diff --git a/jcvi/formats/fasta.py b/jcvi/formats/fasta.py
index 6e1a2546..b794f045 100644
--- a/jcvi/formats/fasta.py
+++ b/jcvi/formats/fasta.py
@@ -4,13 +4,14 @@
import re
import sys
-import os
import os.path as op
import shutil
import logging
import string
import hashlib
+from random import choice
+
from itertools import groupby, zip_longest
from more_itertools import grouper, pairwise
@@ -19,12 +20,13 @@
from Bio.SeqRecord import SeqRecord
from Bio.SeqUtils.CheckSum import seguid
-from jcvi.formats.base import BaseFile, DictFile, must_open
-from jcvi.formats.bed import Bed
-from jcvi.utils.cbook import percentage
-from jcvi.utils.console import printf
-from jcvi.utils.table import write_csv
-from jcvi.apps.base import OptionParser, ActionDispatcher, cleanup, need_update
+from ..apps.base import OptionParser, ActionDispatcher, cleanup, need_update
+from ..utils.cbook import percentage
+from ..utils.console import printf
+from ..utils.table import write_csv
+
+from .base import BaseFile, DictFile, must_open
+from .bed import Bed
class Fasta(BaseFile, dict):
@@ -166,19 +168,17 @@ def sequence(self, f, asstring=True):
return seq
-"""
-Class derived from https://gist.github.com/933737
-Original code written by David Winter (https://github.com/dwinter)
-
-Code writted to answer this challenge at Biostar:
-http://biostar.stackexchange.com/questions/5902/
+class ORFFinder(object):
+ """
+ Class derived from https://gist.github.com/933737
+ Original code written by David Winter (https://github.com/dwinter)
-(Code includes improvements from Brad Chapman)
-"""
+ Code writted to answer this challenge at Biostar:
+ http://biostar.stackexchange.com/questions/5902/
+ (Code includes improvements from Brad Chapman)
-class ORFFinder(object):
- """Find the longest ORF in a given sequence
+ Find the longest ORF in a given sequence
"seq" is a string, if "start" is not provided any codon can be the start of
and ORF. If muliple ORFs have the longest length the first one encountered
is printed
@@ -356,51 +356,48 @@ def rc(s):
def main():
actions = (
+ ("clean", "remove irregular chars in FASTA seqs"),
+ ("diff", "check if two fasta records contain same information"),
(
"extract",
- "given fasta file and seq id, retrieve the sequence " + "in fasta format",
+ "given fasta file and seq id, retrieve the sequence in fasta format",
),
- ("longestorf", "find longest orf for CDS fasta"),
- ("translate", "translate CDS to proteins"),
- ("info", "run `sequence_info` on fasta files"),
- ("summary", "report the real no of bases and N's in fasta files"),
- ("uniq", "remove records that are the same"),
- ("ids", "generate a list of headers"),
+ ("fastq", "combine fasta and qual to create fastq file"),
(
"format",
- "trim accession id to the first space or switch id "
- + "based on 2-column mapping file",
+ "trim accession id to the first space or switch id based on 2-column mapping file",
),
- ("pool", "pool a bunch of fastafiles together and add prefix"),
- ("random", "randomly take some records"),
- ("simulate", "simulate random fasta file for testing"),
- ("diff", "check if two fasta records contain same information"),
- ("identical", "given 2 fasta files, find all exactly identical records"),
- ("trim", "given a cross_match screened fasta, trim the sequence"),
- ("trimsplit", "split sequences at lower-cased letters"),
- ("sort", "sort the records by IDs, sizes, etc."),
("filter", "filter the records by size"),
+ ("fromtab", "convert 2-column sequence file to FASTA format"),
+ ("gaps", "print out a list of gap sizes within sequences"),
+ ("gc", "plot G+C content distribution"),
+ ("identical", "given 2 fasta files, find all exactly identical records"),
+ ("ids", "generate a list of headers"),
+ ("info", "run `sequence_info` on fasta files"),
+ ("ispcr", "reformat paired primers into isPcr query format"),
+ ("join", "concatenate a list of seqs and add gaps in between"),
+ ("longestorf", "find longest orf for CDS fasta"),
("pair", "sort paired reads to .pairs, rest to .fragments"),
(
"pairinplace",
- "starting from fragment.fasta, find if "
- + "adjacent records can form pairs",
+ "starting from fragment.fasta, find if adjacent records can form pairs",
),
- ("fastq", "combine fasta and qual to create fastq file"),
- ("tidy", "normalize gap sizes and remove small components in fasta"),
+ ("pool", "pool a bunch of fastafiles together and add prefix"),
+ ("qual", "generate dummy .qual file based on FASTA file"),
+ ("random", "randomly take some records"),
("sequin", "generate a gapped fasta file for sequin submission"),
- ("gaps", "print out a list of gap sizes within sequences"),
- ("join", "concatenate a list of seqs and add gaps in between"),
+ ("simulate", "simulate random fasta file for testing"),
(
"some",
- "include or exclude a list of records (also performs on "
- + ".qual file if available)",
+ "include or exclude a list of records (also performs on .qual file if available)",
),
- ("qual", "generate dummy .qual file based on FASTA file"),
- ("clean", "remove irregular chars in FASTA seqs"),
- ("ispcr", "reformat paired primers into isPcr query format"),
- ("fromtab", "convert 2-column sequence file to FASTA format"),
- ("gc", "plot G+C content distribution"),
+ ("sort", "sort the records by IDs, sizes, etc."),
+ ("summary", "report the real no of bases and N's in fasta files"),
+ ("tidy", "normalize gap sizes and remove small components in fasta"),
+ ("translate", "translate CDS to proteins"),
+ ("trim", "given a cross_match screened fasta, trim the sequence"),
+ ("trimsplit", "split sequences at lower-cased letters"),
+ ("uniq", "remove records that are the same"),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
@@ -410,8 +407,6 @@ def simulate_one(fw, name, size):
"""
Simulate a random sequence with name and size
"""
- from random import choice
-
seq = Seq("".join(choice("ACGT") for _ in range(size)))
s = SeqRecord(seq, id=name, description="Fake sequence")
SeqIO.write([s], fw, "fasta")
diff --git a/jcvi/formats/gff.py b/jcvi/formats/gff.py
index 46c99b52..d4ee94bb 100644
--- a/jcvi/formats/gff.py
+++ b/jcvi/formats/gff.py
@@ -23,7 +23,7 @@
)
from ..annotation.reformat import atg_name
from ..utils.cbook import AutoVivification
-from ..utils.range import range_minmax
+from ..utils.range import Range, range_minmax
from ..utils.orderedcollections import DefaultOrderedDict, OrderedDict, parse_qs
from .base import DictFile, LineFile, must_open, is_number
@@ -484,8 +484,6 @@ def to_range(obj, score=None, id=None, strand=None):
"""
Given a gffutils object, convert it to a range object
"""
- from jcvi.utils.range import Range
-
if score or id:
_score = score if score else obj.score
_id = id if id else obj.id
@@ -503,39 +501,39 @@ def main():
("addparent", "merge sister features and infer their parent"),
("bed", "parse gff and produce bed file for particular feature type"),
("bed12", "produce bed12 file for coding features"),
- ("fromgtf", "convert gtf to gff3 format"),
- ("gtf", "convert gff3 to gtf format"),
- ("gb", "convert gff3 to genbank format"),
- ("sort", "sort the gff file"),
+ ("chain", "fill in parent features by chaining children"),
+ ("children", "find all children that belongs to the same parent"),
+ ("cluster", "cluster transcripts based on shared splicing structure"),
+ ("extract", "extract contig or features from gff file"),
("filter", "filter the gff file based on Identity and Coverage"),
- ("sizes", "calculate sizes of features in gff file"),
- ("format", "format the gff file, change seqid, etc."),
(
"fixboundaries",
"fix boundaries of parent features by range chaining child features",
),
- ("chain", "fill in parent features by chaining children"),
- ("rename", "change the IDs within the gff3"),
- ("uniq", "remove the redundant gene models"),
- ("liftover", "adjust gff coordinates based on tile number"),
- ("note", "extract certain attribute field for each feature"),
- ("load", "extract the feature (e.g. CDS) sequences and concatenate"),
- ("extract", "extract contig or features from gff file"),
- ("split", "split the gff into one contig per file"),
- ("merge", "merge several gff files into one"),
- ("parents", "find the parents given a list of IDs"),
- ("children", "find all children that belongs to the same parent"),
+ (
+ "fixpartials",
+ "fix 5/3 prime partial transcripts, locate nearest in-frame start/stop",
+ ),
+ ("format", "format the gff file, change seqid, etc."),
("frombed", "convert from bed format to gff3"),
+ ("fromgtf", "convert gtf to gff3 format"),
("fromsoap", "convert from soap format to gff3"),
("gapsplit", "split alignment GFF3 at gaps based on CIGAR string"),
+ ("gb", "convert gff3 to genbank format"),
+ ("gtf", "convert gff3 to gtf format"),
+ ("liftover", "adjust gff coordinates based on tile number"),
+ ("load", "extract the feature (e.g. CDS) sequences and concatenate"),
+ ("merge", "merge several gff files into one"),
+ ("note", "extract certain attribute field for each feature"),
("orient", "orient the coding features based on translation"),
+ ("parents", "find the parents given a list of IDs"),
+ ("rename", "change the IDs within the gff3"),
+ ("sizes", "calculate sizes of features in gff file"),
+ ("sort", "sort the gff file"),
("splicecov", "tag gff introns with coverage info from junctions.bed"),
+ ("split", "split the gff into one contig per file"),
("summary", "print summary stats for features of different types"),
- ("cluster", "cluster transcripts based on shared splicing structure"),
- (
- "fixpartials",
- "fix 5/3 prime partial transcripts, locate nearest in-frame start/stop",
- ),
+ ("uniq", "remove the redundant gene models"),
)
p = ActionDispatcher(actions)