From 48d6eed286ba6d5a8b901c6c3e8405235a9bbd7e Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Fri, 11 Oct 2019 10:51:53 -0400
Subject: [PATCH] fixes
---
downloads-generation/data_curated/GENERATE.sh | 28 +-
...curate_by_pmid.py => curate_ms_by_pmid.py} | 465 +++++++++++++++---
.../data_published/GENERATE.sh | 82 ++-
.../models_class1_pan_variants/GENERATE.sh | 6 +-
mhcflurry/downloads.yml | 6 +-
5 files changed, 491 insertions(+), 96 deletions(-)
rename downloads-generation/data_curated/{curate_by_pmid.py => curate_ms_by_pmid.py} (59%)
diff --git a/downloads-generation/data_curated/GENERATE.sh b/downloads-generation/data_curated/GENERATE.sh
index fd041f93..b35d01fc 100755
--- a/downloads-generation/data_curated/GENERATE.sh
+++ b/downloads-generation/data_curated/GENERATE.sh
@@ -29,23 +29,33 @@ git status
cd $SCRATCH_DIR/$DOWNLOAD_NAME
cp $SCRIPT_DIR/curate.py .
-cp $SCRIPT_DIR/curate_by_pmid.py .
+cp $SCRIPT_DIR/curate_ms_by_pmid.py .
-RAW_DIR="$(mhcflurry-downloads path data_published)/raw"
-cp -r "$RAW_DIR" .
+MS_DIR="$(mhcflurry-downloads path data_published)/ms"
+cp -r "$MS_DIR" .
+
+EXPRESSION_DIR="$(mhcflurry-downloads path data_published)/expression"
+cp -r "$EXPRESSION_DIR" .
CURATE_BY_PMID_ARGS=""
-for pmid in $(ls raw)
+for pmid in $(ls ms)
+do
+ CURATE_BY_PMID_ARGS+=$(echo --ms-item $pmid ms/$pmid/* ' ')
+done
+for item in $(ls expression)
do
- CURATE_BY_PMID_ARGS+=$(echo --item $pmid raw/$pmid/* ' ')
+ CURATE_BY_PMID_ARGS+=$(echo --expression-item $item expression/$item/* ' ')
done
-time python curate_by_pmid.py $CURATE_BY_PMID_ARGS \
- --out nontraining_curated.by_pmid.csv
+time python curate_ms_by_pmid.py $CURATE_BY_PMID_ARGS \
+ --ms-out ms.nontraining_curated.by_pmid.csv \
+ --expression-out rna_expression.csv
+
+bzip2 ms.nontraining_curated.by_pmid.csv
+bzip2 rna_expression.csv
-bzip2 nontraining_curated.by_pmid.csv
-rm -rf raw
+rm -rf ms
# No mass-spec data
time python curate.py \
diff --git a/downloads-generation/data_curated/curate_by_pmid.py b/downloads-generation/data_curated/curate_ms_by_pmid.py
similarity index 59%
rename from downloads-generation/data_curated/curate_by_pmid.py
rename to downloads-generation/data_curated/curate_ms_by_pmid.py
index 4f1950e5..5406e238 100755
--- a/downloads-generation/data_curated/curate_by_pmid.py
+++ b/downloads-generation/data_curated/curate_ms_by_pmid.py
@@ -23,24 +23,35 @@ def normalize_allele_name(s):
parser = argparse.ArgumentParser(usage=__doc__)
parser.add_argument(
- "--item",
+ "--ms-item",
nargs="+",
action="append",
metavar="PMID FILE, ... FILE",
default=[],
- help="Item to curate: PMID and list of files")
+ help="Mass spec item to curate: PMID and list of files")
parser.add_argument(
- "--out",
+ "--expression-item",
+ nargs="+",
+ action="append",
+ metavar="LABEL FILE, ... FILE",
+ default=[],
+ help="Expression data to curate: dataset label and list of files")
+parser.add_argument(
+ "--ms-out",
+ metavar="OUT.csv",
+ help="Out file path (MS data)")
+parser.add_argument(
+ "--expression-out",
metavar="OUT.csv",
- help="Out file path")
+ help="Out file path (RNA-seq expression)")
parser.add_argument(
"--debug",
action="store_true",
default=False,
help="Leave user in pdb if PMID is unsupported")
-HANDLERS = {}
-
+PMID_HANDLERS = {}
+EXPRESSION_HANDLERS = {}
def load(filenames, **kwargs):
result = {}
@@ -146,7 +157,7 @@ def handle_pmid_24616531(filename):
"peptide": peptides,
})
result_df["sample_id"] = "24616531"
- result_df["sample_type"] = "B-lymphoblastoid"
+ result_df["sample_type"] = "B-LCL"
result_df["cell_line"] = "GR"
result_df["pulldown_antibody"] = "W6/32"
@@ -181,7 +192,6 @@ def handle_pmid_25576301(filename):
rows.append((row.Sequence, sample))
result_df = pandas.DataFrame(rows, columns=["peptide", "sample_id"])
- result_df["cell_line"] = ""
result_df["pulldown_antibody"] = "W6/32"
result_df["mhc_class"] = "I"
result_df["format"] = "multiallelic"
@@ -209,11 +219,21 @@ def handle_pmid_25576301(filename):
'HCC1143': "basal like breast cancer",
'JY': "B-cell",
}
+ cell_line = {
+ 'Fib': None,
+ 'HCC1937': "HCC1937",
+ 'SupB15WT': None,
+ 'SupB15RT': None,
+ 'HCT116': "HCT116",
+ 'HCC1143': "HCC1143",
+ 'JY': "JY",
+ }
result_df["hla"] = result_df.sample_id.map(allele_map)
print("Entries before dropping samples with unknown alleles", len(result_df))
result_df = result_df.loc[~result_df.hla.isnull()]
print("Entries after dropping samples with unknown alleles", len(result_df))
result_df["sample_type"] = result_df.sample_id.map(sample_type)
+ result_df["cell_line"] = result_df.sample_id.map(cell_line)
print(result_df.head(3))
return result_df
@@ -266,7 +286,7 @@ def handle_pmid_26992070(*filenames):
"HEK293": "hek",
"HL-60": "neutrophil",
"RPMI8226": "b-cell",
- "MAVER-1": "b-lymphoblast",
+ "MAVER-1": "b-LCL",
"THP-1": "monocyte",
})
result_df["mhc_class"] = "I"
@@ -343,30 +363,30 @@ def handle_pmid_28832583(*filenames):
CM467 B-cell 28832583 HLA-A*01:01 HLA-A*24:02 HLA-B*13:02 HLA-B*39:06 HLA-C*06:02 HLA-C*12:03
GD149 B-cell 28832583 HLA-A*01:01 HLA-A*24:02 HLA-B*38:01 HLA-B*44:03 HLA-C*06:02 HLA-C*12:03
MD155 B-cell 28832583 HLA-A*02:01 HLA-A*24:02 HLA-B*15:01 HLA-B*18:01 HLA-C*03:03 HLA-C*07:01
- PD42 B cell 28832583 HLA-A*02:06 HLA-A*24:02 HLA-B*07:02 HLA-B*55:01 HLA-C*01:02 HLA-C*07:02
- RA957 B cell 28832583 HLA-A*02:20 HLA-A*68:01 HLA-B*35:03 HLA-B*39:01 HLA-C*04:01 HLA-C*07:02
+ PD42 B-cell 28832583 HLA-A*02:06 HLA-A*24:02 HLA-B*07:02 HLA-B*55:01 HLA-C*01:02 HLA-C*07:02
+ RA957 B-cell 28832583 HLA-A*02:20 HLA-A*68:01 HLA-B*35:03 HLA-B*39:01 HLA-C*04:01 HLA-C*07:02
TIL1 TIL 28832583 HLA-A*02:01 HLA-A*02:01 HLA-B*18:01 HLA-B*38:01 HLA-C*05:01
TIL3 TIL 28832583 HLA-A*01:01 HLA-A*23:01 HLA-B*07:02 HLA-B*15:01 HLA-C*12:03 HLA-C*14:02
Apher1 Leukapheresis 28832583 HLA-A*03:01 HLA-A*29:02 HLA-B*44:02 HLA-B*44:03 HLA-C*12:03 HLA-C*16:01
Apher6 Leukapheresis 28832583 HLA-A*02:01 HLA-A*03:01 HLA-B*07:02 HLA-C*07:02
- pat_AC2 B lymphoblast 27841757 HLA-A*03:01 HLA-A*32:01 HLA-B*27:05 HLA-B*45:01
- pat_C B lymphoblast 27841757 HLA-A*02:01 HLA-A*03:01 HLA-B*07:02 HLA-C*07:02
- pat_CELG B lymphoblast 27841757 HLA-A*02:01 HLA-A*24:02 HLA-B*15:01 HLA-B*73:01 HLA-C*03:03 HLA-C*15:05
- pat_CP2 B lymphoblast 27841757 HLA-A*11:01 HLA-B*14:02 HLA-B*44:02
- pat_FL B lymphoblast 27841757 HLA-A*03:01 HLA-A*11:01 HLA-B*44:03 HLA-B*50:01
- pat_J B lymphoblast 27841757 HLA-A*02:01 HLA-A*03:01 HLA-B*07:02 HLA-C*07:02
- pat_JPB3 B lymphoblast 27841757 HLA-A*02:01 HLA-A*11:01 HLA-B*27:05 HLA-B*56:01
- pat_JT2 B lymphoblast 27841757 HLA-A*11:01 HLA-B*18:03 HLA-B*35:01
- pat_M B lymphoblast 27841757 HLA-A*03:01 HLA-A*29:02 HLA-B*08:01 HLA-B*44:03 HLA-C*07:01 HLA-C*16:01
- pat_MA B lymphoblast 27841757 HLA-A*02:01 HLA-A*29:02 HLA-B*44:03 HLA-B*57:01 HLA-C*07:01 HLA-C*16:01
- pat_ML B lymphoblast 27841757 HLA-A*02:01 HLA-A*11:01 HLA-B*40:01 HLA-B*44:03
- pat_NS2 B lymphoblast 27841757 HLA-A*02:01 HLA-B*13:02 HLA-B*41:01
- pat_NT B lymphoblast 27841757 HLA-A*01:01 HLA-A*32:01 HLA-B*08:01
- pat_PF1 B lymphoblast 27841757 HLA-A*01:01 HLA-A*02:01 HLA-B*07:02 HLA-B*44:03 HLA-C*07:02 HLA-C*16:01
- pat_R B lymphoblast 27841757 HLA-A*03:01 HLA-A*29:02 HLA-B*08:01 HLA-B*44:03 HLA-C*07:01 HLA-C*16:01
- pat_RT B lymphoblast 27841757 HLA-A*01:01 HLA-A*02:01 HLA-B*18:01 HLA-B*39:24 HLA-C*05:01 HLA-C*07:01
- pat_SR B lymphoblast 27841757 HLA-A*02:01 HLA-A*23:01 HLA-B*18:01 HLA-B*44:03
- pat_ST B lymphoblast 27841757 HLA-A*03:01 HLA-A*24:02 HLA-B*07:02 HLA-B*27:05
+ pat_AC2 B-LCL 27841757 HLA-A*03:01 HLA-A*32:01 HLA-B*27:05 HLA-B*45:01
+ pat_C B-LCL 27841757 HLA-A*02:01 HLA-A*03:01 HLA-B*07:02 HLA-C*07:02
+ pat_CELG B-LCL 27841757 HLA-A*02:01 HLA-A*24:02 HLA-B*15:01 HLA-B*73:01 HLA-C*03:03 HLA-C*15:05
+ pat_CP2 B-LCL 27841757 HLA-A*11:01 HLA-B*14:02 HLA-B*44:02
+ pat_FL B-LCL 27841757 HLA-A*03:01 HLA-A*11:01 HLA-B*44:03 HLA-B*50:01
+ pat_J B-LCL 27841757 HLA-A*02:01 HLA-A*03:01 HLA-B*07:02 HLA-C*07:02
+ pat_JPB3 B-LCL 27841757 HLA-A*02:01 HLA-A*11:01 HLA-B*27:05 HLA-B*56:01
+ pat_JT2 B-LCL 27841757 HLA-A*11:01 HLA-B*18:03 HLA-B*35:01
+ pat_M B-LCL 27841757 HLA-A*03:01 HLA-A*29:02 HLA-B*08:01 HLA-B*44:03 HLA-C*07:01 HLA-C*16:01
+ pat_MA B-LCL 27841757 HLA-A*02:01 HLA-A*29:02 HLA-B*44:03 HLA-B*57:01 HLA-C*07:01 HLA-C*16:01
+ pat_ML B-LCL 27841757 HLA-A*02:01 HLA-A*11:01 HLA-B*40:01 HLA-B*44:03
+ pat_NS2 B-LCL 27841757 HLA-A*02:01 HLA-B*13:02 HLA-B*41:01
+ pat_NT B-LCL 27841757 HLA-A*01:01 HLA-A*32:01 HLA-B*08:01
+ pat_PF1 B-LCL 27841757 HLA-A*01:01 HLA-A*02:01 HLA-B*07:02 HLA-B*44:03 HLA-C*07:02 HLA-C*16:01
+ pat_R B-LCL 27841757 HLA-A*03:01 HLA-A*29:02 HLA-B*08:01 HLA-B*44:03 HLA-C*07:01 HLA-C*16:01
+ pat_RT B-LCL 27841757 HLA-A*01:01 HLA-A*02:01 HLA-B*18:01 HLA-B*39:24 HLA-C*05:01 HLA-C*07:01
+ pat_SR B-LCL 27841757 HLA-A*02:01 HLA-A*23:01 HLA-B*18:01 HLA-B*44:03
+ pat_ST B-LCL 27841757 HLA-A*03:01 HLA-A*24:02 HLA-B*07:02 HLA-B*27:05
"""
info_df = pandas.read_csv(StringIO(info_text), sep="\t", index_col=0)
info_df.index = info_df.index.str.strip()
@@ -613,59 +633,383 @@ def handle_pmid_31495665(filename):
return result_df
-# Add all functions with names like handle_pmid_XXXX to HANDLERS dict.
+def handle_pmid_27869121(filename):
+ """Bassani-Sternberg, ..., Krackhardt Nature Comm. 2016 [PMID 27869121]"""
+ # Although this dataset has class II data also, we are only extracting
+ # class I for now.
+ df = pandas.read_excel(filename, skiprows=1)
+
+ # Taking these from:
+ # Supplementary Table 2: Information of patients selected for neoepitope
+ # identification
+ # For the Mel5 sample, only two-digit alleles are shown (A*01, A*25,
+ # B*08, B*18) so we are skipping that sample for now.
+ hla_df = pandas.DataFrame([
+ ("Mel-8", "HLA-A*01:01 HLA-A*03:01 HLA-B*07:02 HLA-B*08:01 HLA-C*07:01 HLA-C*07:02"),
+ ("Mel-12", "HLA-A*01:01 HLA-B*08:01 HLA-C*07:01"),
+ ("Mel-15", "HLA-A*03:01 HLA-A*68:01 HLA-B*27:05 HLA-B*35:03 HLA-C*02:02 HLA-C*04:01"),
+ ("Mel-16", "HLA-A*01:01 HLA-A*24:02 HLA-B*07:02 HLA-B*08:01 HLA-C*07:01 HLA-C*07:02"),
+ ], columns=["sample_id", "hla"]).set_index("sample_id")
+
+ # We assert below that none of the class I hit peptides were found in any
+ # of the class II pull downs.
+ class_ii_cols = [
+ c for c in df.columns if c.endswith("HLA-II (arbitrary units)")
+ ]
+ class_ii_hits = set(df.loc[
+ (df[class_ii_cols].fillna(0.0).sum(1) > 0)
+ ].Sequence.unique())
+
+ results = []
+ for (sample_id, hla) in hla_df.hla.items():
+ intensity_col = "Intensity %s_HLA-I (arbitrary units)" % sample_id
+ sub_df = df.loc[
+ (df[intensity_col].fillna(0.0) > 0)
+ ]
+ filtered_sub_df = sub_df.loc[
+ (~sub_df.Sequence.isin(class_ii_hits))
+ ]
+ peptides = filtered_sub_df.Sequence.unique()
+ assert not any(p in class_ii_hits for p in peptides)
+
+ result_df = pandas.DataFrame({
+ "peptide": peptides,
+ })
+ result_df["sample_id"] = sample_id
+ result_df["hla"] = hla_df.loc[sample_id, "hla"]
+ result_df["pulldown_antibody"] = "W6/32"
+ result_df["format"] = "multiallelic"
+ result_df["mhc_class"] = "I"
+ result_df["sample_type"] = "melanoma_met"
+ result_df["cell_line"] = None
+ results.append(result_df)
+
+ result_df = pandas.concat(results, ignore_index=True)
+ return result_df
+
+
+def handle_pmid_31154438(*filenames):
+ """Shraibman, ..., Admon Mol Cell Proteomics 2019"""
+ # Note: this publication also includes analyses of the secreted HLA
+ # peptidedome (sHLA) but we are using only the data from membrane-bound
+ # HLA.
+ (xls, txt) = sorted(filenames, key=lambda s: not s.endswith(".xlsx"))
+
+ info = pandas.read_excel(xls, skiprows=1)
+ df = pandas.read_csv(txt, sep="\t", skiprows=1)
+
+ hla_df = info.loc[
+ ~info["mHLA tissue sample"].isnull()
+ ].set_index("mHLA tissue sample")[["HLA typing"]]
+
+ def fix_hla(string):
+ result = []
+ alleles = string.split(";")
+ for a in alleles:
+ a = a.strip()
+ if "/" in a:
+ (a1, a2) = a.split("/")
+ a2 = a1[:2] + a2
+ lst = [a1, a2]
+ else:
+ lst = [a]
+ for a in lst:
+ normalized = normalize_allele_name(a)
+ # Ignore class II
+ if normalized[4] in ("A", "B", "C"):
+ result.append(normalized)
+ return " ".join(result)
+
+ hla_df["hla"] = hla_df["HLA typing"].map(fix_hla)
+
+ results = []
+ for (sample_id, hla) in hla_df.hla.items():
+ intensity_col = "Intensity %s" % sample_id
+ sub_df = df.loc[
+ (df[intensity_col].fillna(0.0) > 0)
+ ]
+ peptides = sub_df.Sequence.unique()
+
+ result_df = pandas.DataFrame({
+ "peptide": peptides,
+ })
+ result_df["sample_id"] = sample_id
+ result_df["hla"] = hla_df.loc[sample_id, "hla"]
+ result_df["pulldown_antibody"] = "W6/32"
+ result_df["format"] = "multiallelic"
+ result_df["mhc_class"] = "I"
+ result_df["sample_type"] = "glioblastoma_tissue"
+ result_df["cell_line"] = None
+ results.append(result_df)
+
+ result_df = pandas.concat(results, ignore_index=True)
+ return result_df
+
+
+def expression_groups(dataset_identifier, df, groups):
+ result_df = pandas.DataFrame(index=df.index)
+ for (label, columns) in groups.items():
+ result_df[label] = df[columns].mean(1)
+ return result_df
+
+
+def handle_expression_GSE113126(*filenames):
+ """
+ Barry, ..., Krummel Nature Medicine 2018 [PMID 29942093]
+
+ This is the melanoma met RNA-seq dataset.
+
+ """
+
+ df = pandas.read_csv(filenames[0], sep="\t", index_col=0)
+ df = df[[]] # no columns
+
+ for filename in filenames:
+ df[os.path.basename(filename)] = pandas.read_csv(
+ filename, sep="\t", index_col=0)["TPM"]
+
+ assert len(df.columns) == len(filenames)
+
+ groups = {
+ "sample_type:MELANOMA_MET": df.columns.tolist(),
+ }
+ return expression_groups("GSE113126", df, groups)
+
+
+def handle_expression_expression_atlas_22460905(filename):
+ df = pandas.read_csv(filename, sep="\t", skiprows=4, index_col=0)
+ del df["Gene Name"]
+ df.columns = df.columns.str.lower()
+ df = df.fillna(0.0)
+
+ def matches(*strings):
+ return [c for c in df.columns if all(s in c for s in strings)]
+
+ import ipdb ; ipdb.set_trace()
+
+ groups = {
+ "sample_type:B-LCL": (
+ matches("b-cell", "lymphoblast") + matches("b acute lymphoblastic")),
+ "sample_type:B-CELL": matches("b-cell"),
+ "sample_type:MELANOMA_CELL_LINE": matches("melanoma"),
+
+ # For GBM tissue we are just using a mixture of cell lines.
+ "sample_type:GLIOBLASTOMA_TISSUE": matches("glioblastoma"),
+
+ "cell_line:THP-1": ["childhood acute monocytic leukemia, thp-1"],
+ "cell_line:HL-60": ["adult acute myeloid leukemia, hl-60"],
+ "cell_line:U-87": ['glioblastoma, u-87 mg'],
+ "cell_line:LNT-229": ['glioblastoma, ln-229'],
+ "cell_line:T98G": ['glioblastoma, t98g'],
+ "cell_line:SK-MEL-5": ['cutaneous melanoma, sk-mel-5'],
+ 'cell_line:MEWO': ['melanoma, mewo'],
+ "cell_line:HCC1937": ['breast ductal adenocarcinoma, hcc1937'],
+ "cell_line:HCT116": ['colon carcinoma, hct 116'],
+ "cell_line:HCC1143": ['breast ductal adenocarcinoma, hcc1143'],
+ }
+ return expression_groups("expression_atlas_22460905", df, groups)
+
+
+
+def handle_expression_human_protein_atlas(*filenames):
+ (cell_line_filename,) = [f for f in filenames if "celline" in f]
+ (blood_filename,) = [f for f in filenames if "blood" in f]
+ (gtex_filename,) = [f for f in filenames if "gtex" in f]
+
+ cell_line_df = pandas.read_csv(cell_line_filename, sep="\t")
+ blood_df = pandas.read_csv(blood_filename, sep="\t", index_col=0)
+ gtex_df = pandas.read_csv(gtex_filename, sep="\t")
+
+ cell_line_df = cell_line_df.pivot(
+ index="Gene", columns="Cell line", values="TPM")
+
+ gtex_df = gtex_df.pivot(
+ index="Gene", columns="Tissue", values="TPM")
+
+ result_df = pandas.DataFrame(index=cell_line_df.index)
+
+ result_df["sample_type:pbmc"] = blood_df[
+ [c for c in blood_df.columns if "total PBMC" in c]
+ ].mean(1)
+
+ result_df["cell_line:HEK293"] = cell_line_df['HEK 293']
+ result_df["cell_line:RPMI8226"] = cell_line_df['RPMI-8226']
+
+ # EXPI293 is based off HEK293
+ result_df["cell_line:EXPI293"] = cell_line_df['HEK 293']
+
+ # For leukapheresis we use pbmc sample
+ result_df["sample_type:leukapheresis"] = result_df["sample_type:pbmc"]
+
+ for tissue in ["lung", "spleen"]:
+ result_df["sample_type:%s" % tissue.upper()] = gtex_df[tissue]
+ return result_df
+
+
+
+
+
+# Add all functions with names like handle_pmid_XXXX to PMID_HANDLERS dict.
for (key, value) in list(locals().items()):
if key.startswith("handle_pmid_"):
- HANDLERS[key.replace("handle_pmid_", "")] = value
+ PMID_HANDLERS[key.replace("handle_pmid_", "")] = value
+ elif key.startswith("handle_expression_"):
+ EXPRESSION_HANDLERS[key.replace("handle_expression_", "")] = value
def run():
args = parser.parse_args(sys.argv[1:])
- dfs = []
- for (i, item_tpl) in enumerate(args.item):
+ expression_dfs = []
+ for (i, item_tpl) in enumerate(args.expression_item):
+ (label, filenames) = (item_tpl[0], item_tpl[1:])
+ label = label.replace("-", "_")
+ print(
+ "Processing expression item %d of %d" % (i + 1, len(args.expression_item)),
+ label,
+ *[os.path.abspath(f) for f in filenames])
+
+ expression_df = None
+ handler = None
+ if label in EXPRESSION_HANDLERS:
+ handler = EXPRESSION_HANDLERS[label]
+ expression_df = handler(*filenames)
+ elif args.debug:
+ debug(*filenames)
+ else:
+ raise NotImplementedError(label)
+
+ if expression_df is not None:
+ print(
+ "Processed expression data",
+ label,
+ "with shape",
+ expression_df.shape)
+ print(*expression_df.columns)
+ expression_dfs.append(expression_df)
+
+ expression_df = expression_dfs[0]
+ for other in expression_dfs[1:]:
+ expression_df = pandas.merge(
+ expression_df, other, how='outer', left_index=True, right_index=True)
+ expression_df = expression_df.fillna(0)
+
+ print(
+ "Genes in each expression dataframe: ",
+ *[len(e) for e in expression_dfs])
+ print("Genes in merged expression dataframe", len(expression_df))
+
+ ms_dfs = []
+ for (i, item_tpl) in enumerate(args.ms_item):
(pmid, filenames) = (item_tpl[0], item_tpl[1:])
print(
- "Processing item %d / %d" % (i + 1, len(args.item)),
+ "Processing MS item %d of %d" % (i + 1, len(args.ms_item)),
pmid,
*[os.path.abspath(f) for f in filenames])
- df = None
+ ms_df = None
handler = None
- if pmid in HANDLERS:
- handler = HANDLERS[pmid]
- df = handler(*filenames)
+ if pmid in PMID_HANDLERS:
+ handler = PMID_HANDLERS[pmid]
+ ms_df = handler(*filenames)
elif args.debug:
debug(*filenames)
else:
- raise NotImplementedError(args.pmid)
-
- if df is not None:
- df["pmid"] = pmid
- if "original_pmid" not in df.columns:
- df["original_pmid"] = pmid
- df = df.applymap(str).applymap(str.upper)
- print("*** PMID %s: %d peptides ***" % (pmid, len(df)))
+ raise NotImplementedError(pmid)
+
+ if ms_df is not None:
+ ms_df["pmid"] = pmid
+ if "original_pmid" not in ms_df.columns:
+ ms_df["original_pmid"] = pmid
+ if "expression_dataset" not in ms_df.columns:
+ ms_df["expression_dataset"] = ""
+ ms_df = ms_df.applymap(str).applymap(str.upper)
+ ms_df["sample_id"] = ms_df.sample_id.str.replace(" ", "")
+ print("*** PMID %s: %d peptides ***" % (pmid, len(ms_df)))
if handler is not None:
print(handler.__doc__)
print("Counts by sample id:")
- print(df.groupby("sample_id").peptide.nunique())
+ print(ms_df.groupby("sample_id").peptide.nunique())
print("")
print("Counts by sample type:")
- print(df.groupby("sample_type").peptide.nunique())
+ print(ms_df.groupby("sample_type").peptide.nunique())
print("****************************")
- dfs.append(df)
+ for value in ms_df.expression_dataset.unique():
+ if value and value not in expression_df.columns:
+ raise ValueError("No such expression dataset", value)
- df = pandas.concat(dfs, ignore_index=True, sort=False)
+ ms_dfs.append(ms_df)
- df["cell_line"] = df["cell_line"].fillna("")
+ ms_df = pandas.concat(ms_dfs, ignore_index=True, sort=False)
+ ms_df["cell_line"] = ms_df["cell_line"].fillna("")
- cols = ["pmid", "sample_id", "peptide", "format", "mhc_class", "hla", ]
- cols += [c for c in sorted(df.columns) if c not in cols]
- df = df[cols]
+ sample_table = ms_df[
+ ["sample_id", "pmid", "expression_dataset", "cell_line", "sample_type"]
+ ].drop_duplicates().set_index("sample_id")
- null_df = df.loc[df.isnull().any(1)]
+ sample_id_to_expression_dataset = sample_table.expression_dataset.to_dict()
+ for (sample_id, value) in sorted(sample_id_to_expression_dataset.items()):
+ if value:
+ print("Expression dataset for sample", sample_id, "already assigned")
+ continue
+ cell_line_col = "cell_line:" + sample_table.loc[sample_id, "cell_line"]
+ sample_type_col = "sample_type:" + (
+ sample_table.loc[sample_id, "sample_type"])
+
+ expression_dataset = None
+ for col in [cell_line_col, sample_type_col]:
+ if col in expression_df.columns:
+ expression_dataset = col
+ break
+
+ if not expression_dataset:
+ print("*" * 20)
+ print("No expression dataset for sample ", sample_id)
+ print("Sample info:")
+ print(sample_table.loc[sample_id])
+ print("*" * 20)
+
+ sample_id_to_expression_dataset[sample_id] = expression_dataset
+ print(
+ "Sample", sample_id, "assigned exp. dataset", expression_dataset)
+
+ print("Expression dataset usage:")
+ print(pandas.Series(sample_id_to_expression_dataset).value_counts())
+
+ missing = [
+ key for (key, value) in
+ sample_id_to_expression_dataset.items()
+ if value is None
+ ]
+ if missing:
+ print("Missing expression data for samples", *missing)
+ print(
+ "Missing cell lines: ",
+ *sample_table.loc[missing, "cell_line"].dropna().drop_duplicates().tolist())
+ print("Missing sample types: ", *sample_table.loc[
+ missing, "sample_type"].dropna().drop_duplicates().tolist())
+ if args.debug:
+ import ipdb; ipdb.set_trace()
+ else:
+ raise ValueError("Missing expression data for samples: ", missing)
+
+ ms_df["expression_dataset"] = ms_df.sample_id.map(
+ sample_id_to_expression_dataset)
+
+ cols = [
+ "pmid",
+ "sample_id",
+ "peptide",
+ "format",
+ "mhc_class",
+ "hla",
+ "expression_dataset",
+ ]
+ cols += [c for c in sorted(ms_df.columns) if c not in cols]
+ ms_df = ms_df[cols]
+
+ null_df = ms_df.loc[ms_df.isnull().any(1)]
if len(null_df) > 0:
print("Nulls:")
print(null_df)
@@ -673,11 +1017,14 @@ def run():
print("No nulls.")
# Each sample should be coming from only one experiment.
- assert df.groupby("sample_id").pmid.nunique().max() == 1, (
- df.groupby("sample_id").pmid.nunique().sort_values())
+ assert ms_df.groupby("sample_id").pmid.nunique().max() == 1, (
+ ms_df.groupby("sample_id").pmid.nunique().sort_values())
+
+ expression_df.to_csv(args.expression_out, index=True)
+ print("Wrote: %s" % os.path.abspath(args.expression_out))
- df.to_csv(args.out, index=False)
- print("Wrote: %s" % os.path.abspath(args.out))
+ ms_df.to_csv(args.ms_out, index=False)
+ print("Wrote: %s" % os.path.abspath(args.ms_out))
if __name__ == '__main__':
run()
diff --git a/downloads-generation/data_published/GENERATE.sh b/downloads-generation/data_published/GENERATE.sh
index e566526a..f10b85b6 100755
--- a/downloads-generation/data_published/GENERATE.sh
+++ b/downloads-generation/data_published/GENERATE.sh
@@ -33,7 +33,7 @@ wget -q https://github.com/openvax/mhcflurry/releases/download/pre-1.1/bdata.200
wget -q https://github.com/openvax/mhcflurry/releases/download/pre-1.1/bdata.20130222.mhci.public.1.txt
wget -q https://github.com/openvax/mhcflurry/releases/download/pre-1.1/bdata.2013.mhci.public.blind.1.txt
-mkdir raw
+mkdir ms
############################################
# MS: Multiallelic class I
@@ -43,10 +43,10 @@ mkdir raw
# Pearson, ..., Perreault JCI 2016 [PMID 27841757]
# but was reanalyzed in this work, and we download the reanalyzed version here.
PMID=28832583
-mkdir -p raw/$PMID
-wget -q https://doi.org/10.1371/journal.pcbi.1005725.s002 -P raw/$PMID # data generated in this work
-wget -q https://doi.org/10.1371/journal.pcbi.1005725.s003 -P raw/$PMID # data reanalyzed in this work
-cd raw/$PMID
+mkdir -p ms/$PMID
+wget -q https://doi.org/10.1371/journal.pcbi.1005725.s002 -P ms/$PMID # data generated in this work
+wget -q https://doi.org/10.1371/journal.pcbi.1005725.s003 -P ms/$PMID # data reanalyzed in this work
+cd ms/$PMID
unzip *.s002
unzip *.s003
mkdir saved
@@ -58,33 +58,33 @@ cd ../..
# Bassani-Sternberg, ..., Mann Mol Cell Proteomics 2015 [PMID 25576301]
PMID=25576301
-mkdir -p raw/$PMID
-wget -q https://www.mcponline.org/highwire/filestream/35026/field_highwire_adjunct_files/7/mcp.M114.042812-4.xlsx -P raw/$PMID
+mkdir -p ms/$PMID
+wget -q https://www.mcponline.org/highwire/filestream/35026/field_highwire_adjunct_files/7/mcp.M114.042812-4.xlsx -P ms/$PMID
# Mommen, ..., Heck PNAS 2014 [PMID 24616531]
PMID=24616531
-mkdir -p raw/$PMID
-wget -q https://www.pnas.org/highwire/filestream/615485/field_highwire_adjunct_files/1/sd01.xlsx -P raw/$PMID
+mkdir -p ms/$PMID
+wget -q https://www.pnas.org/highwire/filestream/615485/field_highwire_adjunct_files/1/sd01.xlsx -P ms/$PMID
# Gloger, ..., Neri Cancer Immunol Immunother 2016 [PMID 27600516]
# Data extracted from supplemental PDF table.
PMID=27600516
-mkdir -p raw/$PMID
-wget -q https://github.com/openvax/mhcflurry/releases/download/pan-dev1/27600516.peptides.csv -P raw/$PMID
+mkdir -p ms/$PMID
+wget -q https://github.com/openvax/mhcflurry/releases/download/pan-dev1/27600516.peptides.csv -P ms/$PMID
# Ritz, ..., Fugmann Proteomics 2016 [PMID 26992070]
# Supplemental zip downloaded from publication
PMID=26992070
-mkdir -p raw/$PMID
-wget -q https://github.com/openvax/mhcflurry/releases/download/pan-dev1/pmic12297-sup-0001-supinfo.zip -P raw/$PMID
-cd raw/$PMID
+mkdir -p ms/$PMID
+wget -q https://github.com/openvax/mhcflurry/releases/download/pan-dev1/pmic12297-sup-0001-supinfo.zip -P ms/$PMID
+cd ms/$PMID
unzip pmic12297-sup-0001-supinfo.zip
cd ../..
# Shraibman, ..., Admon Mol Cell Proteomics 2016 [PMID 27412690]
PMID=27412690
-mkdir -p raw/$PMID
-wget -q https://www.mcponline.org/lookup/suppl/doi:10.1074/mcp.M116.060350/-/DC1/mcp.M116.060350-2.xlsx -P raw/$PMID
+mkdir -p ms/$PMID
+wget -q https://www.mcponline.org/lookup/suppl/doi:10.1074/mcp.M116.060350/-/DC1/mcp.M116.060350-2.xlsx -P ms/$PMID
# Pearson, ..., Perreault J Clin Invest 2016 [PMID 27841757]
# Note: we do not use the original data from this publicaton, we use 28832583's reanalysis of it.
@@ -92,17 +92,59 @@ wget -q https://www.mcponline.org/lookup/suppl/doi:10.1074/mcp.M116.060350/-/DC1
# Hassan, ..., van Veelen Mol Cell Proteomics 2015 [PMID 23481700]
PMID=23481700
-mkdir -p raw/$PMID
-wget -q https://www.mcponline.org/highwire/filestream/34681/field_highwire_adjunct_files/1/mcp.M112.024810-2.xls -P raw/$PMID
+mkdir -p ms/$PMID
+wget -q https://www.mcponline.org/highwire/filestream/34681/field_highwire_adjunct_files/1/mcp.M112.024810-2.xls -P ms/$PMID
+
+# Shraibman, ..., Admon Mol Cell Proteomics 2019 [PMID 31154438]
+PMID=31154438
+mkdir -p ms/$PMID
+wget -q https://www.mcponline.org/highwire/filestream/51948/field_highwire_adjunct_files/3/zjw006195963st2.txt -P ms/$PMID
+wget -q https://www.mcponline.org/highwire/filestream/51948/field_highwire_adjunct_files/1/zjw006195963st1.xlsx -P ms/$PMID
+
+# Bassani-Sternberg, ..., Krackhardt Nature Comm. 2016 [PMID 27869121]
+PMID=27869121
+mkdir -p ms/$PMID
+wget -q "https://static-content.springer.com/esm/art%3A10.1038%2Fncomms13404/MediaObjects/41467_2016_BFncomms13404_MOESM1318_ESM.xlsx" -P ms/$PMID
############################################
# MS: Monoallelic class II
############################################
# Abelin, ..., Rooney Immunity 2019 [PMID 31495665]
PMID=31495665
-mkdir -p raw/$PMID
-wget -q https://ars.els-cdn.com/content/image/1-s2.0-S1074761319303632-mmc2.xlsx -P raw/$PMID
+mkdir -p ms/$PMID
+wget -q https://ars.els-cdn.com/content/image/1-s2.0-S1074761319303632-mmc2.xlsx -P ms/$PMID
+############################################
+# RNA-seq expression data (TPMs)
+############################################
+# CCLE as processed by expression atlas
+DATASET=expression-atlas-22460905
+mkdir -p expression/$DATASET
+wget -q https://www.ebi.ac.uk/gxa/experiments-content/E-MTAB-2770/resources/ExperimentDownloadSupplier.RnaSeqBaseline/tpms.tsv -P expression/$DATASET
+
+# Human protein atlas
+DATASET=human-protein-atlas
+mkdir -p expression/$DATASET
+cd expression/$DATASET
+wget -q https://www.proteinatlas.org/download/rna_celline.tsv.zip
+wget -q https://www.proteinatlas.org/download/rna_blood_cell_sample_tpm_m.tsv.zip
+wget -q https://www.proteinatlas.org/download/rna_tissue_gtex.tsv.zip
+for i in $(ls *.zip)
+do
+ unzip $i
+ rm $i
+done
+cd ../..
+
+# Melanoma. Original publication
+# Barry, ..., Krummel Nature Medicine 2018 [PMID 29942093].
+DATASET=GSE113126
+mkdir -p expression/$DATASET
+cd expression/$DATASET
+wget -q "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE113126&format=file" -O GSE113126_RAW.tar
+tar -xvf GSE113126_RAW.tar
+rm GSE113126_RAW.tar
+cd ../..
cp $SCRIPT_ABSOLUTE_PATH .
bzip2 LOG.txt
diff --git a/downloads-generation/models_class1_pan_variants/GENERATE.sh b/downloads-generation/models_class1_pan_variants/GENERATE.sh
index bda713e2..48da9927 100755
--- a/downloads-generation/models_class1_pan_variants/GENERATE.sh
+++ b/downloads-generation/models_class1_pan_variants/GENERATE.sh
@@ -62,15 +62,15 @@ if [ "$2" != "continue-incomplete" ]
then
cp $SCRIPT_DIR/generate_hyperparameters.production.py .
cp $SCRIPT_DIR/generate_hyperparameters.py .
- python generate_hyperparameters.production.py > hyperparameters.production.json
- python generate_hyperparameters.py hyperparameters.production.json no_pretrain > hyperparameters.no_pretrain.yaml
+ python generate_hyperparameters.production.py > hyperparameters.production.yaml
+ python generate_hyperparameters.py hyperparameters.production.yaml no_pretrain > hyperparameters.no_pretrain.yaml
python generate_hyperparameters.py hyperparameters.no_pretrain.yaml single_hidden > hyperparameters.single_hidden_no_pretrain.yaml
fi
for kind in single_hidden_no_pretrain no_pretrain 34mer_sequence
do
CONTINUE_INCOMPLETE_ARGS=""
- if [ "$2" == "continue-incomplete" ] && [ -d "models.${kind}" ]
+ if [ "$2" == "continue-incomplete" ] && [ -d "models.unselected.${kind}" ]
then
echo "Will continue existing run: $kind"
CONTINUE_INCOMPLETE_ARGS="--continue-incomplete"
diff --git a/mhcflurry/downloads.yml b/mhcflurry/downloads.yml
index 4089fb78..36eff633 100644
--- a/mhcflurry/downloads.yml
+++ b/mhcflurry/downloads.yml
@@ -37,10 +37,6 @@ releases:
url: https://github.com/openvax/mhcflurry/releases/download/pre-1.4.0/data_mass_spec_annotated.20190930.tar.bz2
default: false
- - name: data_expression
- url: https://github.com/openvax/mhcflurry/releases/download/1.4.0/data_expression.20191009.tar.bz2
- default: false
-
- name: data_references
url: https://github.com/openvax/mhcflurry/releases/download/pre-1.4.0/data_references.20190927.tar.bz2
default: false
@@ -62,7 +58,7 @@ releases:
default: false
- name: data_published
- url: https://github.com/openvax/mhcflurry/releases/download/pre-1.4.0/data_published.20190924.tar.bz2
+ url: https://github.com/openvax/mhcflurry/releases/download/1.4.0/data_published.20191011.tar.bz2
default: false
- name: data_curated
--
GitLab