:
keep = False
break
if keep:
I_keep.append(i)
x = AnnotationMatrix.rowslice(MATRIX, I_keep)
return x
def filter_min_callers_in_any_sample(MATRIX, num_callers):
from genomicode import AnnotationMatrix
assert type(num_callers) is type(0)
x = MATRIX.headers
x = [x for x in x if x.startswith("Num Callers")]
callers_h = x
assert callers_h, 'Missing: "Gene Expression" columns'
I_keep = []
for i in range(MATRIX.num_annots()):
keep = False
for h in callers_h:
if not MATRIX[h][i]:
continue
nc = int(MATRIX[h][i])
if nc >= num_callers:
keep = True
break
if keep:
I_keep.append(i)
x = AnnotationMatrix.rowslice(MATRIX, I_keep)
return x
def sort_vcf_file(filename):
from genomicode import vcflib
from genomicode import jmath
from genomicode import AnnotationMatrix
vcf = vcflib.read(filename)
CHROM = vcf.matrix["#CHROM"]
POS = vcf.matrix["POS"]
POS = [int(x) for x in POS]
# Check if POS is sorted. If it's already sorted, then return.
is_sorted = True
for i in range(len(CHROM) - 1):
c1, p1 = CHROM[i], POS[i]
c2, p2 = CHROM[i + 1], POS[i + 1]
if c1 != c2:
continue
if p2 < p1:
is_sorted = False
break
if is_sorted:
return
# Sort by CHROM and POS.
S = ["%s:%d" % (CHROM[i], POS[i]) for i in range(len(CHROM))]
O = jmath.order_list(S, natural=True)
vcf.matrix = AnnotationMatrix.rowslice(vcf.matrix, O)
vcflib.write(filename, vcf)
def add_snpeff_to_svm(svm_file, snpeff_file, outfile):
import shutil
from genomicode import filelib
from genomicode import SimpleVariantMatrix
from genomicode import AnnotationMatrix
if not filelib.exists_nz(snpeff_file):
shutil.copy2(svm_file, outfile)
return
# Read the annotations.
header = None # includes Chrom, Pos, Ref, Alt
coord2d = {}
for d in filelib.read_row(snpeff_file, header=1):
if header is None:
header = d._header
coord = d.Chrom, d.Pos, d.Ref, d.Alt
coord2d[coord] = d
svm = SimpleVariantMatrix.read_as_am(svm_file)
CHROM = svm.header2annots["______Chrom"]
POS = svm.header2annots["______Pos"]
REF = svm.header2annots["______Ref"]
ALT = svm.header2annots["______Alt"]
snpeff_header = header[4:]
snpeff_matrix = [] # Row major.
for i in range(len(CHROM)):
coord = CHROM[i], POS[i], REF[i], ALT[i]
row = [""] * len(snpeff_header)
d = coord2d.get(coord)
if d:
row = d._cols[4:]
assert len(row) == len(snpeff_header)
snpeff_matrix.append(row)
assert len(snpeff_matrix) == len(CHROM)
# AnnotationMatrix is column major.
snpeff_annots = []
for j in range(len(snpeff_header)):
x = [snpeff_matrix[i][j] for i in range(len(snpeff_matrix))]
snpeff_annots.append(x)
# Convert the headers to SVM format.
snpeff_header = ["SnpEff______%s" % x for x in snpeff_header]
# Make the new SimpleVariantMatrix.
headers = svm.headers[:4] + snpeff_header + svm.headers[4:]
x = [svm.header2annots[x] for x in svm.headers_h]
all_annots = x[:4] + snpeff_annots + x[4:]
merged = AnnotationMatrix.create_from_annotations(
headers, all_annots, headerlines=svm.headerlines)
SimpleVariantMatrix.write_from_am(outfile, merged)
def align_annot(matrix, indexes, null_string):
from genomicode import AnnotationMatrix as AM
name2annots_new = {}
for name, annots in matrix.header2annots.iteritems():
annots_new = []
for i, i_annot in enumerate(indexes):
if i_annot != None:
annots_new.append(annots[i_annot])
#elif name == header:
# annots_new.append(samples[i])
else:
annots_new.append(null_string)
name2annots_new[name] = annots_new
#return AnnotationMatrix(name2annots_new, matrix.name_order)
x = AM.AnnotationMatrix(matrix.headers, matrix.headers_h, name2annots_new)
return x
def check_matrix(X):
import re
import arrayio
import copy
from genomicode import hashlib
from genomicode import AnnotationMatrix
assert arrayio.gct_format.is_matrix(X)
# Make sure gene IDs (NAME) is unique and non-empty.
assert X.row_names()[0].upper() == "NAME", \
"Header of first column should be: NAME"
seen = {}
for i, name in enumerate(X.row_names("NAME")):
assert name.strip(), "Empty gene ID in row %d." % (i + 1)
assert name not in seen, "Duplicate gene ID: %s" % name
seen[name] = 1
# Make sure sample names don't contain spaces or other
# punctuation. GSEA seems to be sensitive to these things.
sample_names = X.col_names(arrayio.tdf.SAMPLE_NAME)
bad_names = []
for i, name in enumerate(sample_names):
if not name:
bad_names.append("<blank>")
elif re.search("[^a-zA-Z0-9_-]", name):
bad_names.append(name)
#assert not bad_names, "Bad sample name: %s" % ", ".join(bad_names)
# If there are bad names, try to fix them.
if bad_names:
X = copy.deepcopy(X)
sample_names = [hashlib.hash_var(x) for x in sample_names]
sample_names = AnnotationMatrix.uniquify_headers(sample_names)
header = X._resolve_synonym(arrayio.tdf.SAMPLE_NAME, X.col_names,
X._synonyms)
X._col_names[header] = sample_names
# Make sure sample names are unique.
seen = {}
for i, name in enumerate(sample_names):
assert name not in seen, "Duplicate sample name: %s" % name
seen[name] = 1
return X
def filter_sift_polyphen_damaging(MATRIX):
from genomicode import AnnotationMatrix
x = [x for x in MATRIX.headers if x.endswith("SIFT_pred")]
assert len(x) == 1
SIFT_pred = MATRIX[x[0]]
x = [x for x in MATRIX.headers if x.endswith("Polyphen2_HDIV_pred")]
assert len(x) == 1
hdiv_pred = MATRIX[x[0]]
x = [x for x in MATRIX.headers if x.endswith("Polyphen2_HVAR_pred")]
assert len(x) == 1
hvar_pred = MATRIX[x[0]]
I_keep = []
for i, (sift, hdiv, hvar) in enumerate(zip(SIFT_pred, hdiv_pred,
hvar_pred)):
if sift == "D" and hdiv in ["D", "P"] and hvar in ["D", "P"]:
I_keep.append(i)
x = AnnotationMatrix.rowslice(MATRIX, I_keep)
return x
def filter_linked_perc(MATRIX, args):
if args is None:
return MATRIX
from genomicode import AnnotationMatrix
filter_perc = float(args)
assert filter_perc >= 0 and filter_perc <= 100
h = "Linkage______Perc Linked"
perc_linked = MATRIX[h]
I = []
for i, perc in enumerate(perc_linked):
if perc == "":
I.append(i)
continue
perc = float(perc)
if perc <= filter_perc:
I.append(i)
return AnnotationMatrix.rowslice(MATRIX, I)
def filter_min_callers(MATRIX, args, germline):
if args is None:
return MATRIX
from genomicode import AnnotationMatrix
num_callers = args
assert num_callers >= 1 and num_callers < 20
I_nc = [
i for (i, x) in enumerate(MATRIX.headers)
if x.startswith("Num Callers")
]
headers_nc = [MATRIX.headers_h[i] for i in I_nc]
for i, h in enumerate(headers_nc):
is_germ = False
for g in germline:
if h.endswith(g):
is_germ = True
break
if is_germ:
headers_nc[i] = None
headers_nc = [x for x in headers_nc if x]
I_remove = []
for i in range(MATRIX.num_annots()):
has_sample = False
for h in headers_nc:
x = MATRIX.header2annots[h][i]
if not x.strip():
continue
nc = int(x)
if nc >= num_callers:
has_sample = True
break
if not has_sample:
I_remove.append(i)
x = {}.fromkeys(I_remove)
I_keep = [i for i in range(MATRIX.num_annots()) if i not in x]
filtered_matrix = AnnotationMatrix.rowslice(MATRIX, I_keep)
return filtered_matrix
def exonic_only(MATRIX, args):
if not args:
return MATRIX
from genomicode import AnnotationMatrix
header = "Annovar______Func.refGene"
assert header in MATRIX.headers_h
I_keep = []
func = MATRIX.header2annots[header]
for i in range(len(func)):
# exonic
# ncRNA_exonic;splicing
# exonic;splicing
x = func[i]
x = x.split(";")
if "exonic" not in x:
continue
I_keep.append(i)
MATRIX = AnnotationMatrix.rowslice(MATRIX, I_keep)
return MATRIX
def filter_nonsynonymous(MATRIX):
# Filter out synonymous variants.
from genomicode import AnnotationMatrix
# Make sure annotated with Annovar.
HEADER = "Annovar______ExonicFunc.refGene"
assert HEADER in MATRIX.headers, "Missing: ExonicFunc.refGene"
exonic_func = MATRIX[HEADER]
I_keep = []
for i, efunc in enumerate(exonic_func):
assert efunc in [
"", "nonsynonymous SNV", "synonymous SNV",
"stopgain", "stoploss",
"frameshift substitution", "nonframeshift substitution",
"unknown"], \
"Unknown exonic_func: %s" % efunc
if efunc in [
"nonsynonymous SNV", "stopgain", "stoploss",
"frameshift substitution"
]:
I_keep.append(i)
x = AnnotationMatrix.rowslice(MATRIX, I_keep)
return x
def annotate_linked_variants(MATRIX, args):
if not args:
return MATRIX
from genomicode import filelib
from genomicode import AnnotationMatrix
link_file = args
filelib.assert_exists_nz(link_file)
coord2perc = {}
for d in filelib.read_row(link_file, header=1):
chrom = d.Chrom
pos = int(d.Pos)
perc = float(d.Perc_Linked)
coord2perc[(chrom, pos)] = perc
chrom = MATRIX.header2annots["______Chrom"]
pos = MATRIX.header2annots["______Pos"]
pos = [int(x) for x in pos]
link_score = [""] * len(chrom)
for i in range(len(chrom)):
link_score[i] = coord2perc.get((chrom[i], pos[i]), "")
# Add after:
# Chrom, Pos, Ref, Alt
header = "Linkage______Score"
assert header not in MATRIX.headers
headers = MATRIX.headers[:4] + [header] + MATRIX.headers[4:]
all_annots = []
for h in headers:
if h != header:
x = MATRIX[h]
else:
x = link_score
all_annots.append(x)
return AnnotationMatrix.create_from_annotations(headers, all_annots,
MATRIX.headerlines)
def main():
import os
import argparse
from genomicode import jmath
from genomicode import AnnotationMatrix
parser = argparse.ArgumentParser(description="")
parser.add_argument("datafile", help="Tab-delimited data file.")
parser.add_argument("header", help="Which column contains data to plot.")
parser.add_argument(
"plot_file", help="Name of image file, e.g. outfile.png. "
"Will generate PNG format by default. If this file name ends with "
".pdf, will generate a PDF file instead.")
parser.add_argument(
"--prism_file", help="Write Prism-formatted results to this file.")
parser.add_argument(
"--ignore_missing_values", action="store_true",
help="Ignore missing values in the file.")
group = parser.add_argument_group(title="Calculations")
group.add_argument(
"--breaks_seq",
help="Set the breakpoints. Format: <start>,<stop>,<skip>.")
group.add_argument(
"--num_breaks", type=int, help="Number of breakpoints.")
group.add_argument(
"--ymax", type=int,
help="Set the maximum value for the Y axis.")
group = parser.add_argument_group(title="Plot Labels")
group.add_argument("--title", help="Put a title on the plot.")
group.add_argument("--xlab", help="Label the X-axis.")
group.add_argument(
"--xlabel_size", default=1.0, type=float,
help="Scale the size of the labels on X-axis. Default 1.0.")
group.add_argument(
"--xlabel_off", action="store_true", help="Do not label the X axis.")
group.add_argument(
"--ylabel_off", action="store_true", help="Do not label the Y axis.")
group.add_argument(
"--xtick_label_off", action="store_true",
help="Do not draw the tick labels on the X axis.")
group = parser.add_argument_group(title="Colors")
group.add_argument(
"--bar_color", help="Set the color of the bars. Default #FFFFFF")
x = _fmt_palettes()
group.add_argument(
"--bar_palette", help="Color the bars according to a palette: %s." % x)
group.add_argument(
"--symmetric_palette", action="store_true",
help="Make the color symmetric.")
group = parser.add_argument_group(title="Appearance")
group.add_argument(
"--height", type=int, help="Height (in pixels) of the plot.")
group.add_argument(
"--width", type=int, help="Width (in pixels) of the plot.")
group.add_argument(
"--mar_left", default=1.0, type=float,
help="Scale margin at left of plot. Default 1.0 (no scaling).")
group.add_argument(
"--mar_bottom", default=1.0, type=float,
help="Scale margin at bottom of plot. Default 1.0.")
group.add_argument(
"--xaxis_off", action="store_true", help="Do not show the X axis.")
group.add_argument(
"--yaxis_off", action="store_true", help="Do not show the Y axis.")
# Parse the input arguments.
args = parser.parse_args()
if not os.path.exists(args.datafile):
parser.error("File not found: %s" % args.datafile)
assert not (args.breaks_seq and args.num_breaks)
if args.num_breaks:
assert args.num_breaks >= 2 and args.num_breaks <= 1000
if args.width is not None:
assert args.width > 10, "too small"
assert args.width < 4096*16, "width too big"
if args.height is not None:
assert args.height > 10, "too small"
assert args.height < 4096*16, "height too big"
assert args.mar_bottom > 0 and args.mar_bottom < 10
assert args.mar_left > 0 and args.mar_left < 10
assert args.xlabel_size > 0 and args.xlabel_size < 10
assert not (args.bar_color and args.bar_palette)
assert not args.symmetric_palette or args.bar_palette
assert args.ymax is None or args.ymax > 0
height = args.height or 2400
width = args.width or 3200
MATRIX = AnnotationMatrix.read(args.datafile, False)
assert MATRIX.num_headers() and MATRIX.num_annots(), "Empty matrix."
assert args.header in MATRIX.headers, "header not found: %s" % args.header
# Pull out the values for the histogram.
x = MATRIX[args.header]
if args.ignore_missing_values:
x = [x for x in x if x.strip()]
values = map(float, x)
value_min = value_max = None
# Start R and set up the environment.
R = jmath.start_R()
main = jmath.R_var("NA")
if args.title:
main = args.title
sub = ""
xlab = ""
if args.xlab:
xlab = args.xlab
ylab = "Frequency"
xtick_labels = jmath.R_var("TRUE")
ytick_labels = jmath.R_var("TRUE")
if args.xlabel_off:
xlab = ""
if args.ylabel_off:
ylab = ""
if args.xtick_label_off:
xtick_labels = jmath.R_var("FALSE")
breaks = "Sturges"
if args.breaks_seq:
breaks = _parse_breaks_seq(args.breaks_seq)
value_min, value_max = min(breaks), max(breaks)
jmath.R_equals(breaks, "breaks")
breaks = jmath.R_var("breaks")
if args.num_breaks:
breaks = args.num_breaks
if value_min is not None:
values = [x for x in values if x >= value_min]
if value_max is not None:
values = [x for x in values if x < value_max]
lwd = 2
cex_lab = 1.5
cex_main = 2.0
cex_sub = 1.5
ylim = jmath.R_var("NULL")
if args.ymax is not None:
ylim = [0, args.ymax]
assert values
jmath.R_equals(values, "X")
# Figure out the colors. Do it after X is assigned.
col = jmath.R_var("NULL")
if args.bar_color:
assert args.bar_color.startswith("#")
col = args.bar_color
elif args.bar_palette:
# Figure out how many breaks there are. Number of bars is num
# breaks + 1.
jmath.R_fn(
"hist", jmath.R_var("X"), breaks=breaks, plot=jmath.R_var("FALSE"),
RETVAL="x")
breaks = [x for x in R["x"].rx2("breaks")]
num_bars = len(breaks) + 1
col = _make_col_palette(
args.bar_palette, num_bars, args.symmetric_palette)
bm_type = "png16m"
if args.plot_file.lower().endswith(".pdf"):
bm_type = "pdfwrite"
jmath.R_fn(
"bitmap", args.plot_file, type=bm_type,
height=height, width=width, units="px", res=300)
# Set the margins.
x = 5*1.2*args.mar_bottom, 4*1.2*args.mar_left, 4, 2
mar = [x+0.1 for x in x]
jmath.R_fn("par", mar=mar, RETVAL="op")
jmath.R_fn(
"hist", jmath.R_var("X"), breaks=breaks, main="", xlab="", ylab="",
ylim=ylim, axes=jmath.R_var("FALSE"), col=col, RETVAL="x")
# Make plot area solid white.
#jmath.R('usr <- par("usr")')
#jmath.R('rect(usr[1], usr[3], usr[2], usr[4], col="#FFFFFF")')
#jmath.R_fn(
# "hist", jmath.R_var("X"), plot=jmath.R_var("FALSE"),
# main=main, xlab="", ylab="", axes=jmath.R_var("FALSE"),
# add=jmath.R_var("TRUE"))
#jmath.R_fn("box", lwd=lwd)
# x-axis
if not args.xaxis_off:
jmath.R_fn(
"axis", 1, lwd=lwd, labels=xtick_labels, **{ "cex.axis" : 1.5 })
# y-axis
if not args.yaxis_off:
jmath.R_fn(
"axis", 2, lwd=lwd, labels=ytick_labels, **{ "cex.axis" : 1.5 })
jmath.R_fn(
"title", main=main, sub=sub, xlab=xlab, ylab=ylab,
**{ "cex.lab" : cex_lab, "cex.main" : cex_main, "cex.sub" : cex_sub })
R("par(op)")
jmath.R_fn("dev.off")
if args.prism_file:
write_prism_file(args.prism_file, R["x"])
def read_as_am(filename, is_csv=False):
# Read file in SVM format. Return an AnnotationMatrix object.
# Does no special processing on any columns (i.e. no parsing as
# integers or Call objects). Everything is a string.
# Header format: <header0>___<header1>___<header2>
# "blanks" are filled in. E.g. "Annovar" occurs in each Annovar
# column in header0.
#
# Headers:
# ______Chrom
# ______Pos
# ______Ref
# ______Alt
# Num Callers______<Sample>
# ...
from genomicode import filelib
from genomicode import AnnotationMatrix
delimiter = "\t"
if is_csv:
delimiter = ","
matrix = []
for x in filelib.read_cols(filename, delimiter=delimiter):
matrix.append(x)
assert len(matrix) >= 3 # at least 3 rows for the header
for i in range(1, len(matrix)):
assert len(matrix[i]) == len(matrix[0])
assert len(matrix[0]) >= 4 # Chrom, Pos, Ref, Alt
assert len(matrix[0]) >= 5, "No calls"
header0 = matrix[0]
header1 = matrix[1]
header2 = matrix[2]
assert header2[:4] == ["Chrom", "Pos", "Ref", "Alt"]
# Fill in the blanks for header1.
for i in range(1, len(header1)):
if header1[i]:
continue
# header1[i] is blank. If header0[i], then this starts a new
# "block". Start with a new header1, and do not copy the old
# one over.
if not header1[i] and not header0[i]:
header1[i] = header1[i - 1]
# Fill in the blanks for header0.
for i in range(1, len(header0)):
if not header0[i]:
header0[i] = header0[i - 1]
# Make a list of all samples.
I = [i for (i, x) in enumerate(header2) if x == "Ref/Alt/VAF"]
assert I
x = [header0[i] for i in I]
x = [x for x in x if x]
# Get rid of duplicates, preserving order.
x = [x[i] for (i, y) in enumerate(x) if y not in x[:i]]
samples = x
# Make a list of all callers.
x = [header1[i] for i in I]
x = [x for x in x if x]
# Get rid of duplicates, preserving order.
x = [x[i] for (i, y) in enumerate(x) if y not in x[:i]]
callers = x
headers = []
for x in zip(header0, header1, header2):
x = "___".join(x)
headers.append(x)
all_annots = []
for j in range(len(headers)):
annots = [x[j] for x in matrix[3:]]
all_annots.append(annots)
matrix = AnnotationMatrix.create_from_annotations(headers, all_annots)
matrix.samples = samples
matrix.callers = callers
return matrix
def main():
import argparse
from genomicode import AnnotationMatrix as AM
SKIP_OUTFILE = "_"
parser = argparse.ArgumentParser(
description="Align a set of matrices. Preserve the order of the "
"first file given.")
parser.add_argument("outfile", nargs="+")
parser.add_argument(
"--express_file", default=[], action="append", help="")
parser.add_argument(
"--annot_file", default=[], action="append", help="")
parser.add_argument(
"--header", default=[], action="append",
help="Specify the header for an annotation file. Should come "
"after the --annot_file that it refers to.")
parser.add_argument(
"--annot_path",
help="Align all the annotation files in a path. "
"If using this argument, no --annot_file or --express_file should "
"be given. "
"--header is still required, and should apply to at least one file. "
'Only one "outfile" should be given, and it should refer to a path '
"in which to store the aligned files.")
#parser.add_argument(
# "--first_annot_header", help="If only aligning annotation files, "
# "find the samples to be matched under this header in the first "
# "annotation file.")
parser.add_argument(
"--clobber", default=False, action="store_true",
help="Overwrite output files, if they already exist.")
group = parser.add_argument_group(title="Comparisons")
group.add_argument(
"--case_insensitive", default=False, action="store_true",
help="Do a case insensitive search of sample names.")
group.add_argument(
"--hash", default=False, action="store_true",
help="Hash the sample names to [a-zA-Z0-9_] before comparison.")
group.add_argument(
"--ignore_nonalnum", default=False, action="store_true",
help="Ignore non-alphanumeric characters in the IDs.")
group.add_argument(
"--ignore_blank", default=False, action="store_true",
help="Ignore IDs that are blank (don't align them.")
group = parser.add_argument_group(title="Joins")
group.add_argument(
"--strict", default=False, action="store_true",
help="Complain if a file is missing a sample.")
group.add_argument(
"--left_join", default=False, action="store_true",
help='By default, does an "inner join" and keeps only the '
'records that are present in all files. A "left join" will '
'keep all records that occur in the first file.')
group.add_argument(
"--outer_join", default=False, action="store_true",
help='By default, does an "inner join" and keeps only the '
'records that are present in all files. An "outer join" will '
'also keep records that occur in any file.')
group = parser.add_argument_group(title="Output")
group.add_argument(
"--null_string", default="",
help='For left_join or outer_join, what to give the missing values.')
group.add_argument(
"--unaligned_only", action="store_true",
help="Show only the rows that are not aligned.")
group.add_argument(
"--dont_add_missing_samples", action="store_true",
help="If a matrix does not have a sample, don't fill in the value "
"from another matrix.")
group = parser.add_argument_group(title="Debug")
group.add_argument(
"--debug_nrows", type=int,
help="Debugging: Only read this many rows from the annotation files.")
args = parser.parse_args()
# If the user specified an --annot_path, revise args to
# contain --annot_files instead.
sys.argv, args = _handle_annot_path(sys.argv, args)
ni, no = len(args.express_file)+len(args.annot_file), len(args.outfile)
assert ni == no, "Mismatch: %d inputs and %d outputs" % (ni, no)
for x in args.express_file + args.annot_file:
assert os.path.exists(x), "I could not find file: %s" % x
for x in args.outfile:
if x == SKIP_OUTFILE:
continue
assert args.clobber or not os.path.exists(x), "File exists: %s" % x
assert not (args.left_join and args.outer_join)
if args.null_string:
assert args.outer_join or args.left_join, \
"null_string given, but only used for outer_join"
# Align the outfiles to the expression and annotation files.
express_file = args.express_file[:]
annot_file = args.annot_file[:]
outfile = args.outfile[:]
matrix_data = [] # list of (infile, outfile, is_express_file)
for arg in sys.argv:
if arg not in ["--express_file", "--annot_file"]:
continue
assert outfile
if arg == "--express_file":
assert express_file
x = express_file.pop(0), outfile.pop(0), True
else:
assert annot_file
x = annot_file.pop(0), outfile.pop(0), False
matrix_data.append(x)
assert not express_file
assert not annot_file
assert not outfile
# Align the --header arguments to the annotation files.
headers = [None] * len(matrix_data)
header_i = -1
for i, arg in enumerate(sys.argv):
if arg == "--header":
assert header_i >= 0, \
"--header given before an --express_file or --annot_file."
assert headers[header_i] is None, "Two --header for one file."
headers[header_i] = sys.argv[i+1]
elif arg in ["--express_file", "--annot_file"]:
header_i += 1
# Add the headers to the matrix_data.
new_matrix_data = [] # list of (infile, outfile, is_express_file, header)
for i in range(len(matrix_data)):
infile, outfile, is_express_file = matrix_data[i]
if is_express_file and headers[i]:
raise NotImplementedError, "No headers for --express_file."
x = infile, outfile, is_express_file, headers[i]
new_matrix_data.append(x)
matrix_data = new_matrix_data
# Read each of the files.
new_matrix_data = [] # list of (infile, outfile, matrix, header)
for x in matrix_data:
infile, outfile, is_express_file, header = x
if is_express_file:
data = read_express(infile)
else:
data = AM.read(infile, nrows=args.debug_nrows)
x = infile, outfile, data, header
new_matrix_data.append(x)
matrix_data = new_matrix_data
# Find the samples in each matrix.
new_matrix_data = [] # list of (infile, outfile, matrix, header, samples)
samples_hint = peek_samples_hint(matrix_data)
for x in matrix_data:
infile, outfile, matrix, header = x
headers_hint = [x for x in headers if x]
x = get_samples(
matrix, header, samples_hint, headers_hint,
args.case_insensitive, args.hash, args.ignore_nonalnum)
assert x, "I could not find the samples for %s" % infile
header, samples = x
x = infile, outfile, matrix, header, samples
new_matrix_data.append(x)
matrix_data = new_matrix_data
if args.left_join:
assert not args.strict, "Can't do a strict left join."
# No duplicates.
samples = list_all_samples(
matrix_data[:1], args.case_insensitive, args.hash,
args.ignore_nonalnum)
assert samples, "No samples."
elif args.outer_join:
assert not args.strict, "Can't do a strict outer join."
samples = list_all_samples(
matrix_data, args.case_insensitive, args.hash,
args.ignore_nonalnum)
assert samples, "No samples."
else: # inner join
samples = list_common_samples(
matrix_data, args.case_insensitive, args.hash,
args.ignore_nonalnum)
assert samples, "No common samples found."
if args.strict:
all_samples = list_all_samples(
matrix_data, args.case_insensitive, args.hash,
args.ignore_nonalnum)
common_samples = list_common_samples(
matrix_data, args.case_insensitive, args.hash,
args.ignore_nonalnum)
if sorted(all_samples) != sorted(common_samples):
missing_samples = []
for x in all_samples:
i = find_sample(
common_samples, x, args.case_insensitive, args.hash,
args.ignore_nonalnum, args.ignore_blank)
if i >= 0:
continue
missing_samples.append(x)
short = missing_samples
if len(short) > 10:
short = short[:10] + ["..."]
short = "\n".join(short)
raise AssertionError, "%d samples not in all data sets.\n%s" % \
(len(missing_samples), short)
# Align each of the matrices.
matrix_data = align_matrices(
matrix_data, samples, args.case_insensitive, args.hash,
args.ignore_nonalnum, args.ignore_blank,
args.left_join, args.outer_join, args.unaligned_only,
args.null_string)
# Add the missing samples back to the matrix.
if not args.dont_add_missing_samples:
matrix_data = add_missing_samples(matrix_data, args.null_string)
# Write out each of the matrices.
for x in matrix_data:
infile, outfile, matrix, header, samples = x
if outfile == SKIP_OUTFILE:
continue
write_matrix(outfile, matrix)
def run(self, network, in_data, out_attributes, user_options, num_cores,
outfile):
import math
from genomicode import filelib
from genomicode import jmath
from genomicode import AnnotationMatrix
from genomicode import SimpleVariantMatrix
from Betsy import module_utils as mlib
svm_node = in_data
filelib.assert_exists_nz(svm_node.identifier)
linked_file = mlib.get_user_option(user_options,
"linked_variants_file",
not_empty=True,
check_file=True)
# Read the variant file.
SVM = SimpleVariantMatrix.read_as_am(svm_node.identifier)
CHROM = SVM["______Chrom"]
POS = SVM["______Pos"]
POS = [int(x) for x in POS]
all_coords = {} # (chrom, pos) -> 1
for x in zip(CHROM, POS):
all_coords[x] = 1
# Read the linked variant file.
# Chrom Pos Perc Linked p
coord2info = {} # (chrom, pos) -> d
for d in filelib.read_row(linked_file, header=1):
pos = int(d.Pos)
if (d.Chrom, pos) not in all_coords:
continue
coord2info[(d.Chrom, pos)] = d
# Align the linked annotations to the matrix.
MAX_SCORE = 1000
min_p = 10**-(MAX_SCORE / 10)
linked_headers = ["Perc Linked", "Score"]
annotations = []
for (chrom, pos) in zip(CHROM, POS):
if (chrom, pos) not in coord2info:
x = [""] * len(linked_headers)
annotations.append(x)
continue
d = coord2info[(chrom, pos)]
score = MAX_SCORE
if float(d.p) >= min_p:
score = -10 * math.log(float(d.p), 10)
x = d.Perc_Linked, score
assert len(x) == len(linked_headers)
annotations.append(x)
# Convert the headers and annotations to SVM format.
linked_headers = ["Linkage______%s" % x for x in linked_headers]
linked_annotations = jmath.transpose(annotations)
# Make the new SimpleVariantMatrix.
# Figure out where to put these annotations.
INDEX = 4
## If Annovar exists, put after.
#I = [i for (i, x) in enumerate(SVM.headers)
# if x.upper().startswith("ANNOVAR")]
#if I:
# INDEX = max(INDEX, max(I)+1)
headers = SVM.headers[:INDEX] + linked_headers + SVM.headers[INDEX:]
x = [SVM.header2annots[x] for x in SVM.headers_h]
all_annots = x[:INDEX] + linked_annotations + x[INDEX:]
merged = AnnotationMatrix.create_from_annotations(
headers, all_annots, headerlines=SVM.headerlines)
SimpleVariantMatrix.write_from_am(outfile, merged)
def run(
self, network, in_data, out_attributes, user_options, num_cores,
outfile):
from genomicode import filelib
from genomicode import jmath
from genomicode import AnnotationMatrix
from genomicode import SimpleVariantMatrix
from Betsy import module_utils as mlib
svm_node = in_data
filelib.assert_exists_nz(svm_node.identifier)
cosmic_file = mlib.get_user_option(
user_options, "cosmic_variants_file", not_empty=True,
check_file=True)
# Read the variant file.
SVM = SimpleVariantMatrix.read_as_am(svm_node.identifier)
CHROM = SVM["______Chrom"]
POS = SVM["______Pos"]
POS = [int(x) for x in POS]
all_coords = {} # (chrom, pos) -> 1
for x in zip(CHROM, POS):
all_coords[x] = 1
# Read the COSMIC variant file.
# Chrom Start End GRCh Count SNP
# Mutation CDS Mutation AA
# FATHMM prediction FATHMM score Mutation somatic status
coord2info = {} # (chrom, pos) -> d
for d in filelib.read_row(cosmic_file, header=1):
start, end = int(d.Start), int(d.End)
in_svm = False
for pos in range(start, end+1):
if (d.Chrom, pos) in all_coords:
in_svm = True
break
if not in_svm:
continue
coord2info[(d.Chrom, pos)] = d
# Align the COSMIC annotations to the matrix.
cosmic_headers = [
"SNP", "Num Tumors", "Mutation CDS", "Mutation AA",
"FATHMM prediction", "FATHMM score", "Mutation somatic status"]
annotations = []
for (chrom, pos) in zip(CHROM, POS):
if (chrom, pos) not in coord2info:
x = [""] * len(cosmic_headers)
annotations.append(x)
continue
d = coord2info[(chrom, pos)]
x = d.SNP, d.Count, d.Mutation_CDS, d.Mutation_AA, \
d.FATHMM_prediction, d.FATHMM_score, \
d.Mutation_somatic_status
annotations.append(x)
# Convert the headers and annotations to SVM format.
cosmic_headers = ["COSMIC______%s" % x for x in cosmic_headers]
cosmic_annotations = jmath.transpose(annotations)
# Make the new SimpleVariantMatrix.
# Figure out where to put these annotations.
INDEX = 4
# If Annovar exists, put after.
I = [i for (i, x) in enumerate(SVM.headers)
if x.upper().startswith("ANNOVAR")]
if I:
INDEX = max(INDEX, max(I)+1)
# If SnpEff exists, put after.
I = [i for (i, x) in enumerate(SVM.headers)
if x.upper().startswith("SNPEFF")]
if I:
INDEX = max(INDEX, max(I)+1)
headers = SVM.headers[:INDEX] + cosmic_headers + SVM.headers[INDEX:]
x = [SVM.header2annots[x] for x in SVM.headers_h]
all_annots = x[:INDEX] + cosmic_annotations + x[INDEX:]
merged = AnnotationMatrix.create_from_annotations(
headers, all_annots, headerlines=SVM.headerlines)
SimpleVariantMatrix.write_from_am(outfile, merged)
def run(self, network, in_data, out_attributes, user_options, num_cores,
out_filename):
from genomicode import filelib
from genomicode import SimpleVariantMatrix
from genomicode import AnnotationMatrix
simple_file = in_data.identifier
metadata = {}
# Read all in memory. Hopefully, not too big.
ds = []
for d in filelib.read_row(simple_file, header=-1):
ds.append(d)
#if len(ds) > 50000: # DEBUG
# break
# MuSE sometimes has alternates.
# Alt A,C
# Num_Alt 13,0
# VAF 0.19,0.0
# Detect this and fix it. Take the alternate with the highest VAF.
for d in ds:
if d.Num_Alt.find(",") < 0:
continue
x1 = d.Num_Alt.split(",")
x2 = d.VAF.split(",")
assert len(x1) == len(x2)
x1 = map(int, x1)
x2 = map(float, x2)
max_vaf = max_i = None
for i in range(len(x2)):
if max_vaf is None or x2[i] > max_vaf:
max_vaf = x2[i]
max_i = i
assert max_i is not None
d.Num_Alt = str(x1[max_i])
d.VAF = str(x2[max_i])
# Make a list of all the positions.
positions = {} # (Chrom, Pos) -> 1
for d in ds:
positions[(d.Chrom, int(d.Pos))] = 1
positions = sorted(positions)
# Make a list of all the callers.
callers = {}
for d in ds:
callers[d.Caller] = 1
callers = sorted(callers)
# Make a list of all the samples.
samples = {}
for d in ds:
samples[d.Sample] = 1
samples = sorted(samples)
# Make a list of the coordinates.
coord_data = {}
for d in ds:
x = d.Chrom, int(d.Pos), d.Ref, d.Alt
coord_data[x] = 1
coord_data = sorted(coord_data)
# Make a list of all DNA calls.
call_data = []
for d in ds:
assert d.Source in ["DNA", "RNA"]
if d.Source != "DNA":
continue
num_ref = num_alt = vaf = None
if d.Num_Ref:
num_ref = int(d.Num_Ref)
if d.Num_Alt:
num_alt = int(d.Num_Alt)
if d.VAF:
vaf = float(d.VAF)
if num_ref is None and num_alt is None and vaf is None:
continue
call = SimpleVariantMatrix.Call(num_ref, num_alt, vaf)
x = d.Chrom, int(d.Pos), d.Ref, d.Alt, d.Sample, d.Caller, call
call_data.append(x)
# sample -> caller -> chrom, pos, ref, alt -> call
samp2caller2coord2call = {}
for x in call_data:
chrom, pos, ref, alt, sample, caller, call = x
coord = chrom, pos, ref, alt
if sample not in samp2caller2coord2call:
samp2caller2coord2call[sample] = {}
caller2coord2call = samp2caller2coord2call[sample]
if caller not in caller2coord2call:
caller2coord2call[caller] = {}
coord2call = caller2coord2call[caller]
# A (sample, caller, coord) may have multiple calls. For
# example, for germline samples that are called with each
# tumor sample. If this is the case, then take the call
# with the highest coverage.
if coord in coord2call:
old_call = coord2call[coord]
cov = old_cov = None
if call.num_ref is not None and call.num_alt is not None:
cov = call.num_ref + call.num_alt
if old_call.num_ref is not None and \
old_call.num_alt is not None:
old_cov = old_call.num_ref + old_call.num_alt
if cov is None and old_cov is not None:
call = old_call
elif cov is not None and old_cov is not None and cov < old_cov:
call = old_call
coord2call[coord] = call
# Count the number of callers that called a variant at each
# position for each sample.
samp2coord2caller = {} # sample -> chrom, pos, ref, alt -> caller -> 1
# Need to do this first, to make sure each caller is counted
# at most once. This is to account for germline samples that
# is called by each caller multiple times.
for x in call_data:
chrom, pos, ref, alt, sample, caller, call = x
coord = chrom, pos, ref, alt
if sample not in samp2coord2caller:
samp2coord2caller[sample] = {}
if coord not in samp2coord2caller[sample]:
samp2coord2caller[sample][coord] = {}
samp2coord2caller[sample][coord][caller] = 1
samp2coord2nc = {} # sample -> chrom, pos, ref, alt -> num_callers
for sample in samp2coord2caller:
samp2coord2nc[sample] = {}
for coord in samp2coord2caller[sample]:
samp2coord2nc[sample][coord] = len(
samp2coord2caller[sample][coord])
#for x in call_data:
# chrom, pos, ref, alt, sample, caller, call = x
# coord = chrom, pos, ref, alt
# if sample not in samp2coord2nc:
# samp2coord2nc[sample] = {}
# nc = samp2coord2nc[sample].get(coord, 0) + 1
# samp2coord2nc[sample][coord] = nc
# Format everything into an annotation matrix.
headers0 = []
headers1 = []
headers2 = []
all_annots = []
# Add the positions.
headers0 += ["", "", "", ""]
headers1 += ["", "", "", ""]
headers2 += ["Chrom", "Pos", "Ref", "Alt"]
for i in range(4):
x = [x[i] for x in coord_data]
x = [str(x) for x in x]
all_annots.append(x)
# Add the number of callers information.
headers0 += ["Num Callers"] * len(samples)
headers1 += [""] * len(samples)
headers2 += samples
for sample in samples:
annots = []
for coord in coord_data:
nc = samp2coord2nc.get(sample, {}).get(coord, "")
annots.append(nc)
all_annots.append(annots)
# Add information about calls.
for sample in samples:
caller2coord2call = samp2caller2coord2call.get(sample, {})
for i, caller in enumerate(callers):
h0 = ""
if not i:
h0 = sample
h1 = caller
h2 = "Ref/Alt/VAF"
headers0.append(h0)
headers1.append(h1)
headers2.append(h2)
coord2call = caller2coord2call.get(caller, {})
annots = []
for coord in coord_data:
x = ""
call = coord2call.get(coord)
if call:
x = SimpleVariantMatrix._format_call(call)
annots.append(x)
all_annots.append(annots)
# Set the headers.
assert len(headers0) == len(headers1)
assert len(headers0) == len(headers2)
assert len(headers0) == len(all_annots)
headers = [None] * len(headers0)
for i, x in enumerate(zip(headers0, headers1, headers2)):
x = "___".join(x)
headers[i] = x
matrix = AnnotationMatrix.create_from_annotations(headers, all_annots)
SimpleVariantMatrix.write_from_am(out_filename, matrix)
#annot_header = ["Chrom", "Pos", "Ref", "Alt"]
#matrix = SimpleVariantMatrix.make_matrix(
# samples, callers, annot_header, coord_data, named_data,
# call_data)
#SimpleVariantMatrix.write(out_filename, matrix)
return metadata
def run(
self, network, in_data, out_attributes, user_options, num_cores,
outfile):
from genomicode import filelib
from genomicode import hashlib
from genomicode import jmath
from genomicode import AnnotationMatrix
from genomicode import SimpleVariantMatrix
from Betsy import module_utils as mlib
simple_node = in_data
filelib.assert_exists_nz(simple_node.identifier)
gene_file = mlib.get_user_option(
user_options, "cancer_genes_file", not_empty=True, check_file=True)
# Read the cancer genes file.
# <Gene ID> <Gene Symbol> <Dataset> ...
symbol2info = {} # symbol -> d
gene_iter = filelib.read_row(gene_file, header=1)
header = None
for d in gene_iter:
assert "Gene Symbol" in d._header
if header is None:
header = [
x for x in d._header
if x not in ["Gene ID", "Gene Symbol"]]
if not d.Gene_Symbol:
continue
symbol2info[d.Gene_Symbol] = d
# Read the variant file.
SVM = SimpleVariantMatrix.read_as_am(simple_node.identifier)
GENE_H = "Annovar______Gene.refGene"
assert GENE_H in SVM.headers, "Missing annotation: %s" % GENE_H
GENES = SVM[GENE_H]
# Align the matrix to the simple variant matrix.
gene_headers = header
gene_annotations = []
for i, gene_str in enumerate(GENES):
# Format of genes:
# PFN1P2
# PMS2P2,PMS2P7
values = [""] * len(gene_headers)
genes = gene_str.split(",")
for gene in genes:
if gene not in symbol2info:
continue
d = symbol2info[gene]
for j, h in enumerate(gene_headers):
h = hashlib.hash_var(h)
assert hasattr(d, h)
x = getattr(d, h)
assert x in ["", "1"]
if x == "1":
values[j] = 1
gene_annotations.append(values)
# Convert the headers and annotations to SVM format.
gene_headers = ["Cancer Genes______%s" % x for x in gene_headers]
gene_annotations = jmath.transpose(gene_annotations)
# Make the new SimpleVariantMatrix.
# Figure out where to put these annotations.
INDEX = 4
# If Annovar exists, put after.
I = [i for (i, x) in enumerate(SVM.headers)
if x.upper().startswith("ANNOVAR")]
if I:
INDEX = max(INDEX, max(I)+1)
# If SnpEff exists, put after.
I = [i for (i, x) in enumerate(SVM.headers)
if x.upper().startswith("SNPEFF")]
if I:
INDEX = max(INDEX, max(I)+1)
# If COSMIC exists, put after.
I = [i for (i, x) in enumerate(SVM.headers)
if x.upper().startswith("COSMIC")]
if I:
INDEX = max(INDEX, max(I)+1)
headers = SVM.headers[:INDEX] + gene_headers + SVM.headers[INDEX:]
x = [SVM.header2annots[x] for x in SVM.headers_h]
all_annots = x[:INDEX] + gene_annotations + x[INDEX:]
merged = AnnotationMatrix.create_from_annotations(
headers, all_annots, headerlines=SVM.headerlines)
SimpleVariantMatrix.write_from_am(outfile, merged)
def run(
self, network, antecedents, out_attributes, user_options, num_cores,
out_filename):
import arrayio
from genomicode import filelib
from genomicode import AnnotationMatrix
from genomicode import SimpleVariantMatrix
simple_node, signal_node = antecedents
filelib.assert_exists_nz(simple_node.identifier)
filelib.assert_exists_nz(signal_node.identifier)
# Read the variant file.
SVM = SimpleVariantMatrix.read(simple_node.identifier)
#AM = SVM.annot_matrix
#assert GENE_H in AM.headers
# Read the gene expression file.
GXP = arrayio.read(signal_node.identifier)
# Make sure the samples from the variant matrix can be found
# in the gene expression matrix.
GXP_samples = GXP.col_names(arrayio.COL_ID)
missing = [x for x in SVM.samples if x not in GXP_samples]
assert len(missing) < len(SVM.samples), (
"SimpleVariantMatrix and gene expression file have "
"no common samples.")
# Actually, may not have all the same samples. For example, a
# gene expression profile might not have been calculated for
# the germline sample. So ignore if something is missing.
#x = missing
#if len(x) > 5:
# x = x[:5] + ["..."]
#msg = "Samples (%d) not found in gene expression file: %s" % (
# len(missing), ", ".join(x))
#assert not missing, msg
# Add all the samples from the gene expression file.
SAMPLES = GXP_samples
# Find the genes in each row.
GENE_H = "Gene.refGene"
annovar_matrix = None
for (name, matrix) in SVM.named_matrices:
if GENE_H in matrix.headers:
annovar_matrix = matrix
break
assert annovar_matrix, "Missing annotation: %s" % GENE_H
GENES = annovar_matrix[GENE_H]
# Make a list of the genes.
genes = {}
for i, gene_str in enumerate(GENES):
# Format of genes:
# PFN1P2
# PMS2P2,PMS2P7
for x in gene_str.split(","):
genes[x] = 1
genes = sorted(genes)
# Make a matrix of the gene expression values for each gene
# and each sample.
#I = [GXP_samples.index(x) for x in SVM.samples]
#GXP_a = GXP.matrix(genes, I) # align the matrices.
GXP_a = GXP.matrix(genes, None)
# Write out the expression matrix for debugging purposes.
arrayio.write(GXP_a, "expression.txt")
# Search for each of the genes in the matrix.
gene2I = {} # gene -> list of row indexes
for gene in genes:
x = GXP_a._index(row=gene)
I_row, i_col = x
if I_row:
gene2I[gene] = I_row
# Align the gene expression matrix to the simple variant
# matrix.
#matrix = [[None]*len(SVM.samples) for i in range(len(GENES))]
matrix = [[None]*len(SAMPLES) for i in range(len(GENES))]
for i, gene_str in enumerate(GENES):
# Format of genes: Format of output
# PFN1P2 5.2
# PMS2P2,PMS2P7 2.2,8.6
# If a gene is missing, then skip it.
genes = gene_str.split(",")
#for j in range(len(SVM.samples)):
for j in range(len(SAMPLES)):
values = [] # expression values for each gene.
for k in range(len(genes)):
if genes[k] not in gene2I:
continue
x = [GXP_a._X[l][j] for l in gene2I[genes[k]]]
# If there are multiple instances of this gene,
# then pick the one with the maximum expression.
x = max(x)
values.append(x)
values = [_pretty_gxp(x) for x in values]
x = ",".join(values)
matrix[i][j] = x
# Add the matrix back to the simple variant matrix.
#headers = SVM.samples
headers = SAMPLES
all_annots = []
for j in range(len(headers)):
x = [matrix[i][j] for i in range(len(matrix))]
all_annots.append(x)
x = AnnotationMatrix.create_from_annotations(headers, all_annots)
SVM.named_matrices.append(("Gene Expression", x))
# Write to file.
SimpleVariantMatrix.write(out_filename, SVM)
def run(self, network, in_data, out_attributes, user_options, num_cores,
out_filename):
import itertools
from genomicode import SimpleVariantMatrix
from genomicode import AnnotationMatrix
from Betsy import module_utils as mlib
summary_file = in_data.identifier
metadata = {}
#x = mlib.get_user_option(
# user_options, "nonsynonymous_and_stopgain_only",
# allowed_values=["no", "yes"])
#nonsynonymous_and_stopgain_only = (x == "yes")
min_alt_reads = mlib.get_user_option(user_options,
"filter_by_min_alt_reads",
not_empty=True,
type=int)
assert min_alt_reads >= 0 and min_alt_reads < 10000
min_total_reads = mlib.get_user_option(user_options,
"filter_by_min_total_reads",
not_empty=True,
type=int)
assert min_total_reads >= 0 and min_total_reads < 10000
min_vaf = mlib.get_user_option(user_options,
"filter_by_min_vaf",
not_empty=True,
type=float)
assert min_vaf >= 0.0 and min_vaf < 1.0
#min_gq = mlib.get_user_option(
# user_options, "filter_by_min_GQ", not_empty=True, type=float)
#assert min_gq >= 0 and min_gq < 1000
assert min_total_reads or min_alt_reads, "No filter"
matrix = SimpleVariantMatrix.read_as_am(summary_file)
#var_matrix = SimpleVariantMatrix.read(summary_file)
#call_matrix = var_matrix.call_matrix
#annot_matrix = var_matrix.annot_matrix
#annovar_matrix = None
#for (name, matrix) in var_matrix.named_matrices:
# if "ExonicFunc.refGene" in matrix.headers:
# annovar_matrix = matrix
# break
#assert annovar_matrix, "Missing annotation: ExonicFunc.refGene"
# copy.deepcopy is very slow. Try to avoid it.
# Strategy:
# 1. Make a list of the changes to be made.
# 2. Save the filtered rows.
# 3. Make the changes.
# 4. Save the non-filtered rows.
I_remove = {} # i -> 1
call_remove = {} # i -> (sample, caller) -> 1
#CHROM = matrix.header2annots["______Chrom"]
#POS = matrix.header2annots["______Pos"]
#POS = [int(x) for x in POS]
#REF = matrix.header2annots["______Ref"]
#ALT = matrix.header2annots["______Alt"]
# Optimization: normalize the headers for the samples and callers.
sc2header = {} # (sample, caller) -> header_h
for sc in itertools.product(matrix.samples, matrix.callers):
sample, caller = sc
header = "%s___%s___Ref/Alt/VAF" % (sample, caller)
header_h = matrix.normalize_header(header)
assert header_h
sc2header[sc] = header_h
for i in range(matrix.num_annots()):
has_calls = False # whether this row has any calls.
for sc in itertools.product(matrix.samples, matrix.callers):
sample, caller = sc
header_h = sc2header[sc]
call_str = matrix.header2annots[header_h][i]
if not call_str:
continue
call = SimpleVariantMatrix._parse_call(call_str)
filt = False
# filter_by_min_alt_reads
if min_alt_reads > 0 and \
(call.num_alt is None or call.num_alt < min_alt_reads):
filt = True
# filter_by_min_total_reads
if min_total_reads > 0 and (call.total is None
or call.total < min_total_reads):
filt = True
# filter_by_min_vaf
if min_vaf >= 1E-6 and (call.vaf is None
or call.vaf < min_vaf):
filt = True
if filt:
if i not in call_remove:
call_remove[i] = {}
call_remove[i][sc] = 1
else:
has_calls = True
# If this coordinate has no more calls, then remove the
# whole row.
if not has_calls:
I_remove[i] = 1
I_remove = sorted(I_remove)
# Write out a matrix of the discarded rows.
filtered_matrix = AnnotationMatrix.rowslice(matrix, I_remove)
SimpleVariantMatrix.write_from_am("discarded.txt", filtered_matrix)
# Remove the calls.
for i in call_remove:
for sc in call_remove[i]:
header_h = sc2header[sc]
call_str = matrix.header2annots[header_h][i]
assert call_str
matrix.header2annots[header_h][i] = ""
# Which rows to keep.
I_remove_dict = {}.fromkeys(I_remove)
I_keep = [
i for i in range(matrix.num_annots()) if i not in I_remove_dict
]
filtered_matrix = AnnotationMatrix.rowslice(matrix, I_keep)
SimpleVariantMatrix.write_from_am(out_filename, filtered_matrix)
## ## Filter out synonymous variants.
## #if nonsynonymous_and_stopgain_only:
## # # Make sure annotated with Annovar.
## # assert "ExonicFunc.refGene" in annovar_matrix.headers
## # exonic_func = annovar_matrix["ExonicFunc.refGene"]
## # for i, efunc in enumerate(exonic_func):
## # efunc = exonic_func[i]
## # assert efunc in [
## # "", "nonsynonymous SNV", "synonymous SNV",
## # "stopgain", "stoploss",
## # "frameshift substitution", "nonframeshift substitution",
## # "unknown"], \
## # "Unknown exonic_func: %s" % efunc
## # if efunc not in ["nonsynonymous SNV", "stopgain"]:
## # I_remove[i] = 1
## # continue
## # Filter based on the calls.
## if min_alt_reads > 0 or min_total_reads > 0:
## all_coord = call_matrix.coord2samplecaller2call.keys()
## for coord in all_coord:
## all_sc = call_matrix.coord2samplecaller2call[coord].keys()
## for sc in all_sc:
## # SimpleVariantMatrix.Call object.
## call = call_matrix.coord2samplecaller2call[coord][sc]
## # filter_by_min_alt_reads
## if min_alt_reads > 0 and \
## (call.num_alt is None or call.num_alt < min_alt_reads):
## if coord not in call_remove:
## call_remove[coord] = {}
## call_remove[coord][sc] = 1
## # filter_by_min_total_reads
## if min_total_reads > 0 and (
## call.total is None or call.total < min_total_reads):
## if coord not in call_remove:
## call_remove[coord] = {}
## call_remove[coord][sc] = 1
## # Filter based on VAF.
## if min_vaf >= 1E-6:
## all_coord = call_matrix.coord2samplecaller2call.keys()
## for coord in all_coord:
## all_sc = call_matrix.coord2samplecaller2call[coord].keys()
## for sc in all_sc:
## call = call_matrix.coord2samplecaller2call[coord][sc]
## # filter_by_min_vaf
## if call.vaf is None or call.vaf < min_vaf:
## if coord not in call_remove:
## call_remove[coord] = {}
## call_remove[coord][sc] = 1
## # If any of these coordinates have no more variants, then
## # remove the whole row.
## if call_remove:
## chrom, pos = annot_matrix["Chrom"], annot_matrix["Pos"]
## ref, alt = annot_matrix["Ref"], annot_matrix["Alt"]
## pos = [int(x) for x in pos]
## coord2i = {}
## for i, coord in enumerate(zip(chrom, pos, ref, alt)):
## coord2i[coord] = i
## for coord in call_remove:
## num_remove = len(call_remove[coord])
## num_calls = len(call_matrix.coord2samplecaller2call[coord])
## assert num_remove <= num_calls
## if num_remove == num_calls:
## i = coord2i[coord]
## I_remove[i] = 1
## # Make a matrix of the discarded rows.
## old_annot_matrix = var_matrix.annot_matrix
## old_named_matrices = var_matrix.named_matrices
## filtered_matrix = var_matrix
## x = AnnotationMatrix.rowslice(var_matrix.annot_matrix, I_remove)
## filtered_matrix.annot_matrix = x
## named_matrices = []
## for (name, matrix) in var_matrix.named_matrices:
## matrix = AnnotationMatrix.rowslice(matrix, I_remove)
## named_matrices.append((name, matrix))
## filtered_matrix.named_matrices = named_matrices
## SimpleVariantMatrix.write("discarded.txt", filtered_matrix)
## var_matrix.annot_matrix = old_annot_matrix
## var_matrix.named_matrices = old_named_matrices
## # Remove the calls.
## for coord in call_remove:
## chrom, pos, ref, alt = coord
## for (sample, caller) in call_remove[coord]:
## var_matrix.call_matrix.set_call(
## chrom, pos, ref, alt, sample, caller, None)
## # Which rows to keep.
## I_keep = [
## i for i in range(var_matrix.num_variants()) if i not in I_remove]
## # Filter annotation matrix
## var_matrix.annot_matrix = AnnotationMatrix.rowslice(
## var_matrix.annot_matrix, I_keep)
## # Filter named matrices.
## for i, (name, matrix) in enumerate(var_matrix.named_matrices):
## matrix = AnnotationMatrix.rowslice(matrix, I_keep)
## var_matrix.named_matrices[i] = (name, matrix)
## SimpleVariantMatrix.write(out_filename, var_matrix)
return metadata
def run(
self, network, in_data, out_attributes, user_options, num_cores,
out_filename):
import os
from genomicode import jmath
from genomicode import AnnotationMatrix
from genomicode import alignlib
#from Betsy import module_utils as mlib
rsem_path = in_data.identifier
assert os.path.exists(rsem_path)
assert os.path.isdir(rsem_path)
result_files = alignlib.find_rsem_result_files(rsem_path)
assert result_files, "No .results files found."
metadata = {}
preprocess = out_attributes.get("preprocess")
assert preprocess in ["tpm", "fpkm"]
#x = mlib.get_user_option(
# user_options, "genes_or_isoforms", not_empty=True,
# allowed_values=["genes", "isoforms"])
#get_genes = x == "genes"
# Figure out whether to align to genome or transcriptome.
x = out_attributes["expression_of"]
assert x in ["gene", "isoform"]
get_genes = x == "gene"
transcript_header = "transcript_id(s)"
if not get_genes:
transcript_header = "transcript_id"
# For each of the gene files, get the expression data.
sample2matrix = {} # sample -> AnnotationMatrix
for x in result_files:
sample, gene_filename, isoform_filename = x
# Get the gene results.
# TODO: Implement isoforms.
filename = gene_filename
if not get_genes:
filename = isoform_filename
assert filename is not None, "Missing: %s" % filename
#if filename is None:
# continue
assert os.path.exists(filename)
matrix = AnnotationMatrix.read(filename)
# Do some checking on the matrix.
assert "gene_id" in matrix.headers
assert transcript_header in matrix.headers
assert "TPM" in matrix.headers
assert "FPKM" in matrix.headers
sample2matrix[sample] = matrix
assert sample2matrix, "No samples"
gene_id = transcript_id = None
# Pull out the gene and transcript IDs.
for matrix in sample2matrix.itervalues():
x1 = matrix["gene_id"]
x2 = matrix[transcript_header]
if gene_id is None:
gene_id = x1
if transcript_id is None:
transcript_id = x2
assert x1 == gene_id
assert x2 == transcript_id
assert gene_id
assert transcript_id
assert len(gene_id) == len(transcript_id)
# Assemble into a gene expression matrix.
header = "TPM"
if preprocess == "fpkm":
header = "FPKM"
t_data = [] # matrix, where each row is a sample.
t_data.append(gene_id)
t_data.append(transcript_id)
samples = []
for sample in sorted(sample2matrix):
matrix = sample2matrix[sample]
exp = matrix[header]
assert len(exp) == len(gene_id)
t_data.append(exp)
samples.append(sample)
data = jmath.transpose(t_data)
header = ["gene_id", transcript_header] + samples
data = [header] + data
# Write out the data file.
handle = open(out_filename, 'w')
for x in data:
print >>handle, "\t".join(map(str, x))
return metadata
def add_coverage_to_svm(svm_file, coverage_file, outfile, is_rna_cov):
from genomicode import jmath
from genomicode import filelib
from genomicode import AnnotationMatrix
from genomicode import SimpleVariantMatrix
# Read the variant file.
SVM = SimpleVariantMatrix.read(svm_file)
AM = SVM.annot_matrix
assert "Chrom" in AM.headers
assert "Pos" in AM.headers
CHROM = AM["Chrom"]
POS = AM["Pos"]
POS = [int(x) for x in POS]
# Read the coverage matrix.
# Chrom Pos <Sample> [<Sample> ...]
# Pos is 1-based.
coord2sample2cov = {} # (chrom, pos) -> sample -> ref/alt/vaf
cov_samples = {}
for d in filelib.read_row(coverage_file, header=1):
coord = d.Chrom, int(d.Pos)
if coord not in coord2sample2cov:
coord2sample2cov[coord] = {}
for i in range(2, len(d._header)):
sample = d._header[i]
cov = d._cols[i]
if not cov:
continue
#coord2sample2cov[coord][sample] = int(cov)
coord2sample2cov[coord][sample] = cov
cov_samples[sample] = 1
# Make sure the samples from the variant matrix can be found
# in the coverage matrix.
missing = [x for x in SVM.samples if x not in cov_samples]
assert len(missing) < len(SVM.samples), (
"SimpleVariantMatrix and coverage file have "
"no common samples.")
# If the samples aren't sequenced at high coverage, it's
# possible they just don't have reads at these positions. Be
# a little lenient here, and accept the file if some of the
# samples overlap.
#x = missing
#if len(x) > 5:
# x = x[:5] + ["..."]
#msg = "Samples (%d) not found in coverage file: %s" % (
# len(missing), ", ".join(x))
#assert not missing, msg
# Report the coverage for the samples at the intersection.
SAMPLES = [x for x in SVM.samples if x in cov_samples]
# Align the matrix to the simple variant matrix.
#matrix = [[None]*len(SVM.samples) for i in range(AM.num_annots())]
matrix = [[None]*len(SAMPLES) for i in range(AM.num_annots())]
for i in range(AM.num_annots()):
coord = CHROM[i], POS[i]
sample2cov = coord2sample2cov.get(coord, {})
x = [sample2cov.get(x, "") for x in SAMPLES]
#x = map(str, x)
matrix[i] = x
# Add the matrix back to the simple variant matrix.
headers = SAMPLES
all_annots = jmath.transpose(matrix)
name = "Coverage"
# If this is being used to add RNA coverage, use a different
# name.
if is_rna_cov:
name = "RNA Coverage"
x = AnnotationMatrix.create_from_annotations(headers, all_annots)
SVM.named_matrices.append((name, x))
# Write to file.
SimpleVariantMatrix.write(outfile, SVM)
def main():
import os
import argparse
from genomicode import jmath
from genomicode import AnnotationMatrix
from genomicode import colorlib
from genomicode import pcalib
parser = argparse.ArgumentParser(description="")
parser.add_argument("datafile", help="Tab-delimited data file.")
#parser.add_argument("x_header", help="Which column for X values.")
#parser.add_argument("y_header", help="Which column for Y values.")
parser.add_argument(
"plot_file",
help="Name of image file, e.g. outfile.png. "
"Will generate PNG format by default. If this file name ends with "
".pdf, will generate a PDF file instead.")
group = parser.add_argument_group(title="Data Series")
group.add_argument(
"--series",
action="append",
help="Add a data series to the plot. At least one series must be "
"plotted. Format: <x_header>;<y_header>")
group = parser.add_argument_group(title="General Appearance")
group.add_argument("--no_box",
action="store_true",
help="Turn off the box around the plot.")
group.add_argument("--height",
type=int,
help="Height (in pixels) of the plot.")
group.add_argument("--width",
type=int,
help="Width (in pixels) of the plot.")
group.add_argument(
"--mar_left",
default=1.0,
type=float,
help="Scale margin at left of plot. Default 1.0 (no scaling).")
group.add_argument("--mar_bottom",
default=1.0,
type=float,
help="Scale margin at bottom of plot. Default 1.0.")
#group.add_argument(
# "--xlabel_size", default=1.0, type=float,
# help="Scale the size of the labels on X-axis. Default 1.0.")
group.add_argument("--log_x",
action="store_true",
help="Plot the X-axis on a log scale.")
group.add_argument("--log_y",
action="store_true",
help="Plot the Y-axis on a log scale.")
group.add_argument(
"--qq",
action="store_true",
help="Make a QQ-plot. Will sort the values to be plotted.")
group = parser.add_argument_group(title="Plot Labels")
group.add_argument("--title", help="Put a title on the plot.")
group.add_argument("--xlab", help="Label the X-axis.")
group.add_argument("--ylab", help="Label the Y-axis.")
group.add_argument("--add_regression",
action="store_true",
help="Put a regression line on the plot.")
group = parser.add_argument_group(title="Legend")
group.add_argument("--add_legend",
action="store_true",
help="Add a legend to the plot.")
group.add_argument("--legend_inset", type=float, default=0.05, help="")
LEGEND_LOCATIONS = [
"bottomright",
"bottom",
"bottomleft",
"left",
"topleft",
"top",
"topright",
"right",
"center",
]
group.add_argument("--legend_loc",
choices=LEGEND_LOCATIONS,
help="Where to draw the legend.")
group = parser.add_argument_group(title="Point Appearance")
group.add_argument("--scale_points",
default=1.0,
type=float,
help="Scale the size of the points. Default 1.0")
group.add_argument("--label_header",
help="Label each point with the values in this column.")
group.add_argument("--label_size",
type=float,
help="Scale the size of the labels by this value.")
group.add_argument("--label_pos",
default="top",
choices=["top", "bottom", "left", "right"],
help="Where to label the points.")
group = parser.add_argument_group(title="Line Appearance")
group.add_argument("--add_lines",
action="store_true",
help="Add lines that connect the points.")
group.add_argument("--scale_lines",
default=1.0,
type=float,
help="Scale the thickness of the lines. Default 1.0")
group = parser.add_argument_group(title="Identity Line")
group.add_argument("--add_identity_line",
action="store_true",
help="Add an identity line to the plot.")
group = parser.add_argument_group(title="Colors")
group.add_argument(
"-c",
"--cluster",
action="append",
help="Group samples into a cluster (e.g. -c 1-5); 1-based, inclusive.")
group.add_argument(
"--indexes_include_headers",
"--iih",
action="store_true",
help="If not given (default), then index 1 is the first row "
"with data. If given, then index 1 is the very first row "
"in the file, including the headers.")
group.add_argument("--default_color",
help="Default color of points. Format: #000000.")
# Parse the input arguments.
args = parser.parse_args()
if not os.path.exists(args.datafile):
parser.error("File not found: %s" % args.datafile)
if args.width is not None:
assert args.width > 10, "too small"
assert args.width < 4096 * 16, "width too big"
if args.height is not None:
assert args.height > 10, "too small"
assert args.height < 4096 * 16, "height too big"
assert args.mar_bottom > 0 and args.mar_bottom < 10
assert args.mar_left > 0 and args.mar_left < 10
#assert args.xlabel_size > 0 and args.xlabel_size < 10
assert args.legend_inset >= 0 and args.legend_inset < 10
if args.legend_loc is None:
args.legend_loc = "bottomright"
if args.default_color:
assert len(args.default_color) == 7
assert args.default_color[0] == "#"
MATRIX = AnnotationMatrix.read(args.datafile, False)
assert MATRIX.num_headers() and MATRIX.num_annots(), "Empty matrix."
assert args.series, "Need to add a data --series to plot."
#assert len(args.series) <= 1, "Not implemented."
#assert args.x_header in MATRIX.headers, \
# "header not found: %s" % args.x_header
#assert args.y_header in MATRIX.headers, \
# "header not found: %s" % args.y_header
if args.label_header:
assert args.label_header in MATRIX.headers, \
"header not found: %s" % args.label_header
if args.label_size is not None:
assert args.label_size > 0 and args.label_size <= 20
assert args.scale_points > 0 and args.scale_points < 20
assert args.scale_lines > 0 and args.scale_lines < 20
series = _parse_series(MATRIX, args.series)
cluster = None
if args.cluster:
cluster = _parse_cluster(args.cluster, args.indexes_include_headers,
MATRIX)
if len(series) > 1:
assert not cluster, "Series and cluster not implemented."
height = args.height or 2400
width = args.width or 3200
# Pull out the values and colors for the plot.
default_color = "#000000"
if args.default_color:
default_color = args.default_color
assert len(series) < len(colorlib.BREWER_QUALITATIVE_SET1)
series_data = [] # list of (x_values, y_values, col) for each series
for i in range(len(series)):
x_header, y_header = series[i]
x = MATRIX[x_header]
y = MATRIX[y_header]
I1 = [j for (j, a) in enumerate(x) if a]
I2 = [j for (j, a) in enumerate(y) if a]
I = [j for j in I1 if j in I2]
x = [x[j] for j in I]
y = [y[j] for j in I]
x = map(float, x)
y = map(float, y)
assert len(x) == len(y)
c = default_color
if len(series) > 1:
rgb = colorlib.BREWER_QUALITATIVE_SET1[i]
c = colorlib.rgb2hex(rgb, prefix="#")
c = [c] * len(x)
x = x, y, c
series_data.append(x)
# Merge all the data point for each series.
x_values = []
y_values = []
col = []
for (x, y, c) in series_data:
x_values.extend(x)
y_values.extend(y)
#c = [c] * len(x)
col.extend(c)
assert len(x_values) == len(y_values)
assert len(x_values) == len(col)
if args.qq:
O = jmath.order(x_values)
x_values = [x_values[i] for i in O]
y_values = [y_values[i] for i in O]
col = [col[i] for i in O]
if cluster is not None:
col_rgb = pcalib.choose_colors(cluster)
col = [default_color] * len(col_rgb)
for i in range(len(col_rgb)):
if col_rgb[i] is None:
continue
col[i] = colorlib.rgb2hex(col_rgb[i], prefix="#")
assert len(col) == len(x_values)
#for i in range(len(x_values)):
# x = x_values[i], y_values[i], cluster[i], col[i]
# print "\t".join(map(str, x))
# Start R and set up the environment.
R = jmath.start_R()
main = jmath.R_var("NA")
if args.title:
main = args.title
sub = ""
xlab = ""
if len(series) == 1:
xlab = x_header
if args.xlab:
xlab = args.xlab
ylab = ""
if len(series) == 1:
ylab = y_header
if args.xlab:
ylab = args.ylab
lwd_box = 2
lwd_axis = 2
lwd_regr = 3
cex = 1.0 * args.scale_points
cex_lab = 1.5
cex_main = 2.0
cex_sub = 1.0
plot_log = ""
if args.log_x:
plot_log += "x"
if args.log_y:
plot_log += "y"
assert x_values
assert y_values
jmath.R_equals(x_values, "X")
jmath.R_equals(y_values, "Y")
bm_type = "png16m"
if args.plot_file.lower().endswith(".pdf"):
bm_type = "pdfwrite"
jmath.R_fn("bitmap",
args.plot_file,
type=bm_type,
height=height,
width=width,
units="px",
res=300)
# Set the margins.
x = 5 * 1.2 * args.mar_bottom, 4 * 1.2 * args.mar_left, 4, 2
mar = [x + 0.1 for x in x]
jmath.R_fn("par", mar=mar, RETVAL="op")
jmath.R_fn("plot",
jmath.R_var("X"),
jmath.R_var("Y"),
main="",
xlab="",
ylab="",
pch=19,
cex=cex,
log=plot_log,
col=col,
axes=jmath.R_var("FALSE"),
RETVAL="x")
# Make plot area solid white.
#jmath.R('usr <- par("usr")')
#jmath.R('rect(usr[1], usr[3], usr[2], usr[4], col="#FFFFFF")')
#jmath.R_fn(
# "hist", jmath.R_var("X"), plot=jmath.R_var("FALSE"),
# main=main, xlab="", ylab="", axes=jmath.R_var("FALSE"),
# add=jmath.R_var("TRUE"))
if args.add_lines:
lwd = 4 * args.scale_lines
i = 0
for (x, y, c) in series_data:
# Cannot use c for the color. It might've been changed by
# --cluster.
assert col and i < len(col)
c = col[i:i + len(x)]
i += len(x)
# The "lines" function takes a scalar for col (except for
# type=h, histogram vertical lines). If there are
# multiple colors, then split up the points based on the
# colors.
l_x, l_y, l_c = [], [], None
for j in range(len(x)):
if c[j] != l_c:
if l_x:
jmath.R_fn("lines", l_x, l_y, lwd=lwd, col=l_c)
# Add the previous point so that the points will
# connect.
if l_x:
l_x = [l_x[-1]]
l_y = [l_y[-1]]
else:
l_x, l_y, l_c = [], [], None
l_x.append(x[j])
l_y.append(y[j])
l_c = c[j]
if l_x:
jmath.R_fn("lines", l_x, l_y, lwd=lwd, col=l_c)
if args.add_identity_line:
lwd = 4
x_min, x_max = min(x_values), max(x_values)
y_min, y_max = min(y_values), max(y_values)
iden_min = max(x_min, y_min)
iden_max = min(x_max, y_max)
l_x = [iden_min, iden_max]
l_y = l_x
l_c = "#FF0000"
jmath.R_fn("lines", l_x, l_y, lwd=lwd, col=l_c)
if args.label_header:
cex = 1
if args.label_size is not None:
cex = args.label_size
pos2specifier = {
"top": 3,
"bottom": 1,
"left": 2,
"right": 4,
}
pos = pos2specifier[args.label_pos]
point_labels = MATRIX[args.label_header]
jmath.R_fn("text",
jmath.R_var("X"),
jmath.R_var("Y"),
labels=point_labels,
cex=cex,
pos=pos)
# Calculate correlation, and other statistics.
# TODO: Should calculate this for each series.
r = jmath.R("cor(X, Y)")
p_value = jmath.R("cor.test(X, Y)$p.value")
r = r[0]
p_value = p_value[0]
print "R = %.2f" % r
print "p = %.2g" % p_value
# Add a regression line.
if args.add_regression:
jmath.R("fit <- lm(Y ~ X)")
coef = jmath.R("fit$coefficients")
assert len(coef) == 2
b, m = coef
x1 = min(x_values)
y1 = x1 * m + b
x2 = max(x_values)
y2 = x2 * m + b
jmath.R_fn("lines", [x1, x2], [y1, y2],
lwd=lwd_regr,
lty=2,
col="#C63F31")
sub = "R=%.2f (p=%.2g)" % (r, p_value)
header = "X", "Y", "R", "p"
print "\t".join(header)
x = xlab, ylab, r, p_value
print "\t".join(map(str, x))
if args.add_legend:
leg = [x[1] for x in series]
fill = [x[-1] for x in series_data]
#jmath.R("x <- rgb(0.5, 0.5, 0.5, 0.5)")
# alpha does not seem to be supported here.
jmath.R_fn("legend",
args.legend_loc,
legend=leg,
fill=fill,
inset=args.legend_inset)
if not args.no_box:
jmath.R_fn("box", lwd=lwd_box)
jmath.R_fn("axis", 1, lwd=lwd_axis, **{"cex.axis": 1.5})
jmath.R_fn("axis", 2, lwd=lwd_axis, **{"cex.axis": 1.5})
jmath.R_fn("title",
main=main,
sub=sub,
xlab=xlab,
ylab=ylab,
**{
"cex.lab": cex_lab,
"cex.main": cex_main,
"cex.sub": cex_sub
})
R("par(op)")
jmath.R_fn("dev.off")
def run(self, network, in_data, out_attributes, user_options, num_cores,
outfile):
import StringIO
import arrayio
from genomicode import arrayplatformlib
from genomicode import parallel
from genomicode import filelib
from genomicode import AnnotationMatrix
from Betsy import module_utils as mlib
M = arrayio.read(in_data.identifier)
metadata = {}
# Add GENE_ID, GENE_SYMBOL, and DESCRIPTION. Figure out which
# platforms provide each one of this.
CATEGORIES = [
arrayplatformlib.GENE_ID,
arrayplatformlib.GENE_SYMBOL,
# biomaRt doesn't convert description. So just ignore it
# for now.
# TODO: implement DESCRIPTION.
#arrayplatformlib.DESCRIPTION,
]
#all_platforms = arrayplatformlib.identify_all_platforms_of_matrix(M)
#assert all_platforms, "Unknown platform: %s" % in_data.identifier
#header, platform_name = all_platforms[0]
scores = arrayplatformlib.score_matrix(M)
scores = [x for x in scores if x.max_score >= 0.75]
assert scores, "I could not identify any platforms."
# Find all the platforms not in the matrix.
platforms = [
arrayplatformlib.find_platform_by_name(x.platform_name)
for x in scores
]
categories = [x.category for x in platforms]
missing = [x for x in CATEGORIES if x not in categories]
score = scores[0]
platform = platforms[0]
to_add = [] # list of platform names
for category in missing:
x = arrayplatformlib.PLATFORMS
x = [x for x in x if x.category == category]
x = [x for x in x if x.bm_organism == platform.bm_organism]
x = [x for x in x if x.name != score.platform_name]
# Take the first one, if any.
if x:
to_add.append(x[0].name)
if to_add:
annotate = mlib.get_config("annotate_matrix",
which_assert_file=True)
sq = parallel.quote
cmd = [
"python",
sq(annotate),
"--no_na",
"--header",
sq(score.header),
]
for x in to_add:
x = ["--platform", sq(x)]
cmd.extend(x)
cmd.append(in_data.identifier)
cmd = " ".join(cmd)
data = parallel.sshell(cmd)
metadata["commands"] = [cmd]
assert data.find("Traceback") < 0, data
else:
data = open(in_data.identifier).read()
# Clean up the headers.
platform2pretty = {
"Entrez_ID_human": "Gene ID",
"Entrez_Symbol_human": "Gene Symbol",
"Entrez_ID_mouse": "Gene ID",
"Entrez_Symbol_mouse": "Gene Symbol",
}
handle = open(outfile, 'w')
header_written = False
for cols in filelib.read_cols(StringIO.StringIO(data)):
if not header_written:
cols = [platform2pretty.get(x, x) for x in cols]
cols = AnnotationMatrix.uniquify_headers(cols)
header_written = True
print >> handle, "\t".join(cols)
return metadata
def run(self, network, in_data, out_attributes, user_options, num_cores,
out_filename):
#import shutil
from genomicode import filelib
from genomicode import parallel
from genomicode import alignlib
from genomicode import SimpleVariantMatrix
from genomicode import AnnotationMatrix
from Betsy import module_utils as mlib
summary_node = in_data
summary_filename = summary_node.identifier
metadata = {}
buildver = mlib.get_user_option(user_options,
"annovar_buildver",
allowed_values=["hg19"],
not_empty=True)
# Name files.
p, root, ext = mlib.splitpath(summary_filename)
annovar_infile = "pos.txt"
log_filename = "annovar.log"
# Annovar takes a filestem, without the ".vcf".
annovar_outstem = "annotations"
# Produces file:
# <annovar_outstem>.hg19_multianno.txt
multianno_file = "%s.hg19_multianno.txt" % annovar_outstem
#temp_file = "temp.txt"
# Make the infile for Annovar.
# <chrom> <start> <end> <ref> <alt>
handle = open(annovar_infile, 'w')
for d in filelib.read_row(summary_filename, skip=2, header=1):
x = d.Chrom, d.Pos, d.Pos, d.Ref, d.Alt
print >> handle, "\t".join(x)
handle.close()
cmd = alignlib.make_annovar_command(annovar_infile,
log_filename,
annovar_outstem,
buildver,
vcf_input=False)
parallel.sshell(cmd)
metadata["commands"] = [cmd]
filelib.assert_exists_nz(log_filename)
filelib.assert_exists_nz(multianno_file)
matrix = SimpleVariantMatrix.read(summary_filename)
annot_matrix = matrix.annot_matrix
#headers = annot_matrix.headers + anno_header[5:]
chrom, pos = annot_matrix["Chrom"], annot_matrix["Pos"]
ref, alt = annot_matrix["Ref"], annot_matrix["Alt"]
pos = [int(x) for x in pos]
# Read in the multianno output file.
pos2d = {} # (chrom, start, ref, alt) -> d
anno_header = None
for d in filelib.read_row(multianno_file, header=1):
key = d.Chr, int(d.Start), d.Ref, d.Alt
assert key not in pos2d, "Duplicate pos: %s" % str(key)
pos2d[key] = d
if not anno_header:
anno_header = d._header
assert anno_header
# Multianno starts with:
# Chr Start End Ref Alt
# Ignore these.
assert anno_header[:5] == ["Chr", "Start", "End", "Ref", "Alt"]
headers = anno_header[5:]
all_annots = []
#for h in annot_matrix.headers_h:
# x = annot_matrix.header2annots[h]
# all_annots.append(x)
for i in range(5, len(anno_header)):
annots = []
for coord in zip(chrom, pos, ref, alt):
d = pos2d.get(coord)
x = ""
if d:
x = d._cols[i]
annots.append(x)
all_annots.append(annots)
x = AnnotationMatrix.create_from_annotations(headers, all_annots)
matrix.named_matrices.insert(0, ("Annovar", x))
SimpleVariantMatrix.write(out_filename, matrix)
## cols_to_add = len(anno_header) - 5
## assert cols_to_add > 0
## # Merge the multianno file with the simple call summary. Add
## # these columns before the <Sample>.
## # Sample <Sample>
## # Caller <Caller>
## # Chrom Pos Ref Alt Ref/Alt/VAF
## handle = open(temp_file, 'w')
## it = filelib.read_cols(summary_filename)
## header1 = it.next()
## header2 = it.next()
## header3 = it.next()
## assert len(header1) == len(header2), "%d %d %d %s" % (
## len(header1), len(header2), len(header3), summary_filename)
## assert len(header1) == len(header3), "%d %d %d %s" % (
## len(header1), len(header2), len(header3), summary_filename)
## assert header1[0] == "Sample"
## assert header2[0] == "Caller"
## assert header3[:4] == ["Chrom", "Pos", "Ref", "Alt"]
## header1 = header1[:4] + [""]*cols_to_add + header1[4:]
## header2 = header2[:4] + [""]*cols_to_add + header2[4:]
## header3 = header3[:4] + anno_header[5:] + header3[4:]
## print >>handle, "\t".join(header1)
## print >>handle, "\t".join(header2)
## print >>handle, "\t".join(header3)
## for cols in it:
## chrom, pos, ref, alt = cols[:4]
## pos = int(pos)
## d = pos2d.get((chrom, pos))
## if not d:
## cols = cols[:4] + [""]*cols_to_add + cols[4:]
## continue
## assert ref == d.Ref, "%s %s %s %s %s %s" % (
## chrom, pos, ref, alt, d.Ref, d.Alt)
## assert alt == d.Alt, "%s %s %s %s %s %s" % (
## chrom, pos, ref, alt, d.Ref, d.Alt)
## x = d._cols[5:]
## assert len(x) == cols_to_add
## cols = cols[:4] + x + cols[4:]
## print >>handle, "\t".join(cols)
## handle.close()
## shutil.move(temp_file, out_filename)
return metadata