From 11b13122c033a3b0221a5542edb0632c8be0777f Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Mon, 30 Sep 2019 11:45:02 -0400
Subject: [PATCH] add flanking sequence
---
.../data_mass_spec_annotated/GENERATE.sh | 4 +-
.../data_mass_spec_annotated/annotate.py | 61 +++++++++++++++++--
2 files changed, 59 insertions(+), 6 deletions(-)
diff --git a/downloads-generation/data_mass_spec_annotated/GENERATE.sh b/downloads-generation/data_mass_spec_annotated/GENERATE.sh
index e5851c1e..f1897cf5 100755
--- a/downloads-generation/data_mass_spec_annotated/GENERATE.sh
+++ b/downloads-generation/data_mass_spec_annotated/GENERATE.sh
@@ -15,8 +15,8 @@ rm -rf "$SCRATCH_DIR/$DOWNLOAD_NAME"
mkdir "$SCRATCH_DIR/$DOWNLOAD_NAME"
# Send stdout and stderr to a logfile included with the archive.
-exec > >(tee -ia "$SCRATCH_DIR/$DOWNLOAD_NAME/LOG.txt")
-exec 2> >(tee -ia "$SCRATCH_DIR/$DOWNLOAD_NAME/LOG.txt" >&2)
+#exec > >(tee -ia "$SCRATCH_DIR/$DOWNLOAD_NAME/LOG.txt")
+#exec 2> >(tee -ia "$SCRATCH_DIR/$DOWNLOAD_NAME/LOG.txt" >&2)
# Log some environment info
date
diff --git a/downloads-generation/data_mass_spec_annotated/annotate.py b/downloads-generation/data_mass_spec_annotated/annotate.py
index 56b6b3a6..4dc93fac 100755
--- a/downloads-generation/data_mass_spec_annotated/annotate.py
+++ b/downloads-generation/data_mass_spec_annotated/annotate.py
@@ -5,6 +5,7 @@ import argparse
import os
import time
import collections
+import re
from six.moves import StringIO
import pandas
@@ -32,13 +33,26 @@ parser.add_argument(
"--out",
metavar="OUT.csv",
help="Out file path")
+parser.add_argument(
+ "--flanking-length",
+ metavar="N",
+ type=int,
+ default=15,
+ help="Length of flanking sequence to include")
+parser.add_argument(
+ "--debug-max-rows",
+ metavar="N",
+ type=int,
+ default=None,
+ help="Max rows to process. Useful for debugging. If specified an ipdb "
+ "debugging session is also opened at the end of the script")
def run():
args = parser.parse_args(sys.argv[1:])
df = pandas.read_csv(args.peptides)
- df["hit_id"] = "hit." + df.index.map(str)
+ df["hit_id"] = "hit." + df.index.map('{0:07d}'.format)
df = df.set_index("hit_id")
print("Read peptides", df.shape, *df.columns.tolist())
@@ -54,12 +68,46 @@ def run():
for (hit_id, row) in tqdm.tqdm(df.iterrows(), total=len(df)):
matches = fm.search(row.peptide)
for match in matches:
- join_df.append((hit_id, match.doc_id, len(matches)))
+ reference_row = reference_df.iloc[match.doc_id]
+ starts = [
+ m.start() for m in
+ re.finditer(row.peptide, reference_row.seq)
+ ]
+ assert len(starts) > 0, (row.peptide, reference_row.seq)
+ for start in starts:
+ end_pos = start + len(row.peptide)
+ n_flank = reference_row.seq[
+ max(start - args.flanking_length, 0) : start
+ ].rjust(args.flanking_length, 'X')
+ c_flank = reference_row.seq[
+ end_pos : (end_pos + args.flanking_length)
+ ].ljust(args.flanking_length, 'X')
+ join_df.append((
+ hit_id,
+ match.doc_id,
+ len(matches),
+ len(starts),
+ start,
+ start / len(reference_row.seq),
+ n_flank,
+ c_flank,
+ ))
+
+ if args.debug_max_rows and len(join_df) > args.debug_max_rows:
+ break
join_df = pandas.DataFrame(
join_df,
- columns=["hit_id", "match_index", "num_proteins"],
- )
+ columns=[
+ "hit_id",
+ "match_index",
+ "num_proteins",
+ "num_occurrences_in_protein",
+ "start_position",
+ "start_fraction_in_protein",
+ "n_flank",
+ "c_flank",
+ ]).drop_duplicates()
join_df["protein_accession"] = join_df.match_index.map(
reference_df.index.to_series().reset_index(drop=True))
@@ -84,6 +132,11 @@ def run():
merged_df.to_csv(args.out, index=False)
print("Wrote: %s" % os.path.abspath(args.out))
+ if args.debug_max_rows:
+ # Leave user in a debugger
+ import ipdb
+ ipdb.set_trace()
+
if __name__ == '__main__':
run()
--
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