# HG changeset patch
# User sanbi-uwc
# Date 1658231879 0
# Node ID f2a7aaf93a1dd0f5005061649e0c3edf55802b86
# Parent 7e49c6b19f5e23920d691b9644415ecc6fca5c71
planemo upload for repository https://github.com/pvanheus/polio_report commit a99e10fec2fac5aae70974c977eb3b362a1a8429-dirty
diff -r 7e49c6b19f5e -r f2a7aaf93a1d CITATION.cff
--- a/CITATION.cff Tue Jul 19 11:47:08 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-cff-version: 1.2.0
-message: "If you use this software, please cite it as below."
-authors:
-- family-names: "van Heusden"
- given-names: "Peter"
- orcid: "https://orcid.org/0000-0001-6553-5274"
-title: "Poliovirus variation reporting scripts"
-version: 0.1.0
-date-released: 2022-07-19
-url: "https://github.com/pvanheus/polio_report"
\ No newline at end of file
diff -r 7e49c6b19f5e -r f2a7aaf93a1d LICENSE
--- a/LICENSE Tue Jul 19 11:47:08 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,674 +0,0 @@
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-OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
-THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
-IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
-ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
-
- 16. Limitation of Liability.
-
- IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
-WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
-THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
-GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
-USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
-DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
-PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
-EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
-SUCH DAMAGES.
-
- 17. Interpretation of Sections 15 and 16.
-
- If the disclaimer of warranty and limitation of liability provided
-above cannot be given local legal effect according to their terms,
-reviewing courts shall apply local law that most closely approximates
-an absolute waiver of all civil liability in connection with the
-Program, unless a warranty or assumption of liability accompanies a
-copy of the Program in return for a fee.
-
- END OF TERMS AND CONDITIONS
-
- How to Apply These Terms to Your New Programs
-
- If you develop a new program, and you want it to be of the greatest
-possible use to the public, the best way to achieve this is to make it
-free software which everyone can redistribute and change under these terms.
-
- To do so, attach the following notices to the program. It is safest
-to attach them to the start of each source file to most effectively
-state the exclusion of warranty; and each file should have at least
-the "copyright" line and a pointer to where the full notice is found.
-
-
- Copyright (C)
-
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see .
-
-Also add information on how to contact you by electronic and paper mail.
-
- If the program does terminal interaction, make it output a short
-notice like this when it starts in an interactive mode:
-
- Copyright (C)
- This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
- This is free software, and you are welcome to redistribute it
- under certain conditions; type `show c' for details.
-
-The hypothetical commands `show w' and `show c' should show the appropriate
-parts of the General Public License. Of course, your program's commands
-might be different; for a GUI interface, you would use an "about box".
-
- You should also get your employer (if you work as a programmer) or school,
-if any, to sign a "copyright disclaimer" for the program, if necessary.
-For more information on this, and how to apply and follow the GNU GPL, see
-.
-
- The GNU General Public License does not permit incorporating your program
-into proprietary programs. If your program is a subroutine library, you
-may consider it more useful to permit linking proprietary applications with
-the library. If this is what you want to do, use the GNU Lesser General
-Public License instead of this License. But first, please read
-.
diff -r 7e49c6b19f5e -r f2a7aaf93a1d README
--- a/README Tue Jul 19 11:47:08 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-This repository contains some Galaxy tools for processing the output of a poliovirus variation reporting pipeline.
\ No newline at end of file
diff -r 7e49c6b19f5e -r f2a7aaf93a1d assess_alignment.py
--- a/assess_alignment.py Tue Jul 19 11:47:08 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,192 +0,0 @@
-#!/usr/bin/env python
-
-import argparse
-import json
-import sys
-from dataclasses import dataclass
-from typing import TextIO
-
-
-@dataclass
-class Sample:
- name: str
- reference: str
- mismatches: int
- quality: str
-
-
-def load_json(json_file: TextIO) -> dict:
- data = json.load(json_file)
- if "msa" not in data:
- raise ValueError("MSA missing from JSON, cannot proceed")
- if "gappedTraces" not in data:
- raise ValueError("gappedTraces missing from JSON, cannot proceed")
- return data
-
-
-def analyse_mismatches(
- json_file: TextIO,
- offset: int,
- length: int,
- vp1only: bool = True,
- sec_is_conflict: bool = False,
-) -> list:
- data = load_json(json_file)
- msas = [al for al in data["msa"] if not al["reference"]]
- reference = None
- for al in data["msa"]:
- if al["reference"]:
- if reference is None:
- reference = al
- else:
- sys.exit(
- "more than one reference found in JSON MSA list, cannot proceed"
- )
- min_start = min([int(al["leadingGaps"]) for al in msas])
- max_end = max([int(al["leadingGaps"]) + len(al["align"]) for al in msas])
- base_state = ["n"] * len(reference["align"])
- mismatch_bases = {}
- for i, base in enumerate(reference["align"]):
- for k, al in enumerate(msas):
- leading_gaps = int(al["leadingGaps"])
- align_len = len(al["align"])
- if leading_gaps < i and (leading_gaps + align_len) > i:
- vp1pos = i - offset
- if vp1only and vp1pos < 0 or vp1pos > length:
- # skip positions outside of vp1 gene region
- continue
- al_base = al["align"][i - leading_gaps]
- has_secondary_basecall = False
- if sec_is_conflict:
- gappedTrace = data["gappedTraces"][k]
- pos = i - int(gappedTrace["leadingGaps"])
- # print(len(gappedTrace['basecallPos']), pos, k, len(gappedTrace['basecalls']), gappedTrace['basecallPos'][pos])
- basecall_str = gappedTrace["basecalls"][
- str(gappedTrace["basecallPos"][pos])
- ]
- if "|" in basecall_str:
- has_secondary_basecall = True
- # set this position to conflicted
- base_state[i] = "C"
- if al_base != base:
- # let's deal with all the cases where the base state doesn't match the reference
- if base_state[i] == "G":
- # the base state was G (a trace matches reference) and now we see a mismatch
- base_state[i] = "C"
- elif base_state[i] == "C":
- # already marked as conflicting - a mismatch doesn't change that
- pass
- elif base_state[i] == "n" or base_state[i] == "M":
- # we never saw this before or its already marked as a mismatch
- base_state[i] = "M"
- mismatch_bases[i] = al_base
- else:
- sys.exit("unexpected base state: " + base_state[i])
- else:
- if base_state[i] == "G" or base_state[i] == "n":
- # we saw this before and got a match or
- # we never saw this before
- base_state[i] = "G"
- elif base_state[i] == "M":
- # we saw this before but it was a mismatch - mark this as a conflict
- base_state[i] = "C"
- if i in mismatch_bases:
- del mismatch_bases[i]
- elif base_state[i] == "C":
- # we have seen a conflict here before
- pass
- else:
- sys.exit("unexpected base_state: " + base_state[i])
- conflicts = base_state.count("C")
- matches = base_state.count("G")
- mismatches = base_state.count("M")
- mismatch_list = []
- for i, state in enumerate(base_state):
- # i is in zero-based genome coordinates
- if state == "M":
- # for mismatch store [pos_in_genome, pos_in_vp1, reference_base, sequenced_base]
- mismatch_list.append(
- [i, i - offset, reference["align"][i], mismatch_bases[i]]
- )
- return [conflicts, matches, mismatches, mismatch_list]
-
-
-def analyse_trace_quality(json_file: TextIO) -> float:
- data = load_json(json_file)
-
- traces = data["gappedTraces"]
- overall_avg = 0
- for trace in traces:
- start = min(trace["basecallPos"])
- end = max(trace["basecallPos"])
- call_quality = {}
- avg_ratio = 0
- for base in ("A", "C", "G", "T"):
- calls = trace["peak" + base][start : end + 1]
- min_call = min(calls)
- max_call = max(calls)
- avg_call = sum(calls) / len(calls)
- ratio = max_call / avg_call
- call_quality["avg" + base] = avg_call
- call_quality["min" + base] = min_call
- call_quality["max" + base] = max_call
- call_quality["ratio" + base] = ratio
- avg_ratio += ratio
- avg_ratio = avg_ratio / 4
- overall_avg += avg_ratio
- overall_avg = overall_avg / len(traces)
- return overall_avg
-
-
-def comma_split(args: str) -> list[str]:
- return args.split(",")
-
-
-if __name__ == "__main__":
- parser = argparse.ArgumentParser()
- parser.add_argument("--output_filename", help="Path to output file")
- parser.add_argument("--sample_name", help="Name of sample being analysed")
- parser.add_argument(
- "--dataset_names", type=comma_split, help="Comma separated names for datasets"
- )
- parser.add_argument("--datasets", nargs="+")
- args = parser.parse_args()
-
- offsets = {
- "poliovirus1sabin": 2480,
- "poliovirus2sabin": 2482,
- "poliovirus3sabin": 2477,
- }
-
- lengths = {
- "poliovirus1sabin": 906,
- "poliovirus2sabin": 903,
- "poliovirus3sabin": 900,
- }
-
- min_mismatches = None
- for file_index, json_filename in enumerate(args.datasets):
- dataset_name = args.dataset_names[file_index].replace(
- ".json", ""
- ) # take the name but remove any json suffix
- offset = offsets[dataset_name]
- length = lengths[dataset_name]
- (conflicts, matches, mismatches, mismatch_list) = analyse_mismatches(
- open(json_filename), offset, length
- )
- # analyse_mismatches(json_filename, True)
- quality = analyse_trace_quality(open(json_filename))
- if min_mismatches is None or mismatches < min_mismatches:
- min_mismatches = mismatches
- best_match_mismatch_list = mismatch_list
- best_match_quality = quality
- best_match_reference = dataset_name
-
- info = {
- "sample_name": args.sample_name,
- "best_reference": best_match_reference,
- "mismatches": min_mismatches,
- "mismatch_list": best_match_mismatch_list,
- "quality": best_match_quality,
- }
- json.dump(info, open(args.output_filename, "w"))
diff -r 7e49c6b19f5e -r f2a7aaf93a1d assess_poliovirus_alignment.xml
--- a/assess_poliovirus_alignment.xml Tue Jul 19 11:47:08 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,51 +0,0 @@
-
-
- python
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff -r 7e49c6b19f5e -r f2a7aaf93a1d summarize_poliovirus_alignment.xml
--- a/summarize_poliovirus_alignment.xml Tue Jul 19 11:47:08 2022 +0000
+++ b/summarize_poliovirus_alignment.xml Tue Jul 19 11:57:59 2022 +0000
@@ -1,4 +1,4 @@
-
+
python