mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-15 20:04:43 +08:00
Nicola Soranzo
90a729e431
Found by running `ack --type=python -f | grep -v '^tools/' | xargs pyupgrade --py36-plus`
234 lines
9.2 KiB
Python
234 lines
9.2 KiB
Python
#!/usr/bin/env python
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# Dan Blankenberg
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import sys
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assert sys.version_info[:2] >= (2, 4)
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# genbank_to_bed
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class Region:
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def __init__(self):
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self.qualifiers = {}
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self.start = None
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self.end = None
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self.strand = '+'
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def set_coordinates_by_location(self, location):
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location = location.strip().lower().replace('..', ',')
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if "complement(" in location: # if part of the sequence is on the negative strand, it all is?
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self.strand = '-' # default of + strand
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for remove_text in ["join(", "order(", "complement(", ")"]:
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location = location.replace(remove_text, "")
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for number in location.split(','):
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number = number.strip('\n\r\t <>,()')
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if number:
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if "^" in number:
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# a single point
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# check that this is correct for points, ie: 413/NC_005027.gbk: misc_feature 6636286^6636287 ===> 6636285,6636286
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end = int(number.split('^')[0])
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start = end - 1
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else:
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end = int(number)
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start = end - 1 # match BED coordinates
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if self.start is None or start < self.start:
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self.start = start
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if self.end is None or end > self.end:
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self.end = end
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class GenBankFeatureParser:
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"""Parses Features from Single Locus GenBank file"""
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def __init__(self, fh):
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self.fh = fh
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self.features = {}
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fh.seek(0)
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in_features = False
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last_feature_name = None
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base_indent = 0
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last_attr_name = None
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for line in fh:
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if not in_features and line.startswith('FEATURES'):
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in_features = True
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continue
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if in_features:
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lstrip = line.lstrip()
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if line and lstrip == line:
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break # end of feature block
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cur_indent = len(line) - len(lstrip)
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if last_feature_name is None:
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base_indent = cur_indent
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if cur_indent == base_indent:
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# a new feature
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last_attr_name = None
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fields = lstrip.split(None, 1)
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last_feature_name = fields[0].strip()
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if last_feature_name not in self.features:
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self.features[last_feature_name] = []
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region = Region()
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region.set_coordinates_by_location(fields[1])
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self.features[last_feature_name].append(region)
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else:
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# add info to last known feature
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line = line.strip()
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if line.startswith('/'):
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fields = line[1:].split('=', 1)
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if len(fields) == 2:
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last_attr_name, content = fields
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else:
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# No data
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last_attr_name = line[1:]
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content = ""
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content = content.strip('"')
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if last_attr_name not in self.features[last_feature_name][-1].qualifiers:
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self.features[last_feature_name][-1].qualifiers[last_attr_name] = []
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self.features[last_feature_name][-1].qualifiers[last_attr_name].append(content)
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elif last_attr_name is None and last_feature_name:
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# must still be working on location
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self.features[last_feature_name][-1].set_coordinates_by_location(line)
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else:
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# continuation of multi-line qualifier content
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if last_feature_name.lower() in ['translation']:
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self.features[last_feature_name][-1].qualifiers[last_attr_name][-1] = "{}{}".format(self.features[last_feature_name][-1].qualifiers[last_attr_name][-1], line.rstrip('"'))
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else:
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self.features[last_feature_name][-1].qualifiers[last_attr_name][-1] = "{} {}".format(self.features[last_feature_name][-1].qualifiers[last_attr_name][-1], line.rstrip('"'))
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def get_features_by_type(self, feature_type):
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if feature_type not in self.features:
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return []
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else:
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return self.features[feature_type]
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# Parse A GenBank file and return arrays of BED regions for the corresponding features
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def get_bed_from_genbank(gb_file, chrom, feature_list):
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genbank_parser = GenBankFeatureParser(open(gb_file))
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features = {}
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for feature_type in feature_list:
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features[feature_type] = []
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for feature in genbank_parser.get_features_by_type(feature_type):
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name = ""
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for name_tag in ['gene', 'locus_tag', 'db_xref']:
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if name_tag in feature.qualifiers:
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if name:
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name = name + ";"
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name = name + feature.qualifiers[name_tag][0].replace(" ", "_")
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if not name:
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name = "unknown"
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features[feature_type].append(f"{chrom}\t{feature.start}\t{feature.end}\t{name}\t{0}\t{feature.strand}") # append new bed field here
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return features
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# geneMark to bed
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# converts GeneMarkHMM to bed
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# returns an array of bed regions
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def get_bed_from_GeneMark(geneMark_filename, chr):
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orfs = open(geneMark_filename).readlines()
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while True:
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line = orfs.pop(0).strip()
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if line.startswith("--------"):
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orfs.pop(0)
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break
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orfs = "".join(orfs)
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ctr = 0
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regions = []
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for block in orfs.split("\n\n"):
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if block.startswith("List of Regions of interest"):
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break
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best_block = {'start': 0, 'end': 0, 'strand': '+', 'avg_prob': -sys.maxsize, 'start_prob': -sys.maxsize, 'name': 'DNE'}
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ctr += 1
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ctr2 = 0
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for line in block.split("\n"):
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ctr2 += 1
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fields = line.split()
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start = int(fields.pop(0)) - 1
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end = int(fields.pop(0))
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strand = fields.pop(0)
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if strand == 'complement':
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strand = "-"
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else:
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strand = "+"
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frame = fields.pop(0)
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frame = frame + " " + fields.pop(0)
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avg_prob = float(fields.pop(0))
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try:
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start_prob = float(fields.pop(0))
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except Exception:
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start_prob = 0
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name = "orf_" + str(ctr) + "_" + str(ctr2)
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if avg_prob >= best_block['avg_prob'] and start_prob > best_block['start_prob']:
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best_block = {'start': start, 'end': end, 'strand': strand, 'avg_prob': avg_prob, 'start_prob': start_prob, 'name': name}
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regions.append(chr + "\t" + str(best_block['start']) + "\t" + str(best_block['end']) + "\t" + best_block['name'] + "\t" + str(int(best_block['avg_prob'] * 1000)) + "\t" + best_block['strand'])
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return regions
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# geneMarkHMM to bed
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# converts GeneMarkHMM to bed
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# returns an array of bed regions
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def get_bed_from_GeneMarkHMM(geneMarkHMM_filename, chr):
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orfs = open(geneMarkHMM_filename).readlines()
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while True:
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line = orfs.pop(0).strip()
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if line == "Predicted genes":
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orfs.pop(0)
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orfs.pop(0)
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break
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regions = []
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for line in orfs:
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fields = line.split()
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name = "gene_number_" + fields.pop(0)
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strand = fields.pop(0)
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start = fields.pop(0)
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if start.startswith("<"):
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start = 1
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start = int(start) - 1
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end = fields.pop(0)
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if end.startswith(">"):
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end = end[1:]
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end = int(end)
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score = 0 # no scores provided
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regions.append(chr + "\t" + str(start) + "\t" + str(end) + "\t" + name + "\t" + str(score) + "\t" + strand)
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return regions
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# glimmer3 to bed
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# converts glimmer3 to bed, doing some linear scaling (probably not correct?) on scores
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# returns an array of bed regions
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def get_bed_from_glimmer3(glimmer3_filename, chr):
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max_score = -sys.maxsize
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min_score = sys.maxsize
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orfs = []
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for line in open(glimmer3_filename).readlines():
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if line.startswith(">"):
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continue
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fields = line.split()
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name = fields.pop(0)
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start = int(fields.pop(0))
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end = int(fields.pop(0))
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if int(fields.pop(0)) < 0:
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strand = "-"
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temp = start
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start = end
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end = temp
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else:
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strand = "+"
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start = start - 1
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score = (float(fields.pop(0)))
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if score > max_score:
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max_score = score
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if score < min_score:
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min_score = score
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orfs.append((chr, start, end, name, score, strand))
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delta = 0
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if min_score < 0:
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delta = min_score * -1
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regions = []
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for (chr, start, end, name, score, strand) in orfs:
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# need to cast to str because was having the case where 1000.0 was rounded to 999 by int, some sort of precision bug?
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my_score = int(float(str(((score + delta) * (1000 - 0 - (min_score + delta))) / ((max_score + delta) + 0))))
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regions.append(chr + "\t" + str(start) + "\t" + str(end) + "\t" + name + "\t" + str(my_score) + "\t" + strand)
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return regions
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