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Python3 Functionality #11

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Python3 Functionality #11

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d1ddd83
Create setup.py
iPsychonaut Feb 13, 2025
da58294
Update code for Python 3 compatibility
iPsychonaut Feb 13, 2025
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16 changes: 8 additions & 8 deletions GFFParser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
import re
import os
import sys
import urllib
import urllib.request, urllib.parse, urllib.error
import numpy as np
import helper as utils
from collections import defaultdict
Expand Down Expand Up @@ -62,7 +62,7 @@ def attribute_tags(col9):
# replace the double qoutes from feature identifier
val = re.sub('"', '', val)
# replace the web formating place holders to plain text format
info[key].extend([urllib.unquote(v) for v in val.split(',') if v])
info[key].extend([urllib.parse.unquote(v) for v in val.split(',') if v])

return is_gff, info

Expand All @@ -87,7 +87,7 @@ def spec_features_keywd(gff_parts):
pass
## TODO key words
for flat_name in ["Transcript", "CDS"]:
if gff_parts["info"].has_key(flat_name):
if flat_name in gff_parts["info"]:
# parents
if gff_parts['type'] in [flat_name] or re.search(r'transcript', gff_parts['type'], re.IGNORECASE):
if not gff_parts['id']:
Expand Down Expand Up @@ -158,7 +158,7 @@ def Parse(ga_file):
gff_info = spec_features_keywd(gff_info)

# link the feature relationships
if gff_info['info'].has_key('Parent'):
if 'Parent' in gff_info['info']:
for p in gff_info['info']['Parent']:
if p == gff_info['id']:
gff_info['id'] = ''
Expand Down Expand Up @@ -217,7 +217,7 @@ def format_gene_models(parent_nf_map, child_nf_map):
g_cnt = 0
gene = np.zeros((len(parent_nf_map),), dtype = utils.init_gene())

for pkey, pdet in parent_nf_map.items():
for pkey, pdet in list(parent_nf_map.items()):
# considering only gene features
#if not re.search(r'gene', pdet.get('type', '')):
# continue
Expand Down Expand Up @@ -284,7 +284,7 @@ def format_gene_models(parent_nf_map, child_nf_map):

# make general ascending order of coordinates
if orient == '-':
for etype, excod in child_feat.items():
for etype, excod in list(child_feat.items()):
if len(excod) > 1:
if excod[0][0] > excod[-1][0]:
excod.reverse()
Expand Down Expand Up @@ -412,7 +412,7 @@ def format_gene_models(parent_nf_map, child_nf_map):
break

if XPFLG==1:
XQC = range(XP, len(gene)+1)
XQC = list(range(XP, len(gene)+1))
gene = np.delete(gene, XQC)

return gene
Expand Down Expand Up @@ -445,7 +445,7 @@ def create_missing_feature_type(p_feat, c_feat):
"""

child_n_map = defaultdict(list)
for fid, det in c_feat.items():
for fid, det in list(c_feat.items()):
# get the details from grand child
GID = STRD = SCR = None
SPOS, EPOS = [], []
Expand Down
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