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Cleanup gff
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@tanghaibao
tanghaibao committed Apr 30, 2024
1 parent 9cdf9ac commit b8f4447
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Showing 3 changed files with 66 additions and 66 deletions.
5 changes: 3 additions & 2 deletions jcvi/formats/bed.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -26,8 +26,6 @@
popen,
sh,
)
from ..formats.base import DictFile, LineFile, must_open, is_number, get_number
from ..formats.sizes import Sizes
from ..utils.cbook import SummaryStats, thousands, percentage
from ..utils.grouper import Grouper
from ..utils.range import (
Expand All @@ -38,6 +36,9 @@
range_intersect,
)

from .base import DictFile, LineFile, get_number, is_number, must_open
from .sizes import Sizes


class BedLine(object):
# the Bed format supports more columns. we only need
Expand Down
122 changes: 60 additions & 62 deletions jcvi/formats/gff.py
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Original file line number Diff line number Diff line change
@@ -1,33 +1,34 @@
#!/usr/bin/env python
# -*- coding: UTF-8 -*-

import sys
import os
import os.path as op
import logging
import re
import sys

from collections import defaultdict
from urllib.parse import quote, unquote

from jcvi.utils.cbook import AutoVivification
from jcvi.formats.base import DictFile, LineFile, must_open, is_number
from jcvi.formats.fasta import Fasta, SeqIO
from jcvi.formats.bed import Bed, BedLine, natsorted
from jcvi.annotation.reformat import atg_name
from jcvi.utils.range import range_minmax
from jcvi.utils.orderedcollections import DefaultOrderedDict, OrderedDict, parse_qs
from jcvi.apps.base import (
from ..apps.base import (
OptionParser,
OptionGroup,
ActionDispatcher,
cleanup,
flatten,
logger,
mkdir,
need_update,
parse_multi_values,
sh,
)
from ..annotation.reformat import atg_name
from ..utils.cbook import AutoVivification
from ..utils.range import range_minmax
from ..utils.orderedcollections import DefaultOrderedDict, OrderedDict, parse_qs

from .base import DictFile, LineFile, must_open, is_number
from .bed import Bed, BedLine, natsorted
from .fasta import Fasta, SeqIO


Valid_strands = ("+", "-", "?", ".")
Expand Down Expand Up @@ -356,7 +357,7 @@ def __init__(
if filename in ("-", "stdin") or filename.endswith(".gz"):
if ".gtf" in filename:
self.gff3 = False
logging.debug("File is not gff3 standard.")
logger.debug("File is not gff3 standard.")
return

self.set_gff_type()
Expand All @@ -368,7 +369,7 @@ def set_gff_type(self):
break
gff3 = False if not row else "=" in row.attributes_text
if not gff3:
logging.debug("File is not gff3 standard.")
logger.debug("File is not gff3 standard.")

self.gff3 = gff3
self.fp.seek(0)
Expand Down Expand Up @@ -564,9 +565,7 @@ def addparent(args):
continue
data[g.parent].append(g)

logging.debug(
"A total of {0} {1} features clustered".format(len(data), opts.childfeat)
)
logger.debug("A total of %d %s features clustered", len(data), opts.childfeat)

parents = []
for parent, dd in data.items():
Expand All @@ -588,7 +587,7 @@ def addparent(args):
)
parents.append(GffLine(gffline))
parents.sort(key=lambda x: (x.seqid, x.start))
logging.debug("Merged feature sorted")
logger.debug("Merged feature sorted")

fw = must_open(opts.outfile, "w")
for parent in parents:
Expand Down Expand Up @@ -627,9 +626,8 @@ def is_valid_codon(codon, type="start"):
if not any(_codon == codon for _codon in ("TGA", "TAG", "TAA")):
return False
else:
logging.error(
"`{0}` is not a valid codon type. ".format(type)
+ "Should be one of (`start` or `stop`)"
logger.error(
"`%s` is not a valid codon type. Should be one of (`start` or `stop`)", type
)
sys.exit()

Expand Down Expand Up @@ -739,14 +737,15 @@ def fixpartials(args):
stop_codon, strand, seqid, genome, type="stop"
)

logging.debug(
"feature={0} ({1})".format(trid, strand)
+ ", 5'={0}, 3'={1}".format(five_prime, three_prime)
+ ", {0} <== {1} ==> {2}".format(
nstart if strand == "+" else nstop,
cds_span,
nstop if strand == "+" else nstart,
)
logger.debug(
"feature=%s (%s), 5'=%s, 3'=%s, %d <== %d ==> %d",
trid,
strand,
five_prime,
three_prime,
nstart if strand == "+" else nstop,
cds_span,
nstop if strand == "+" else nstart,
)

if not five_prime or not three_prime:
Expand Down Expand Up @@ -989,7 +988,7 @@ def summary(args):

if ids:
ids = SetFile(ids)
logging.debug("Total ids loaded: {0}".format(len(ids)))
logger.debug("Total ids loaded: %d", len(ids))

if opts.isoform:
pids = set()
Expand All @@ -1006,14 +1005,14 @@ def summary(args):
continue
pids.add(g.id)
ids = pids
logging.debug("After checking longest: {0}".format(len(ids)))
logger.debug("After checking longest: %d", len(ids))

# Collects aliases
gff = Gff(gff_file)
for g in gff:
if g.name in ids:
ids.add(g.id)
logging.debug("Total ids including aliases: {0}".format(len(ids)))
logger.debug("Total ids including aliases: %d", len(ids))

gff = Gff(gff_file)
beds = defaultdict(list)
Expand Down Expand Up @@ -1104,7 +1103,7 @@ def orient(args):

print(g)

logging.debug("A total of {0} features flipped.".format(flipped))
logger.debug("A total of %d features flipped.", flipped)


def rename(args):
Expand Down Expand Up @@ -1225,7 +1224,7 @@ def filter(args):
if identity < oid or coverage < ocov:
bad.add(g.id)

logging.debug("{0} bad accns marked.".format(len(bad)))
logger.debug("%d bad accns marked.", len(bad))

fw = must_open(opts.outfile, "w")
for g in gffdb.features_of_type(ptype, order_by=("seqid", "start")):
Expand Down Expand Up @@ -1770,10 +1769,9 @@ def format(args):
mod_remove_attrs.append(remove_attr)

if mod_remove_attrs:
logging.error(
"Attributes `{0}` cannot be removed and modified".format(
",".join(mod_remove_attrs)
)
logger.error(
"Attributes `%s` cannot be removed and modified",
",".join(mod_remove_attrs),
)
sys.exit()

Expand Down Expand Up @@ -1912,9 +1910,7 @@ def format(args):
if origid in mapping:
g.seqid = mapping[origid]
else:
logging.error(
"{0} not found in `{1}`. ID unchanged.".format(origid, mapfile)
)
logger.error("%s not found in `%s`. ID unchanged.", origid, mapfile)
else:
g.seqid = mapfile

Expand Down Expand Up @@ -2247,7 +2243,7 @@ def import_feats(gffile, type="gene"):
continue
allgenes.append(g)

logging.debug("A total of {0} {1} features imported.".format(len(allgenes), type))
logger.debug("A total of %d %s features imported.", len(allgenes), type)
allgenes.sort(key=lambda x: (x.seqid, x.start))
return allgenes

Expand Down Expand Up @@ -2319,8 +2315,8 @@ def uniq(args):
def populate_children(outfile, ids, gffile, iter="2", types=None):
ids = set(ids)
fw = must_open(outfile, "w")
logging.debug("A total of {0} features selected.".format(len(ids)))
logging.debug("Populate children. Iteration 1..")
logger.debug("A total of %d features selected.", len(ids))
logger.debug("Populate children. Iteration 1..")
gff = Gff(gffile)
children = set()
for g in gff:
Expand All @@ -2333,7 +2329,7 @@ def populate_children(outfile, ids, gffile, iter="2", types=None):
children.add(g.accn)

if iter == "2":
logging.debug("Populate grand children. Iteration 2..")
logger.debug("Populate grand children. Iteration 2..")
gff = Gff(gffile)
for g in gff:
if "Parent" not in g.attributes:
Expand All @@ -2342,7 +2338,7 @@ def populate_children(outfile, ids, gffile, iter="2", types=None):
if parent in children:
children.add(g.accn)

logging.debug("Populate parents..")
logger.debug("Populate parents..")
gff = Gff(gffile)
parents = set()
for g in gff:
Expand All @@ -2354,12 +2350,12 @@ def populate_children(outfile, ids, gffile, iter="2", types=None):
parents.add(parent)

combined = ids | children | parents
logging.debug("Original: {0}".format(len(ids)))
logging.debug("Children: {0}".format(len(children)))
logging.debug("Parents: {0}".format(len(parents)))
logging.debug("Combined: {0}".format(len(combined)))
logger.debug("Original: %d", len(ids))
logger.debug("Children: %d", len(children))
logger.debug("Parents: %d", len(parents))
logger.debug("Combined: %d", len(combined))

logging.debug("Filter gff file..")
logger.debug("Filter gff file..")
gff = Gff(gffile)
seen = set()
for g in gff:
Expand Down Expand Up @@ -2409,7 +2405,7 @@ def sort(args):
if opts.method == "topo" or (
opts.method == "unix" and gffile in ("-", "stdin")
):
logging.error(
logger.error(
"Cannot perform inplace sort when method is `topo`"
+ " or method is `unix` and input is `stdin` stream"
)
Expand All @@ -2427,7 +2423,7 @@ def sort(args):
elif opts.method == "topo":
GT_HOME = opts.gt_home
if not op.isdir(GT_HOME):
logging.error("GT_HOME={0} directory does not exist".format(GT_HOME))
logger.error("GT_HOME=%s directory does not exist", GT_HOME)
sys.exit()
cmd = "{0}".format(op.join(GT_HOME, "bin", "gt"))
cmd += " gff3 -sort -tidy -retainids -addids no {0}".format(gffile)
Expand Down Expand Up @@ -2490,7 +2486,7 @@ def fromgtf(args):
print(g, file=fw)
nfeats += 1

logging.debug("A total of {0} features written.".format(nfeats))
logger.debug("A total of %d features written.", nfeats)


def frombed(args):
Expand Down Expand Up @@ -2656,7 +2652,7 @@ def merge(args):
fw = must_open(outfile, "w")
fastarecs = {}
for gffile in natsorted(gffiles, key=lambda x: op.basename(x)):
logging.debug(gffile)
logger.debug(gffile)
fp = open(gffile)
for row in fp:
row = row.rstrip()
Expand Down Expand Up @@ -3109,15 +3105,17 @@ def bed(args):

sorted = not opts.nosort
b.print_to_file(opts.outfile, sorted=sorted)
logging.debug(
"Extracted {} features (type={} id={} parent={})".format(
len(b), ",".join(type), key, parent_key
)
logger.debug(
"Extracted %d features (type=%s id=%s parent=%s)",
len(b),
",".join(type),
key,
parent_key,
)
if primary_only:
logging.debug("Skipped non-primary: %d", skipped_non_primary)
logger.debug("Skipped non-primary: %d", skipped_non_primary)
if ensembl_cds:
logging.debug("Skipped due to identical range: %d", skipped_identical_range)
logger.debug("Skipped due to identical range: %d", skipped_identical_range)


def make_index(gff_file):
Expand All @@ -3130,10 +3128,10 @@ def make_index(gff_file):

if need_update(gff_file, db_file):
cleanup(db_file)
logging.debug("Indexing `{0}`".format(gff_file))
logger.debug("Indexing `%s`", gff_file)
gffutils.create_db(gff_file, db_file, merge_strategy="create_unique")
else:
logging.debug("Load index `{0}`".format(gff_file))
logger.debug("Load index `%s`", gff_file)

return gffutils.FeatureDB(db_file)

Expand Down Expand Up @@ -3333,7 +3331,7 @@ def load(args):
try:
g_fparent = g[fparent]
except gffutils.exceptions.FeatureNotFoundError:
logging.error("{} not found in index .. skipped".format(fparent))
logger.error("%s not found in index .. skipped", fparent)
continue
if desc_attr in g_fparent.attributes:
desc = ",".join(g_fparent.attributes[desc_attr])
Expand Down
5 changes: 3 additions & 2 deletions jcvi/graphics/chromosome.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,8 @@
from ..formats.base import DictFile, get_number
from ..formats.bed import Bed
from ..formats.sizes import Sizes
from ..graphics.base import (

from .base import (
CirclePolygon,
Polygon,
Rectangle,
Expand All @@ -31,7 +32,7 @@
set1_n,
set3_n,
)
from ..graphics.glyph import BaseGlyph, plot_cap
from .glyph import BaseGlyph, plot_cap


class Chromosome(BaseGlyph):
Expand Down

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