Mercurial > repos > galaxyp > iedb_netmhcpan

annotate nextgen_iedb_api.py @ 0:88e44dab2988 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
author galaxyp
date Wed, 09 Jul 2025 12:56:30 +0000
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88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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1 #!/usr/bin/env python
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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3 """
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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4 This file was adapted from the iedb_apy.py file of the iedb_api tool.
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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5 It uses the newer "Next-Generation" IEDB API, and is constrained to
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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6 the mhci and mhcii tool groups.
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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7 """
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8
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9 import argparse
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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10 import json
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11 import os.path
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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12 import re
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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13 import sys
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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14 import time
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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15 import urllib.request
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16 from urllib.error import HTTPError
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18 # IEDB tool groups and predictor methods
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19 mhci_methods = ['netmhcpan_el', 'netmhcpan_ba']
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20 mhcii_methods = ['netmhciipan_el', 'netmhciipan_ba']
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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21 tool_group_methods = {'mhci': mhci_methods,
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22 'mhcii': mhcii_methods}
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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23 all_methods = set(mhci_methods + mhcii_methods)
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25 # Values for polling backoff
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26 max_backoff_count = 25
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27 init_poll_sleep = 10
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28 poll_retries = 50
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29 requests_before_backoff = 5
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32 def parse_alleles(allelefile):
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33 """Returns a dictionary with alleles from input file."""
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34 alleles = []
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35 with open(allelefile, 'r') as fh:
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36 for line in fh:
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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37 allele = line.strip()
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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38 alleles.append(allele)
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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39 return alleles
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42 def parse_sequence_column(sequence_file_lines, col):
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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43 """Sequences may come from a specific column in a TSV file.
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44
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45 Parse these sequences out while checking each against a regex for validity.
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46 """
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47 aapat = '^[ABCDEFGHIKLMNPQRSTVWY]+$'
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48 sequences = []
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49 for i, line in enumerate(sequence_file_lines):
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50 fields = line.split('\t')
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51 if len(fields) > col:
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52 seq = re.sub('[_*]', '', fields[col].strip())
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53 if not re.match(aapat, seq):
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54 warn_err(f'Line {i}, Not a peptide: {seq}')
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55 else:
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56 sequences.append(seq)
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57 else:
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58 warn_err('Invalid value for -c/--column')
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59 break
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60 return sequences
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61
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63 def iedb_request(req, timeout, retries, error_retry_sleep, response_fn=None, req_data=None):
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64 """Handles HTTP request and exceptions. Allows for a callback to parse IEDB response."""
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65 for retry in range(1, retries + 1):
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66 response = None
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67 try:
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68 response = urllib.request.urlopen(req, req_data, timeout=timeout)
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69 except HTTPError as e:
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70 warn_err(f'{retry} of {retries} Error connecting to IEDB server. \
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71 HTTP status code: {e.code}')
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72 time.sleep(error_retry_sleep)
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73 except Exception as e:
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74 warn_err(f'Error getting results from IEDB server: {e}')
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75 return None
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76
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77 if response and response.getcode() == 200:
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78 # If no callback, return results
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79 if not response_fn:
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80 response_string = response.read().decode('utf-8')
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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81 response_json = json.loads(response_string)
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82 return response_json
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83
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84 # Retry if response_fn callback deems necessary, i.e. results from job are not ready.
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
85 response_json = response_fn(response, retry)
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
86 if response_json:
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
87 return response_json
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
88 else:
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
89 code = response.getcode() if response else 1
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
90 warn_err(f'Error connecting to IEDB server. HTTP status code: {code}')
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
91
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
92 warn_err(f'No successful response from IEDB in {retries} retries')
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
93 return None
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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diff changeset
94
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
95
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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diff changeset
96 def pipeline_request(url, tool_group, sequence_text, alleles, length_range,
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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97 methods, peptide_shift, timeout=300, retries=3, error_retry_sleep=300):
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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98 """Submits job to IEDB pipeline and polls API until results are ready.
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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diff changeset
99
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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100 Returns response JSON from IEDB.
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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101 """
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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102
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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103 # Set up input parameters for IEDB NetMHCPan or NetMHCIIPan job
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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104 input_parameters = {
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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105 'alleles': alleles,
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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106 'peptide_length_range': length_range,
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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107 'predictors': [{'type': 'binding', 'method': m} for m in methods],
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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108 'peptide_shift': peptide_shift
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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109 }
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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110
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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diff changeset
111 if peptide_shift:
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
112 input_parameters['peptide_shift'] = peptide_shift
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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diff changeset
113
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
114 stage = {
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
115 'stage_number': 1,
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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116 'tool_group': tool_group,
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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117 'input_sequence_text': sequence_text,
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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diff changeset
118 'input_parameters': input_parameters
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
119 }
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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120
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galaxyp
parents:
diff changeset
121 params = {
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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122 'pipeline_id': "",
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
123 'run_stage_range': [1, 1],
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
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124 'stages': [stage]
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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125 }
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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126
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127 req = urllib.request.Request(url, method='POST')
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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128 req_data = json.dumps(params).encode('utf-8')
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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129 req.add_header('Content-Type', 'application/json; charset=utf-8')
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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130 req.add_header('Content-Length', len(req_data))
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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131
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132 # Make an initial request to submit job
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galaxyp
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133 response_json = iedb_request(req, timeout, retries, error_retry_sleep, req_data=req_data)
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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134 if not response_json:
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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135 warn_err('Initial request failed.')
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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136 return None
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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137
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galaxyp
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138 # Check response from job submission
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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139 warnings = response_json.get('warnings')
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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140 if warnings and len(warnings) > 0:
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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141 invalid_alleles = False
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142 for warning in warnings:
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143 if 'cannot predict binding for allele' in warning:
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144 warn_err(f"Error: Bad allelle input. {warning}")
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145 invalid_alleles = True
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146 if invalid_alleles:
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147 return None
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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148
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galaxyp
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149 warn_err(f'Warnings from IEDB: {warnings}')
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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150
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galaxyp
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diff changeset
151 errors = response_json.get('errors')
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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152 if errors:
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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153 warn_err(f'Errors from IEDB: {errors}')
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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154 return None
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155
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galaxyp
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diff changeset
156 results_uri = response_json.get('results_uri')
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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157 if not results_uri:
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galaxyp
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diff changeset
158 warn_err('No results URI provided from IEDB.')
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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159 return None
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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160
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galaxyp
parents:
diff changeset
161 # Callback function to rate-limit poll requests
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
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162 def poll_response_fn(response, retry):
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galaxyp
parents:
diff changeset
163 response_string = response.read().decode('utf-8')
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
164 response_json = json.loads(response_string)
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
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165 if response_json['status'] != 'done':
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
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166 if retry == poll_retries:
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galaxyp
parents:
diff changeset
167 warn_err('Job not finished in maximum allowed time.')
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
168 backoff_count = min(retry, max_backoff_count)
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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169
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170 # Double sleep every requests_before_backoff requests
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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171 sleep_duration = init_poll_sleep * 2 ** (backoff_count // requests_before_backoff)
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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172 time.sleep(sleep_duration)
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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173 return None
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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174 return response_json
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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175
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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176 # Submit polling for results
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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177 response_json = iedb_request(results_uri, timeout, poll_retries,
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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178 error_retry_sleep, response_fn=poll_response_fn)
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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179 if not response_json:
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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180 warn_err('Retrieving results failed.')
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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181 return response_json
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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182
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183
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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184 def warn_err(msg, exit_code=None):
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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185 sys.stderr.write(f"{msg}\n")
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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186 sys.stderr.flush()
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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187 if exit_code:
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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188 sys.exit(exit_code)
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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189
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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190
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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191 def add_reversed_sequences(file_lines, file_format):
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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192 """Adds a reversed sequence after each input sequence.
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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193
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194 Takes a plain list of sequences, or FASTA file. Each reversed FASTA sequence has
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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195 the same header prefixed with 'reversed_'.
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196 """
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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197 sequences_with_reversed = []
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198 if file_format == 'fasta':
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199 i = 0
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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200 while i < len(file_lines):
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galaxyp
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201
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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202 # Validate header from next sequence
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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203 seq_header = file_lines[i]
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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204 if seq_header[0] != '>':
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
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205 print('Invalid FASTA. Exiting.', file=sys.stderr)
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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206 sys.exit(1)
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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207
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galaxyp
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208 # Aggregate sequence into a single line
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
209 j = i + 1
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
210 seq = ''
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
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211 while j < len(file_lines):
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
212 next_line = file_lines[j]
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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213 if next_line[0] == '>':
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galaxyp
parents:
diff changeset
214 break
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
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215 seq = seq + file_lines[j]
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
216 j += 1
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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217
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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diff changeset
218 # Add non-reversed sequence
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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diff changeset
219 sequences_with_reversed.append(seq_header)
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
220 sequences_with_reversed.append(seq)
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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diff changeset
221
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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222 # Add reversed header and sequence
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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diff changeset
223 rev_header = seq_header.replace('>', '>reversed_')
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
224 sequences_with_reversed.append(rev_header)
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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diff changeset
225
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galaxyp
parents:
diff changeset
226 rev_seq = seq[::-1]
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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diff changeset
227 sequences_with_reversed.append(rev_seq)
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diff changeset
228
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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diff changeset
229 # Advance index to what should be the next sequence header
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galaxyp
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diff changeset
230 i = j
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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231
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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diff changeset
232 # If not FASTA, should be a simple list of peptides to reverse sequentially
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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diff changeset
233 else:
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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diff changeset
234 for seq in file_lines:
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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diff changeset
235
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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diff changeset
236 # Reverse seq
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
237 rev_seq = f'{seq[::-1]}'
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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diff changeset
238
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
239 # Add original and reversed sequences
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
240 sequences_with_reversed.append(seq)
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
241 sequences_with_reversed.append(rev_seq)
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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diff changeset
242
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galaxyp
parents:
diff changeset
243 return sequences_with_reversed
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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244
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galaxyp
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diff changeset
245
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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diff changeset
246 def __main__():
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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247 # Parse Command Line
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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diff changeset
248 parser = argparse.ArgumentParser()
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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diff changeset
249 parser.add_argument('-T', '--tool-group',
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
250 dest='tool_group',
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
251 default='mhci',
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
252 choices=tool_group_methods.keys(),
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
253 help='IEDB API Tool Group')
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
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diff changeset
254 parser.add_argument('-m', '--method',
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
255 action="append",
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
256 required=True,
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
257 choices=all_methods,
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
258 help='prediction method')
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
259 parser.add_argument('-A', '--allelefile',
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
260 required=True,
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
261 help='File of HLA alleles')
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
262 parser.add_argument('-l', '--lengthrange',
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
263 help='length range for which to make predictions for alleles')
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
264 parser.add_argument('-P', '--peptide_shift',
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
265 type=int,
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
266 default=None,
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
267 help='Peptide Shift')
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
268 parser.add_argument('-i', '--input',
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
269 required=True,
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
270 help='Input file for peptide sequences '
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
271 + '(fasta or tabular)')
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
272 parser.add_argument('-c', '--column',
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
273 default=None,
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
274 help='Zero-indexed peptide column in a tabular input file')
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
275 parser.add_argument('-o', '--output',
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
276 required=True,
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
277 help='Output file for query results')
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
278 parser.add_argument('-t', '--timeout',
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
279 type=int,
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
280 default=600,
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
281 help='Seconds to wait for server response')
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
282 parser.add_argument('-r', '--retries',
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
283 type=int,
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
284 default=5,
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
285 help='Number of times to retry failed server query')
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
286 parser.add_argument('-S', '--sleep',
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
287 type=int,
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
288 default=300,
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
289 help='Seconds to wait between failed server query retries')
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
290 parser.add_argument('-R', '--add-reversed',
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
291 dest='add_reversed',
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
292 action='store_true',
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
293 help='Input has every other sequence reversed. Identify in output.')
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
294 args = parser.parse_args()
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
295
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
296 allele_string = ','.join(parse_alleles(args.allelefile))
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
297
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
298 length_range = [int(i) for i in args.lengthrange.split(',')]
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
299
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
300 pipeline_url = 'https://api-nextgen-tools.iedb.org/api/v1/pipeline'
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
301
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
302 # If sequences submitted as a file, parse out sequences.
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
303 try:
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
304 with open(args.input) as inf:
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
305 sequence_file_contents = inf.read()
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
306 except Exception as e:
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
307 warn_err(f'Unable to open input file: {e}', exit_code=1)
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
308
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
309 sequence_file_lines = sequence_file_contents.splitlines()
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
310
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
311 # Pick out sequences if input file has multiple columns,
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
312 # otherwise submit list of sequences as-is.
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
313 if not args.column:
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
314 # IEDB may take FASTA files directly, so input contents as-is
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
315 if args.add_reversed:
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
316 sequence_text = '\n'.join(add_reversed_sequences(sequence_file_lines, 'fasta'))
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
317 else:
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
318 sequence_text = sequence_file_contents
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
319 else:
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
320 sequences = parse_sequence_column(sequence_file_lines, int(args.column))
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
321 if args.add_reversed:
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
322 sequence_text = '\n'.join(add_reversed_sequences(sequences, 'tsv'))
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
323 else:
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
324 sequence_text = '\n'.join(sequences)
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
325
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
326 if len(sequence_text) == 0:
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
327 warn_err('Error parsing sequences', exit_code=1)
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
328
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
329 # Submit job and return results
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
330 results = pipeline_request(pipeline_url, args.tool_group, sequence_text,
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
331 allele_string, length_range, args.method,
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
332 peptide_shift=args.peptide_shift, timeout=args.timeout,
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
333 retries=args.retries, error_retry_sleep=args.sleep)
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
334 if not results:
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
335 warn_err('Job failed. Exiting.', exit_code=1)
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
336
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
337 try:
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
338 peptide_table = [t for t in results['data']['results'] if t['type'] == 'peptide_table'][0]
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
339 peptide_table_data = peptide_table['table_data']
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
galaxyp
parents:
diff changeset
340 peptide_table_columns = peptide_table['table_columns']
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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341
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342 # If we reversed peptides prior to IEDB input,
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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343 # find column index of sequence number so we can identify which come from reversed input.
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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344 if args.add_reversed:
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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345 for i, column in enumerate(peptide_table_columns):
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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346 if column['display_name'] == 'seq #':
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347 seq_num_index = i
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348 break
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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349 except (KeyError, IndexError) as e:
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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350 warn_err(f'Error parsing IEDB results: {e}', exit_code=1)
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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351
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352 output_path = os.path.abspath(args.output)
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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353 with open(output_path, 'w') as output_file:
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354 # Write column names
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355 display_names = '\t'.join([c['display_name'] for c in peptide_table_columns] + ['reversed'])
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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356 print(display_names, file=output_file)
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357
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358 # Write data
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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359 for values in peptide_table_data:
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360 if args.add_reversed:
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361 seq_number = values[seq_num_index]
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362 # Every original input sequence is followed by its reversed sequence,
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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363 # so we know even sequence numbers are reversed.
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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364 reversed_val = str(seq_number % 2 == 0).lower()
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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365 else:
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366 reversed_val = 'false'
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367 values = '\t'.join([str(v) for v in values] + [reversed_val])
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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368 print(values, file=output_file)
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369
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370
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371 if __name__ == "__main__":
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372 __main__()