In [1]:

    

import collections


    

In [3]:

    

Foo = collections.namedtuple('Foo', ('bar', 'baz'))
foo = Foo(None, None)
foo


    

    
Out[3]:





Foo(bar=None, baz=None)

In [4]:

    

bool(-1)


    

    
Out[4]:





True

In [6]:

    

-3 % 3


    

    
Out[6]:





0

In [129]:

    

from __future__ import division
import numpy as np
import petl.interactive as etl
import petlx.all
import collections
import operator
import pyfasta
from Bio.Seq import Seq


CodingPosition = collections.namedtuple('CodingPosition', 
                                        ('gene_id', 'gene_start', 'gene_stop',
                                         'transcript_id', 'transcript_start', 'transcript_stop',
                                         'exon_id', 'exon_start', 'exon_stop',
                                         'strand',
                                         'chrom',
                                         'pos',
                                         'ref',
                                         'ref_start',
                                         'ref_stop',
                                         'ref_cds_start',
                                         'ref_cds_stop'))

CodonChange = collections.namedtuple('CodonChange',
                                     CodingPosition._fields + ('alt', 'ref_codon', 'alt_codon', 'codon_change'))

AminoAcidChange = collections.namedtuple('AminoAcidChange', 
                                         CodonChange._fields + ('aa_pos', 'ref_aa', 'alt_aa', 'aa_change'))


class EffectPredictor(object):
    
    
    def __init__(self, fasta_fn, gff3_fn, 
                 gff3_id_attribute='ID', 
                 gff3_parent_attribute='Parent',
                 gff3_gene_types=['gene', 'pseudogene'],
                 gff3_transcript_types=['mRNA', 'pseudogenic_transcript'],
                 gff3_exon_types=['CDS', 'pseudogenic_exon']):
        """Create a variant effect predictor.
        
        Parameters
        ----------
        
        fasta_fn : string
            Path to reference genome FASTA file.
        gff3_fn : string
            Path to genome annotations GFF3 file.
        gff3_id_attribute : string, optional
            Name of attribute containing feature identifier.
        gff3_parent_attribute : string, optional
            Name of attribute containing parent feature identifier. 
        gff3_gene_types : list of strings, optional
            Feature types to consider as genes.
        gff3_transcript_types : list of strings, optional
            Feature types to consider as transcripts.
        gff3_exon_types : list of strings, optional
            Feature types to consider as exons.
            
        """
        
        # store parameters
        self._fasta_fn = fasta_fn
        self._gff3_fn = gff3_fn
        self._gff3_id_attribute = gff3_id_attribute
        self._gff3_parent_attribute = gff3_parent_attribute
        self._gff3_gene_types = gff3_gene_types
        self._gff3_transcript_types = gff3_transcript_types
        self._gff3_exon_types = gff3_exon_types
        
        # setup reference sequence
        self._fasta = pyfasta.Fasta(fasta_fn)
        
        # setup access to GFF3 as a table
        self._tbl_features = (etl
            .fromgff3(gff3_fn)
            .unpackdict('attributes', [gff3_id_attribute, gff3_parent_attribute])
            .rename({gff3_id_attribute: 'feature_id', gff3_parent_attribute: 'parent_id'})
        )
        # TODO remove hack for testing
        self._tbl_features = self._tbl_features.eq('seqid', 'Pf3D7_01_v3')
        # index features by ID
        self._lkp_feature = self._tbl_features.recordlookupone('feature_id')
        # index features by parent ID
        self._lkp_children = self._tbl_features.recordlookup('parent_id')
        # index features by genomic location
        self._interval_trees = self._tbl_features.facetintervalrecordlookup('seqid', 'start', 'end', proximity=1)
        
        
    def get_feature(self, feature_id):
        """Look up a feature by ID."""
        return self._lkp_feature[feature_id]
    
    
    def get_feature_children(self, feature_id):
        """Look up the children of a feature."""
        return self._lkp_children[feature_id]
    
    
    def find_features(self, chrom, start, stop=None):
        """Look up features overlapping a given genomic location."""
        if stop is None:
            stop = start
        return self._interval_trees[chrom].find(start, stop)
    
    
    def get_coding_positions(self, chrom, pos, ref):
        """Calculate position of the reference allele relative to the start 
        of gene coding sequences.
        
        Parameters
        ----------
        
        chrom : string
            Chromosome.
        pos : int
            Position.
        ref : string
            Reference allele.
            
        Returns
        -------
        
        Generator of `CodingPosition`s.
                
        """
        
        # ensure types and case
        ref = str(ref).upper()

        # convenience
        fasta = self._fasta

        # obtain start and end coordinates of the reference allele
        # N.B., use one-based inclusive coordinate system (like GFF3) throughout
        ref_start = pos
        ref_stop = pos + len(ref) - 1

        # check the reference allele matches the reference sequence
        ref_seq = fasta.sequence({'chr': chrom, 
                                  'start': ref_start, 
                                  'stop': ref_stop})
        ref_seq = str(ref_seq).lower()
        assert ref_seq == ref.lower(), 'reference allele does not match reference sequence, expected %r, found %r' % (ref_seq, ref.lower())
        
        # find overlapping features
        overlapping_features = self.find_features(chrom, ref_start, ref_stop)
        
        # filter to find overlapping exons
        overlapping_exons = [f for f in overlapping_features 
                             if f.type in self._gff3_exon_types]
        
        for overlapping_exon in overlapping_exons:
            
            strand = overlapping_exon.strand
            transcript = self.get_feature(overlapping_exon.parent_id)
            gene = self.get_feature(transcript.parent_id)
            
            # find all exons in transcript
            exons = self.get_feature_children(transcript.feature_id)
            
            if strand == '+':
                
                # sort exons
                exons = sorted(exons, key=operator.itemgetter('start'))
                
                # find index of overlapping exons in all exons
                exon_ids = [exon.feature_id for exon in exons]
                exon_index = exon_ids.index(overlapping_exon.feature_id)
                
                # find offset
                offset = sum([exon.end - exon.start + 1 for exon in exons[:exon_index]])
                
                # find ref cds start position relative to overlapping exon
                if ref_start < overlapping_exon.start:
                    ref_cds_start = -1
                else:
                    ref_cds_start = offset + (ref_start - overlapping_exon.start)
                
                # find ref cds stop position relative to overlapping exon
                if ref_stop > overlapping_exon.end:
                    ref_cds_stop = -1
                else:
                    ref_cds_stop = offset + (ref_stop - overlapping_exon.start)
                                    
            else:
                
                # sort exons (backwards this time)
                exons = sorted(exons, key=operator.itemgetter('end'), reverse=True)
                    
                # find index of overlapping exons in all exons
                exon_ids = [exon.feature_id for exon in exons]
                exon_index = exon_ids.index(overlapping_exon.feature_id)

                # find offset
                offset = sum([exon.end - exon.start + 1 for exon in exons[:exon_index]])
                
                # find ref cds start position relative to overlapping exon
                # N.B., have to think back-to-front
                if ref_stop > overlapping_exon.end:
                    ref_cds_start = -1
                else:
                    ref_cds_start = offset + (overlapping_exon.end - ref_stop)
                
                # find ref cds stop position relative to overlapping exon
                # N.B., have to think back-to-front
                if ref_start < overlapping_exon.start:
                    ref_cds_stop = -1
                else:
                    ref_cds_stop = offset + (overlapping_exon.end - ref_start)
            
            yield CodingPosition(gene.feature_id, gene.start, gene.end,
                                 transcript.feature_id, transcript.start, transcript.end,
                                 overlapping_exon.feature_id, overlapping_exon.start, overlapping_exon.end,
                                 strand,
                                 chrom, 
                                 pos,
                                 ref,
                                 ref_start,
                                 ref_stop,
                                 ref_cds_start,
                                 ref_cds_stop)


    def get_codon_changes(self, chrom, pos, ref, alt):
        """Calculate the codon changes resulting from a given variant.
        
        Parameters
        ----------
        
        chrom : string
            Chromosome.
        pos : int
            Position.
        ref : string
            Reference allele.
        alt : string
            Alternate allele.
            
        Returns
        -------
        
        Generator of `CodonChange`s.
        
        """
        
        # ensure types and case
        ref = str(ref).upper()
        alt = str(alt).upper()

        # convenience
        fasta = self._fasta

        for coding_position in self.get_coding_positions(chrom, pos, ref):
            
            # convenience
            strand = coding_position.strand
            ref_start = coding_position.ref_start
            ref_stop = coding_position.ref_stop
            ref_cds_start = coding_position.ref_cds_start
            ref_cds_stop = coding_position.ref_cds_stop
            
            if ref_cds_start >= 0 and ref_cds_stop >= 0:
            
                # lookup exon
                exon = self.get_feature(coding_position.exon_id)

                if strand == '+':

                    # calculate position of reference allele start within codon
                    ref_start_phase = ref_cds_start % 3

                    # obtain any previous nucleotides to complete the first codon
                    prefix = fasta.sequence({'chr': chrom, 
                                             'start': ref_start - ref_start_phase, 
                                             'stop': ref_start - 1})
                    prefix = str(prefix).lower()

                    # begin constructing reference and alternate codon sequences
                    ref_codon = prefix + ref
                    alt_codon = prefix + alt

                    # obtain any subsequence nucleotides to complete the last codon
                    if len(ref_codon) % 3:
                        ref_stop_phase = len(ref_codon) % 3
                        suffix = fasta.sequence({'chr': chrom, 
                                                 'start': ref_stop + 1, 
                                                 'stop': ref_stop + 3 - ref_stop_phase})
                        suffix = str(suffix).lower()
                        ref_codon += suffix

                    if len(alt_codon) % 3:
                        alt_stop_phase = len(alt_codon) % 3
                        suffix = fasta.sequence({'chr': chrom, 
                                                 'start': ref_stop + 1, 
                                                 'stop': ref_stop + 3 - alt_stop_phase})
                        suffix = str(suffix).lower()
                        alt_codon += suffix

                else:

                    # N.B., we are on the reverse strand, so position reported for 
                    # variant is actually position at the *end* of the reference allele
                    # which is particularly important for deletions

                    # we will construct everything for the forward strand (i.e., back-to-front)
                    # then take reverse complement afterwards at the end of this code block

                    # calculate position of reference allele start within codon
                    ref_start_phase = ref_cds_start % 3

                    # obtain any previous nucleotides to complete the first codon
                    prefix = fasta.sequence({'chr': chrom, 
                                             'start': ref_stop + 1, 
                                             'stop': ref_stop + ref_start_phase})
                    prefix = str(prefix).lower()

                    # begin constructing reference and alternate codon sequences
                    ref_codon = ref + prefix
                    alt_codon = alt + prefix

                    # obtain any subsequence nucleotides to complete the last codon
                    if len(ref_codon) % 3:
                        ref_stop_phase = len(ref_codon) % 3
                        suffix = fasta.sequence({'chr': chrom, 
                                                 'start': ref_start - 3 + ref_stop_phase, 
                                                 'stop': ref_start - 1})
                        suffix = str(suffix).lower()
                        ref_codon = suffix + ref_codon

                    if len(alt_codon) % 3:
                        alt_stop_phase = len(alt_codon) % 3
                        suffix = fasta.sequence({'chr': chrom, 
                                                 'start': ref_start - 3 + alt_stop_phase, 
                                                 'stop': ref_start - 1})
                        suffix = str(suffix).lower()
                        alt_codon = suffix + alt_codon

                    # take reverse complement
                    ref_codon = str(Seq(ref_codon).reverse_complement())
                    alt_codon = str(Seq(alt_codon).reverse_complement())

                codon_change = '%s/%s' % (ref_codon, alt_codon)
                yield CodonChange(*(coding_position + (alt, ref_codon, alt_codon, codon_change)))

            
    def get_amino_acid_changes(self, chrom, pos, ref, alt):
        """Calculate the amino acid changes resulting from a given variant.
        
        Parameters
        ----------
        
        chrom : string
            Chromosome.
        pos : int
            Position.
        ref : string
            Reference allele.
        alt : string
            Alternate allele.
            
        Returns
        -------
        
        Generator of `AminoAcidChange`s.
        
        """
        
        for codon_change in self.get_codon_changes(chrom, pos, ref, alt):
            
            ref_aa = str(Seq(codon_change.ref_codon).translate())
            alt_aa = str(Seq(codon_change.alt_codon).translate()) 
            aa_pos = (codon_change.ref_cds_start // 3) + 1
            aa_change = '%s%s%s' % (ref_aa, aa_pos, alt_aa) 
                
            yield AminoAcidChange(*(codon_change + (aa_pos, ref_aa, alt_aa, aa_change)))
            
            
    def get_amino_acid_change(self, chrom, pos, ref, alt, transcript_id):
        """TODO"""

        coding_pos = self.get_coding_
        # ensure types and case
        ref = str(ref).upper()
        alt = str(alt).upper()

        # convenience
        fasta = self._fasta
        
        # look up transcript
        transcript = self.get_feature(transcript_id)
        
        # obtain start and end coordinates of the reference allele
        # N.B., use one-based inclusive coordinate system (like GFF3) throughout
        ref_start = pos
        ref_stop = pos + len(ref) - 1

        # check the reference allele matches the reference sequence
        ref_seq = fasta.sequence({'chr': chrom, 
                                  'start': ref_start, 
                                  'stop': ref_stop})
        ref_seq = str(ref_seq).lower()
        assert ref_seq == ref.lower(), 'reference allele does not match reference sequence, expected %r, found %r' % (ref_seq, ref.lower())
        
        if ref_start < transcript.start or ref_stop > transcript.end:
            
            raise Exception('reference allele does not overlap transcript or overlaps transcript boundary')
            
        else:
            
            


            
    def get_effects(chrom, pos, ref, alt):
        """TODO"""

        # ensure types and case
        ref = str(ref).upper()
        alt = str(alt).upper()

        # convenience
        fasta = self._fasta

        # obtain start and end coordinates of the reference allele
        # N.B., use one-based inclusive coordinate system (like GFF3) throughout
        ref_start = pos
        ref_stop = pos + len(ref) - 1

        # check the reference allele matches the reference sequence
        ref_seq = fasta.sequence({'chr': chrom, 
                                  'start': ref_start, 
                                  'stop': ref_stop})
        ref_seq = str(ref_seq).lower()
        assert ref_seq == ref.lower(), 'reference allele does not match reference sequence, expected %r, found %r' % (ref_seq, ref.lower())
        
        # find overlapping genome features
        overlapping_features = self.find_features(chrom, ref_start, ref_stop)

        # filter to find overlapping genes
        genes = [f for f in overlapping_features 
                 if f.type in self._gff3_gene_types]
        
        if not genes:
            
            yield EffectIntergenic()
            
        else:
            
            for gene in genes:
                
                transcripts = self.get_children(gene.feature_id)
            
                if not transcripts:

                    yield EffectIntragenic(gene.feature_id)

                else:

                    for transcript in transcripts:

                        if ref_start >= transcript.start and ref_stop <= transcript.end:
                            
                            aa_change = self._get_amino_acid_change(chrom, pos, ref, alt, transcript)

                            if aa_change.ref_cds_start < 0 and aa_change.ref_cds_stop < 0:

                                yield EffectIntronic(*aa_change)
                                
                            elif ref_cds_start < 0 or ref_cds_stop < 0:
                                
                                yield EffectNotImplemented(*aa_change)
                                
                            else:
                                                                
                                if len(ref) == len(alt) == 1:
                                    
                                    # SNPs
                                    if aa_change.ref_aa == aa_change.alt_aa:
                                        
                                        yield EffectSynonymousCoding(*aa_change)
                                        
                                    elif aa_change.ref_aa == 'M' and ref_cds_start == 0:
                                        
                                        yield EffectStartLost(*aa_change)
                                        
                                    elif aa_change.ref_aa == '*':
                                        
                                        yield EffectStopLost(*aa_change)
                                        
                                    elif aa_change.alt_aa == '*':
                                        
                                        yield EffectStopGained(*aa_change)
                                        
                                    else:
                                        
                                        yield EffectNonSynonymousCoding(*aa_change)
                                
                                else:
                                    
                                    # TODO INDELs
                            
                        else:
                            
                            yield EffectNotImplemented(gene.feature_id, transcript.feature_id)


    

In [229]:

    

eff._tbl_features.counts('type').displayall()


    

    








type
count
frequency




CDS
374
0.406080347448


polypeptide
148
0.160694896851


gene
141
0.153094462541


mRNA
135
0.14657980456


polypeptide_motif
39
0.042345276873


pseudogenic_exon
36
0.0390879478827


pseudogene
13
0.014115092291


pseudogenic_transcript
13
0.014115092291


repeat_region
12
0.0130293159609


rRNA
5
0.00542888165038


ncRNA
4
0.0043431053203


centromere
1
0.00108577633008

In [130]:

    

fasta_fn = '../../../data/genome/sanger/version3/September_2012/Pf3D7_v3.fa'
gff3_fn = '../../../data/genome/sanger/version3/September_2012/Pf3D7_v3.gff'
eff = EffectPredictor(fasta_fn, gff3_fn)


    

In [131]:

    

import pprint
pp = pprint.PrettyPrinter(indent=1, width=80, depth=3)

def dbg(results):
    pp.pprint([x._asdict().items() for x in results])


    

In [132]:

    

eff._tbl_features.eq('type', 'gene').rowslice(15, 19)


    

    
Out[132]:







seqid
source
type
start
end
score
strand
phase
feature_id
parent_id




Pf3D7_01_v3
chado
gene
98819
102282
.
+
.
PF3D7_0102200
None


Pf3D7_01_v3
chado
gene
104704
105209
.
+
.
PF3D7_0102300
None


Pf3D7_01_v3
chado
gene
110750
115799
.
-
.
PF3D7_0102500
None


Pf3D7_01_v3
chado
gene
119041
121249
.
-
.
PF3D7_0102600
None

In [133]:

    

eff._fasta['Pf3D7_01_v3'][98815:98824]


    

    
Out[133]:





u'attatgaga'

In [134]:

    

dbg(eff.get_coding_positions('Pf3D7_01_v3', 98818, 'TAT'))


    

    




[[('gene_id', 'PF3D7_0102200'),
  ('gene_start', 98819),
  ('gene_stop', 102282),
  ('transcript_id', 'PF3D7_0102200.1'),
  ('transcript_start', 98819),
  ('transcript_stop', 102282),
  ('exon_id', 'PF3D7_0102200.1:exon:1'),
  ('exon_start', 98819),
  ('exon_stop', 99013),
  ('strand', '+'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 98818),
  ('ref', 'TAT'),
  ('ref_start', 98818),
  ('ref_stop', 98820),
  ('ref_cds_start', -1),
  ('ref_cds_stop', 1)]]

In [135]:

    

dbg(eff.get_coding_positions('Pf3D7_01_v3', 98819, 'A'))


    

    




[[('gene_id', 'PF3D7_0102200'),
  ('gene_start', 98819),
  ('gene_stop', 102282),
  ('transcript_id', 'PF3D7_0102200.1'),
  ('transcript_start', 98819),
  ('transcript_stop', 102282),
  ('exon_id', 'PF3D7_0102200.1:exon:1'),
  ('exon_start', 98819),
  ('exon_stop', 99013),
  ('strand', '+'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 98819),
  ('ref', 'A'),
  ('ref_start', 98819),
  ('ref_stop', 98819),
  ('ref_cds_start', 0),
  ('ref_cds_stop', 0)]]

In [136]:

    

dbg(eff.get_coding_positions('Pf3D7_01_v3', 98820, 'T'))


    

    




[[('gene_id', 'PF3D7_0102200'),
  ('gene_start', 98819),
  ('gene_stop', 102282),
  ('transcript_id', 'PF3D7_0102200.1'),
  ('transcript_start', 98819),
  ('transcript_stop', 102282),
  ('exon_id', 'PF3D7_0102200.1:exon:1'),
  ('exon_start', 98819),
  ('exon_stop', 99013),
  ('strand', '+'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 98820),
  ('ref', 'T'),
  ('ref_start', 98820),
  ('ref_stop', 98820),
  ('ref_cds_start', 1),
  ('ref_cds_stop', 1)]]

In [137]:

    

dbg(eff.get_coding_positions('Pf3D7_01_v3', 98821, 'G'))


    

    




[[('gene_id', 'PF3D7_0102200'),
  ('gene_start', 98819),
  ('gene_stop', 102282),
  ('transcript_id', 'PF3D7_0102200.1'),
  ('transcript_start', 98819),
  ('transcript_stop', 102282),
  ('exon_id', 'PF3D7_0102200.1:exon:1'),
  ('exon_start', 98819),
  ('exon_stop', 99013),
  ('strand', '+'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 98821),
  ('ref', 'G'),
  ('ref_start', 98821),
  ('ref_stop', 98821),
  ('ref_cds_start', 2),
  ('ref_cds_stop', 2)]]

In [138]:

    

eff._fasta['Pf3D7_01_v3'][99010:99016]


    

    
Out[138]:





u'aatgta'

In [139]:

    

dbg(eff.get_coding_positions('Pf3D7_01_v3', 99013, 'T'))


    

    




[[('gene_id', 'PF3D7_0102200'),
  ('gene_start', 98819),
  ('gene_stop', 102282),
  ('transcript_id', 'PF3D7_0102200.1'),
  ('transcript_start', 98819),
  ('transcript_stop', 102282),
  ('exon_id', 'PF3D7_0102200.1:exon:1'),
  ('exon_start', 98819),
  ('exon_stop', 99013),
  ('strand', '+'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 99013),
  ('ref', 'T'),
  ('ref_start', 99013),
  ('ref_stop', 99013),
  ('ref_cds_start', 194),
  ('ref_cds_stop', 194)]]

In [140]:

    

dbg(eff.get_coding_positions('Pf3D7_01_v3', 99013, 'TG'))


    

    




[[('gene_id', 'PF3D7_0102200'),
  ('gene_start', 98819),
  ('gene_stop', 102282),
  ('transcript_id', 'PF3D7_0102200.1'),
  ('transcript_start', 98819),
  ('transcript_stop', 102282),
  ('exon_id', 'PF3D7_0102200.1:exon:1'),
  ('exon_start', 98819),
  ('exon_stop', 99013),
  ('strand', '+'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 99013),
  ('ref', 'TG'),
  ('ref_start', 99013),
  ('ref_stop', 99014),
  ('ref_cds_start', 194),
  ('ref_cds_stop', -1)]]

In [141]:

    

eff._fasta['Pf3D7_01_v3'][115796:115799]


    

    
Out[141]:





u'cat'

In [142]:

    

dbg(eff.get_coding_positions('Pf3D7_01_v3', 115799, 'T'))


    

    




[[('gene_id', 'PF3D7_0102500'),
  ('gene_start', 110750),
  ('gene_stop', 115799),
  ('transcript_id', 'PF3D7_0102500.1'),
  ('transcript_start', 110750),
  ('transcript_stop', 115799),
  ('exon_id', 'PF3D7_0102500.1:exon:4'),
  ('exon_start', 111338),
  ('exon_stop', 115799),
  ('strand', '-'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 115799),
  ('ref', 'T'),
  ('ref_start', 115799),
  ('ref_stop', 115799),
  ('ref_cds_start', 0),
  ('ref_cds_stop', 0)]]

In [143]:

    

dbg(eff.get_coding_positions('Pf3D7_01_v3', 115798, 'A'))


    

    




[[('gene_id', 'PF3D7_0102500'),
  ('gene_start', 110750),
  ('gene_stop', 115799),
  ('transcript_id', 'PF3D7_0102500.1'),
  ('transcript_start', 110750),
  ('transcript_stop', 115799),
  ('exon_id', 'PF3D7_0102500.1:exon:4'),
  ('exon_start', 111338),
  ('exon_stop', 115799),
  ('strand', '-'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 115798),
  ('ref', 'A'),
  ('ref_start', 115798),
  ('ref_stop', 115798),
  ('ref_cds_start', 1),
  ('ref_cds_stop', 1)]]

In [144]:

    

dbg(eff.get_coding_positions('Pf3D7_01_v3', 115797, 'C'))


    

    




[[('gene_id', 'PF3D7_0102500'),
  ('gene_start', 110750),
  ('gene_stop', 115799),
  ('transcript_id', 'PF3D7_0102500.1'),
  ('transcript_start', 110750),
  ('transcript_stop', 115799),
  ('exon_id', 'PF3D7_0102500.1:exon:4'),
  ('exon_start', 111338),
  ('exon_stop', 115799),
  ('strand', '-'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 115797),
  ('ref', 'C'),
  ('ref_start', 115797),
  ('ref_stop', 115797),
  ('ref_cds_start', 2),
  ('ref_cds_stop', 2)]]

In [145]:

    

dbg(eff.get_coding_positions('Pf3D7_01_v3', 115799, 'TA'))


    

    




[[('gene_id', 'PF3D7_0102500'),
  ('gene_start', 110750),
  ('gene_stop', 115799),
  ('transcript_id', 'PF3D7_0102500.1'),
  ('transcript_start', 110750),
  ('transcript_stop', 115799),
  ('exon_id', 'PF3D7_0102500.1:exon:4'),
  ('exon_start', 111338),
  ('exon_stop', 115799),
  ('strand', '-'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 115799),
  ('ref', 'TA'),
  ('ref_start', 115799),
  ('ref_stop', 115800),
  ('ref_cds_start', -1),
  ('ref_cds_stop', 0)]]

In [146]:

    

dbg(eff.get_coding_positions('Pf3D7_01_v3', 111338, 'T'))


    

    




[[('gene_id', 'PF3D7_0102500'),
  ('gene_start', 110750),
  ('gene_stop', 115799),
  ('transcript_id', 'PF3D7_0102500.1'),
  ('transcript_start', 110750),
  ('transcript_stop', 115799),
  ('exon_id', 'PF3D7_0102500.1:exon:4'),
  ('exon_start', 111338),
  ('exon_stop', 115799),
  ('strand', '-'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 111338),
  ('ref', 'T'),
  ('ref_start', 111338),
  ('ref_stop', 111338),
  ('ref_cds_start', 4461),
  ('ref_cds_stop', 4461)]]

In [147]:

    

dbg(eff.get_coding_positions('Pf3D7_01_v3', 111337, 'C'))


    

    




[]

In [148]:

    

dbg(eff.get_coding_positions('Pf3D7_01_v3', 111337, 'CT'))


    

    




[[('gene_id', 'PF3D7_0102500'),
  ('gene_start', 110750),
  ('gene_stop', 115799),
  ('transcript_id', 'PF3D7_0102500.1'),
  ('transcript_start', 110750),
  ('transcript_stop', 115799),
  ('exon_id', 'PF3D7_0102500.1:exon:4'),
  ('exon_start', 111338),
  ('exon_stop', 115799),
  ('strand', '-'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 111337),
  ('ref', 'CT'),
  ('ref_start', 111337),
  ('ref_stop', 111338),
  ('ref_cds_start', 4461),
  ('ref_cds_stop', -1)]]

In [149]:

    

dbg(eff.get_amino_acid_changes('Pf3D7_01_v3', 98819, 'A', 'T'))


    

    




[[('gene_id', 'PF3D7_0102200'),
  ('gene_start', 98819),
  ('gene_stop', 102282),
  ('transcript_id', 'PF3D7_0102200.1'),
  ('transcript_start', 98819),
  ('transcript_stop', 102282),
  ('exon_id', 'PF3D7_0102200.1:exon:1'),
  ('exon_start', 98819),
  ('exon_stop', 99013),
  ('strand', '+'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 98819),
  ('ref', 'A'),
  ('ref_start', 98819),
  ('ref_stop', 98819),
  ('ref_cds_start', 0),
  ('ref_cds_stop', 0),
  ('alt', 'T'),
  ('ref_codon', 'Atg'),
  ('alt_codon', 'Ttg'),
  ('codon_change', 'Atg/Ttg'),
  ('aa_pos', 1),
  ('ref_aa', 'M'),
  ('alt_aa', 'L'),
  ('aa_change', 'M1L')]]

In [150]:

    

dbg(eff.get_amino_acid_changes('Pf3D7_01_v3', 98820, 'T', 'C'))


    

    




[[('gene_id', 'PF3D7_0102200'),
  ('gene_start', 98819),
  ('gene_stop', 102282),
  ('transcript_id', 'PF3D7_0102200.1'),
  ('transcript_start', 98819),
  ('transcript_stop', 102282),
  ('exon_id', 'PF3D7_0102200.1:exon:1'),
  ('exon_start', 98819),
  ('exon_stop', 99013),
  ('strand', '+'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 98820),
  ('ref', 'T'),
  ('ref_start', 98820),
  ('ref_stop', 98820),
  ('ref_cds_start', 1),
  ('ref_cds_stop', 1),
  ('alt', 'C'),
  ('ref_codon', 'aTg'),
  ('alt_codon', 'aCg'),
  ('codon_change', 'aTg/aCg'),
  ('aa_pos', 1),
  ('ref_aa', 'M'),
  ('alt_aa', 'T'),
  ('aa_change', 'M1T')]]

In [152]:

    

dbg(eff.get_amino_acid_changes('Pf3D7_01_v3', 98821, 'G', 'C'))


    

    




[[('gene_id', 'PF3D7_0102200'),
  ('gene_start', 98819),
  ('gene_stop', 102282),
  ('transcript_id', 'PF3D7_0102200.1'),
  ('transcript_start', 98819),
  ('transcript_stop', 102282),
  ('exon_id', 'PF3D7_0102200.1:exon:1'),
  ('exon_start', 98819),
  ('exon_stop', 99013),
  ('strand', '+'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 98821),
  ('ref', 'G'),
  ('ref_start', 98821),
  ('ref_stop', 98821),
  ('ref_cds_start', 2),
  ('ref_cds_stop', 2),
  ('alt', 'C'),
  ('ref_codon', 'atG'),
  ('alt_codon', 'atC'),
  ('codon_change', 'atG/atC'),
  ('aa_pos', 1),
  ('ref_aa', 'M'),
  ('alt_aa', 'I'),
  ('aa_change', 'M1I')]]

In [153]:

    

dbg(eff.get_amino_acid_changes('Pf3D7_01_v3', 98822, 'A', 'C'))


    

    




[[('gene_id', 'PF3D7_0102200'),
  ('gene_start', 98819),
  ('gene_stop', 102282),
  ('transcript_id', 'PF3D7_0102200.1'),
  ('transcript_start', 98819),
  ('transcript_stop', 102282),
  ('exon_id', 'PF3D7_0102200.1:exon:1'),
  ('exon_start', 98819),
  ('exon_stop', 99013),
  ('strand', '+'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 98822),
  ('ref', 'A'),
  ('ref_start', 98822),
  ('ref_stop', 98822),
  ('ref_cds_start', 3),
  ('ref_cds_stop', 3),
  ('alt', 'C'),
  ('ref_codon', 'Aga'),
  ('alt_codon', 'Cga'),
  ('codon_change', 'Aga/Cga'),
  ('aa_pos', 2),
  ('ref_aa', 'R'),
  ('alt_aa', 'R'),
  ('aa_change', 'R2R')]]

In [154]:

    

dbg(eff.get_amino_acid_changes('Pf3D7_01_v3', 98819, 'A', 'ATTT'))


    

    




[[('gene_id', 'PF3D7_0102200'),
  ('gene_start', 98819),
  ('gene_stop', 102282),
  ('transcript_id', 'PF3D7_0102200.1'),
  ('transcript_start', 98819),
  ('transcript_stop', 102282),
  ('exon_id', 'PF3D7_0102200.1:exon:1'),
  ('exon_start', 98819),
  ('exon_stop', 99013),
  ('strand', '+'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 98819),
  ('ref', 'A'),
  ('ref_start', 98819),
  ('ref_stop', 98819),
  ('ref_cds_start', 0),
  ('ref_cds_stop', 0),
  ('alt', 'ATTT'),
  ('ref_codon', 'Atg'),
  ('alt_codon', 'ATTTtg'),
  ('codon_change', 'Atg/ATTTtg'),
  ('aa_pos', 1),
  ('ref_aa', 'M'),
  ('alt_aa', 'IL'),
  ('aa_change', 'M1IL')]]

In [155]:

    

dbg(eff.get_amino_acid_changes('Pf3D7_01_v3', 98820, 'T', 'TAAA'))


    

    




[[('gene_id', 'PF3D7_0102200'),
  ('gene_start', 98819),
  ('gene_stop', 102282),
  ('transcript_id', 'PF3D7_0102200.1'),
  ('transcript_start', 98819),
  ('transcript_stop', 102282),
  ('exon_id', 'PF3D7_0102200.1:exon:1'),
  ('exon_start', 98819),
  ('exon_stop', 99013),
  ('strand', '+'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 98820),
  ('ref', 'T'),
  ('ref_start', 98820),
  ('ref_stop', 98820),
  ('ref_cds_start', 1),
  ('ref_cds_stop', 1),
  ('alt', 'TAAA'),
  ('ref_codon', 'aTg'),
  ('alt_codon', 'aTAAAg'),
  ('codon_change', 'aTg/aTAAAg'),
  ('aa_pos', 1),
  ('ref_aa', 'M'),
  ('alt_aa', 'IK'),
  ('aa_change', 'M1IK')]]

In [156]:

    

dbg(eff.get_amino_acid_changes('Pf3D7_01_v3', 98819, 'ATG', 'A'))


    

    




[[('gene_id', 'PF3D7_0102200'),
  ('gene_start', 98819),
  ('gene_stop', 102282),
  ('transcript_id', 'PF3D7_0102200.1'),
  ('transcript_start', 98819),
  ('transcript_stop', 102282),
  ('exon_id', 'PF3D7_0102200.1:exon:1'),
  ('exon_start', 98819),
  ('exon_stop', 99013),
  ('strand', '+'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 98819),
  ('ref', 'ATG'),
  ('ref_start', 98819),
  ('ref_stop', 98821),
  ('ref_cds_start', 0),
  ('ref_cds_stop', 2),
  ('alt', 'A'),
  ('ref_codon', 'ATG'),
  ('alt_codon', 'Aag'),
  ('codon_change', 'ATG/Aag'),
  ('aa_pos', 1),
  ('ref_aa', 'M'),
  ('alt_aa', 'K'),
  ('aa_change', 'M1K')]]

In [158]:

    

dbg(eff.get_amino_acid_changes('Pf3D7_01_v3', 98820, 'TGAG', 'T'))


    

    




[[('gene_id', 'PF3D7_0102200'),
  ('gene_start', 98819),
  ('gene_stop', 102282),
  ('transcript_id', 'PF3D7_0102200.1'),
  ('transcript_start', 98819),
  ('transcript_stop', 102282),
  ('exon_id', 'PF3D7_0102200.1:exon:1'),
  ('exon_start', 98819),
  ('exon_stop', 99013),
  ('strand', '+'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 98820),
  ('ref', 'TGAG'),
  ('ref_start', 98820),
  ('ref_stop', 98823),
  ('ref_cds_start', 1),
  ('ref_cds_stop', 4),
  ('alt', 'T'),
  ('ref_codon', 'aTGAGa'),
  ('alt_codon', 'aTa'),
  ('codon_change', 'aTGAGa/aTa'),
  ('aa_pos', 1),
  ('ref_aa', 'MR'),
  ('alt_aa', 'I'),
  ('aa_change', 'MR1I')]]

In [159]:

    

dbg(eff.get_amino_acid_changes('Pf3D7_01_v3', 98819, 'AT', 'GG'))


    

    




[[('gene_id', 'PF3D7_0102200'),
  ('gene_start', 98819),
  ('gene_stop', 102282),
  ('transcript_id', 'PF3D7_0102200.1'),
  ('transcript_start', 98819),
  ('transcript_stop', 102282),
  ('exon_id', 'PF3D7_0102200.1:exon:1'),
  ('exon_start', 98819),
  ('exon_stop', 99013),
  ('strand', '+'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 98819),
  ('ref', 'AT'),
  ('ref_start', 98819),
  ('ref_stop', 98820),
  ('ref_cds_start', 0),
  ('ref_cds_stop', 1),
  ('alt', 'GG'),
  ('ref_codon', 'ATg'),
  ('alt_codon', 'GGg'),
  ('codon_change', 'ATg/GGg'),
  ('aa_pos', 1),
  ('ref_aa', 'M'),
  ('alt_aa', 'G'),
  ('aa_change', 'M1G')]]

In [160]:

    

dbg(eff.get_amino_acid_changes('Pf3D7_01_v3', 98820, 'TG', 'CC'))


    

    




[[('gene_id', 'PF3D7_0102200'),
  ('gene_start', 98819),
  ('gene_stop', 102282),
  ('transcript_id', 'PF3D7_0102200.1'),
  ('transcript_start', 98819),
  ('transcript_stop', 102282),
  ('exon_id', 'PF3D7_0102200.1:exon:1'),
  ('exon_start', 98819),
  ('exon_stop', 99013),
  ('strand', '+'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 98820),
  ('ref', 'TG'),
  ('ref_start', 98820),
  ('ref_stop', 98821),
  ('ref_cds_start', 1),
  ('ref_cds_stop', 2),
  ('alt', 'CC'),
  ('ref_codon', 'aTG'),
  ('alt_codon', 'aCC'),
  ('codon_change', 'aTG/aCC'),
  ('aa_pos', 1),
  ('ref_aa', 'M'),
  ('alt_aa', 'T'),
  ('aa_change', 'M1T')]]

In [161]:

    

dbg(eff.get_amino_acid_changes('Pf3D7_01_v3', 98821, 'GA', 'CC'))


    

    




[[('gene_id', 'PF3D7_0102200'),
  ('gene_start', 98819),
  ('gene_stop', 102282),
  ('transcript_id', 'PF3D7_0102200.1'),
  ('transcript_start', 98819),
  ('transcript_stop', 102282),
  ('exon_id', 'PF3D7_0102200.1:exon:1'),
  ('exon_start', 98819),
  ('exon_stop', 99013),
  ('strand', '+'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 98821),
  ('ref', 'GA'),
  ('ref_start', 98821),
  ('ref_stop', 98822),
  ('ref_cds_start', 2),
  ('ref_cds_stop', 3),
  ('alt', 'CC'),
  ('ref_codon', 'atGAga'),
  ('alt_codon', 'atCCga'),
  ('codon_change', 'atGAga/atCCga'),
  ('aa_pos', 1),
  ('ref_aa', 'MR'),
  ('alt_aa', 'IR'),
  ('aa_change', 'MR1IR')]]

In [199]:

    

eff._fasta['Pf3D7_01_v3'][257823:257830]


    

    
Out[199]:





u'ttgatta'

In [198]:

    

dbg(eff.get_amino_acid_changes('Pf3D7_01_v3', 257826, 'G', 'GATTATTATTATTATT'))


    

    




[[('gene_id', 'PF3D7_0106000'),
  ('gene_start', 255775),
  ('gene_stop', 258543),
  ('transcript_id', 'PF3D7_0106000.1'),
  ('transcript_start', 255775),
  ('transcript_stop', 258543),
  ('exon_id', 'PF3D7_0106000.1:exon:1'),
  ('exon_start', 255775),
  ('exon_stop', 258543),
  ('strand', '-'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 257826),
  ('ref', 'G'),
  ('ref_start', 257826),
  ('ref_stop', 257826),
  ('ref_cds_start', 717),
  ('ref_cds_stop', 717),
  ('alt', 'GATTATTATTATTATT'),
  ('ref_codon', 'Caa'),
  ('alt_codon', 'AATAATAATAATAATCaa'),
  ('codon_change', 'Caa/AATAATAATAATAATCaa'),
  ('aa_pos', 240),
  ('ref_aa', 'Q'),
  ('alt_aa', 'NNNNNQ'),
  ('aa_change', 'Q240NNNNNQ')]]

In [197]:

    

vcf_fn = '../../../data/public/20141022/3d7_hb3.combined.final.vcf.gz'
tbl = (etl
    .fromvcf(vcf_fn, samples=None)
    .unpackinfo('EFF')
    .addfield('my_eff', lambda row: list(eff.get_amino_acid_changes(row.CHROM, row.POS, row.REF, row.ALT[0])))
    .convert(['EFF', 'my_eff'], lambda v: v[0] if v else None)
    .addfield('eff_effect', lambda row: row.EFF.split('(')[0] if row.EFF is not None else None)
    .addfield('eff_codon_change', lambda row: row.EFF.split('|')[2] if row.EFF is not None else None)
    .addfield('my_codon_change', lambda row: row.my_eff.codon_change if row.my_eff is not None else None)
    .addfield('eff_a_change', lambda row: row.EFF.split('|')[3] if row.EFF is not None else None)
    .addfield('my_aa_change', lambda row: row.my_eff.aa_change if row.my_eff is not None else None)
    .cutout('ID', 'my_eff', 'QUAL', 'FILTER', 'EFF')
    .selectnotin('eff_effect', ['INTERGENIC', 'INTRON'])
)
tbl.display(200)


    

    








CHROM
POS
REF
ALT
eff_effect
eff_codon_change
my_codon_change
eff_a_change
my_aa_change




Pf3D7_01_v3
95518
G
[T]
NON_SYNONYMOUS_CODING
aGa/aTa
aGa/aTa
R156I
R156I


Pf3D7_01_v3
95621
T
[A]
NON_SYNONYMOUS_CODING
caT/caA
caT/caA
H190Q
H190Q


Pf3D7_01_v3
95632
G
[A]
NON_SYNONYMOUS_CODING
tGt/tAt
tGt/tAt
C194Y
C194Y


Pf3D7_01_v3
95641
G
[A]
NON_SYNONYMOUS_CODING
tGt/tAt
tGt/tAt
C197Y
C197Y


Pf3D7_01_v3
95680
A
[G]
NON_SYNONYMOUS_CODING
aAt/aGt
aAt/aGt
N210S
N210S


Pf3D7_01_v3
95685
G
[T]
NON_SYNONYMOUS_CODING
Gat/Tat
Gat/Tat
D212Y
D212Y


Pf3D7_01_v3
95686
A
[C]
NON_SYNONYMOUS_CODING
gAt/gCt
gAt/gCt
D212A
D212A


Pf3D7_01_v3
95710
G
[C]
NON_SYNONYMOUS_CODING
tGt/tCt
tGt/tCt
C220S
C220S


Pf3D7_01_v3
95715
A
[G]
NON_SYNONYMOUS_CODING
Agt/Ggt
Agt/Ggt
S222G
S222G


Pf3D7_01_v3
95716
G
[T]
NON_SYNONYMOUS_CODING
aGt/aTt
aGt/aTt
S222I
S222I


Pf3D7_01_v3
95742
G
[A]
NON_SYNONYMOUS_CODING
Gct/Act
Gct/Act
A231T
A231T


Pf3D7_01_v3
95754
G
[T]
NON_SYNONYMOUS_CODING
Gct/Tct
Gct/Tct
A235S
A235S


Pf3D7_01_v3
98868
A
[G]
NON_SYNONYMOUS_CODING
gAt/gGt
gAt/gGt
D17G
D17G


Pf3D7_01_v3
101269
G
[T]
NON_SYNONYMOUS_CODING
Gta/Tta
Gta/Tta
V749L
V749L


Pf3D7_01_v3
101790
AAAT
[A]
CODON_DELETION
aat/-
gaAAAT/gaA
N923-
EN922E


Pf3D7_01_v3
107756
T
[G]
STOP_LOST
tAa/tCa
tAa/tCa
*198S
*198S


Pf3D7_01_v3
107823
T
[C]
NON_SYNONYMOUS_CODING
Atg/Gtg
Atg/Gtg
M176V
M176V


Pf3D7_01_v3
114473
T
[G]
NON_SYNONYMOUS_CODING
Aaa/Caa
Aaa/Caa
K443Q
K443Q


Pf3D7_01_v3
120736
T
[A]
NON_SYNONYMOUS_CODING
aaA/aaT
aaA/aaT
K116N
K116N


Pf3D7_01_v3
127256
AATT
[A]
CODON_DELETION
aat/-
AATTgt/Tgt
N295-
NC295C


Pf3D7_01_v3
127692
G
[GTTATTA]
CODON_CHANGE_PLUS_CODON_INSERTION
aac/aTAATAAac
aaC/aaTAATAAC
N150IIN
N150NNN


Pf3D7_01_v3
127725
G
[A]
SYNONYMOUS_CODING
aaC/aaT
aaC/aaT
N139
N139N


Pf3D7_01_v3
130339
C
[T]
NON_SYNONYMOUS_CODING
Gca/Aca
Gca/Aca
A168T
A168T


Pf3D7_01_v3
135874
ATTTTCCTTTTCC
[A]
CODON_CHANGE_PLUS_CODON_DELETION
aaggaaaaggaaaat/aat
aaGGAAAAGGAAAAT/aaT
KEKEN1124N
KEKEN1124N


Pf3D7_01_v3
136422
G
[T]
NON_SYNONYMOUS_CODING
Caa/Aaa
Caa/Aaa
Q946K
Q946K


Pf3D7_01_v3
137201
ATAT
[A]
CODON_CHANGE_PLUS_CODON_DELETION
aatata/ata
aATATa/aTa
NI685I
NI685I


Pf3D7_01_v3
137258
G
[A]
NON_SYNONYMOUS_CODING
aCg/aTg
aCg/aTg
T667M
T667M


Pf3D7_01_v3
138966
G
[C]
NON_SYNONYMOUS_CODING
Caa/Gaa
Caa/Gaa
Q98E
Q98E


Pf3D7_01_v3
139191
C
[T]
NON_SYNONYMOUS_CODING
Gca/Aca
Gca/Aca
A23T
A23T


Pf3D7_01_v3
145560
A
[T]
SYNONYMOUS_CODING
tcT/tcA
tcT/tcA
S279
S279S


Pf3D7_01_v3
146124
TTTA
[T]
CODON_CHANGE_PLUS_CODON_DELETION
aataaa/aaa
aaTAAA/aaA
NK90K
NK90K


Pf3D7_01_v3
147952
T
[TTTTTAC]
CODON_INSERTION
-/GTAAAA
aAt/aGTAAAAAt
-1609VK
N1609SKN


Pf3D7_01_v3
148490
A
[C]
NON_SYNONYMOUS_CODING
Tca/Gca
Tca/Gca
S1430A
S1430A


Pf3D7_01_v3
148768
TCACGGTGGAAATTATCAC
[T]
CODON_CHANGE_PLUS_CODON_DELETION
ggtgataatttccaccgtgat/gat
gGTGATAATTTCCACCGTGAt/gAt
GDNFHRD1331D
GDNFHRD1331D


Pf3D7_01_v3
148917
A
[T]
NON_SYNONYMOUS_CODING
aaT/aaA
aaT/aaA
N1287K
N1287K


Pf3D7_01_v3
155281
A
[T]
NON_SYNONYMOUS_CODING
tAt/tTt
tAt/tTt
Y369F
Y369F


Pf3D7_01_v3
155819
A
[AAATAATAAT]
CODON_INSERTION
-/AATAATAAT
ctA/ctAAATAATAAT
-549NNN
L548LNNN


Pf3D7_01_v3
155877
G
[A]
NON_SYNONYMOUS_CODING
Gac/Aac
Gac/Aac
D568N
D568N


Pf3D7_01_v3
155977
G
[A]
NON_SYNONYMOUS_CODING
gGc/gAc
gGc/gAc
G601D
G601D


Pf3D7_01_v3
155978
C
[T]
SYNONYMOUS_CODING
ggC/ggT
ggC/ggT
G601
G601G


Pf3D7_01_v3
156910
A
[G]
NON_SYNONYMOUS_CODING
Agt/Ggt
Agt/Ggt
S867G
S867G


Pf3D7_01_v3
159562
A
[G]
SYNONYMOUS_CODING
ttA/ttG
ttA/ttG
L1623
L1623L


Pf3D7_01_v3
161439
C
[CAAT]
CODON_INSERTION
-/AAT
gaC/gaCAAT
-104N
D103DN


Pf3D7_01_v3
161640
T
[C]
SYNONYMOUS_CODING
acT/acC
acT/acC
T170
T170T


Pf3D7_01_v3
161865
G
[T]
NON_SYNONYMOUS_CODING
aaG/aaT
aaG/aaT
K245N
K245N


Pf3D7_01_v3
162124
C
[CATGATCAAGTAAAAAATAAACATGATCAAGTAAAAAATAAAGATGATAAAATAAAAAATAAAG]
CODON_INSERTION
cat/cATGATCAAGTAAAAAATAAACATGATCAAGTAAAAAATAAAGATGATAAAATAAAAAATAAAGat
Cat/CATGATCAAGTAAAAAATAAACATGATCAAGTAAAAAATAAAGATGATAAAATAAAAAATAAAGat
H332HDQVKNKHDQVKNKDDKIKNKD
H332HDQVKNKHDQVKNKDDKIKNKD


Pf3D7_01_v3
162967
C
[CATAATA]
CODON_INSERTION
cat/cATAATAat
Cat/CATAATAat
H613HNN
H613HNN


Pf3D7_01_v3
162981
C
[G]
NON_SYNONYMOUS_CODING
atC/atG
atC/atG
I617M
I617M


Pf3D7_01_v3
163145
A
[T]
NON_SYNONYMOUS_CODING
cAt/cTt
cAt/cTt
H672L
H672L


Pf3D7_01_v3
164206
G
[GTAAACAAAAATATAAATA]
CODON_INSERTION
gta/gTAAACAAAAATATAAATAta
Gta/GTAAACAAAAATATAAATAta
V1026VNKNINI
V1026VNKNINI


Pf3D7_01_v3
167312
A
[G]
NON_SYNONYMOUS_CODING
tAt/tGt
tAt/tGt
Y267C
Y267C


Pf3D7_01_v3
173982
C
[CAAT]
CODON_INSERTION
-/AAT
taC/taCAAT
-374N
Y373YN


Pf3D7_01_v3
178726
G
[A]
NON_SYNONYMOUS_CODING
Gtt/Att
Gtt/Att
V214I
V214I


Pf3D7_01_v3
179265
A
[G]
NON_SYNONYMOUS_CODING
gAa/gGa
gAa/gGa
E284G
E284G


Pf3D7_01_v3
179346
G
[A]
NON_SYNONYMOUS_CODING
gGa/gAa
gGa/gAa
G311E
G311E


Pf3D7_01_v3
179347
A
[G]
SYNONYMOUS_CODING
ggA/ggG
ggA/ggG
G311
G311G


Pf3D7_01_v3
179969
G
[A]
NON_SYNONYMOUS_CODING
Gaa/Aaa
Gaa/Aaa
E519K
E519K


Pf3D7_01_v3
180034
A
[T]
NON_SYNONYMOUS_CODING
gaA/gaT
gaA/gaT
E540D
E540D


Pf3D7_01_v3
180063
C
[A]
NON_SYNONYMOUS_CODING
aCt/aAt
aCt/aAt
T550N
T550N


Pf3D7_01_v3
180073
C
[G]
SYNONYMOUS_CODING
gtC/gtG
gtC/gtG
V553
V553V


Pf3D7_01_v3
180075
A
[G]
NON_SYNONYMOUS_CODING
aAa/aGa
aAa/aGa
K554R
K554R


Pf3D7_01_v3
180076
A
[G]
SYNONYMOUS_CODING
aaA/aaG
aaA/aaG
K554
K554K


Pf3D7_01_v3
180077
A
[G]
NON_SYNONYMOUS_CODING
Aaa/Gaa
Aaa/Gaa
K555E
K555E


Pf3D7_01_v3
180078
A
[C]
NON_SYNONYMOUS_CODING
aAa/aCa
aAa/aCa
K555T
K555T


Pf3D7_01_v3
180159
C
[A]
NON_SYNONYMOUS_CODING
aCt/aAt
aCt/aAt
T582N
T582N


Pf3D7_01_v3
180160
T
[A]
SYNONYMOUS_CODING
acT/acA
acT/acA
T582
T582T


Pf3D7_01_v3
180161
A
[G]
NON_SYNONYMOUS_CODING
Acg/Gcg
Acg/Gcg
T583A
T583A


Pf3D7_01_v3
180162
C
[A]
NON_SYNONYMOUS_CODING
aCg/aAg
aCg/aAg
T583K
T583K


Pf3D7_01_v3
180170
A
[C]
NON_SYNONYMOUS_CODING
Aaa/Caa
Aaa/Caa
K586Q
K586Q


Pf3D7_01_v3
180174
T
[G]
NON_SYNONYMOUS_CODING
aTt/aGt
aTt/aGt
I587S
I587S


Pf3D7_01_v3
180175
T
[G]
NON_SYNONYMOUS_CODING
atT/atG
atT/atG
I587M
I587M


Pf3D7_01_v3
180181
T
[C]
SYNONYMOUS_CODING
ttT/ttC
ttT/ttC
F589
F589F


Pf3D7_01_v3
180186
A
[G]
NON_SYNONYMOUS_CODING
gAa/gGa
gAa/gGa
E591G
E591G


Pf3D7_01_v3
180192
A
[T]
NON_SYNONYMOUS_CODING
aAt/aTt
aAt/aTt
N593I
N593I


Pf3D7_01_v3
180217
C
[T]
SYNONYMOUS_CODING
atC/atT
atC/atT
I601
I601I


Pf3D7_01_v3
180230
G
[C]
NON_SYNONYMOUS_CODING
Gag/Cag
Gag/Cag
E606Q
E606Q


Pf3D7_01_v3
180233
A
[G]
NON_SYNONYMOUS_CODING
Aat/Gat
Aat/Gat
N607D
N607D


Pf3D7_01_v3
180277
G
[A]
SYNONYMOUS_CODING
caG/caA
caG/caA
Q621
Q621Q


Pf3D7_01_v3
180285
G
[T]
NON_SYNONYMOUS_CODING
aGa/aTa
aGa/aTa
R624I
R624I


Pf3D7_01_v3
180288
A
[C]
NON_SYNONYMOUS_CODING
aAt/aCt
aAt/aCt
N625T
N625T


Pf3D7_01_v3
180297
A
[G]
NON_SYNONYMOUS_CODING
gAt/gGt
gAt/gGt
D628G
D628G


Pf3D7_01_v3
180299
G
[C]
NON_SYNONYMOUS_CODING
Gga/Cga
Gga/Cga
G629R
G629R


Pf3D7_01_v3
180304
G
[A]
NON_SYNONYMOUS_CODING
atG/atA
atG/atA
M630I
M630I


Pf3D7_01_v3
180305
G
[A]
NON_SYNONYMOUS_CODING
Gat/Aat
Gat/Aat
D631N
D631N


Pf3D7_01_v3
180306
A
[T]
NON_SYNONYMOUS_CODING
gAt/gTt
gAt/gTt
D631V
D631V


Pf3D7_01_v3
180309
A
[C]
NON_SYNONYMOUS_CODING
gAa/gCa
gAa/gCa
E632A
E632A


Pf3D7_01_v3
180311
C
[A]
NON_SYNONYMOUS_CODING
Cat/Aat
Cat/Aat
H633N
H633N


Pf3D7_01_v3
183844
G
[C]
NON_SYNONYMOUS_CODING
Caa/Gaa
Caa/Gaa
Q127E
Q127E


Pf3D7_01_v3
183845
A
[T]
SYNONYMOUS_CODING
gcT/gcA
gcT/gcA
A126
A126A


Pf3D7_01_v3
190317
CATAATA
[C]
CODON_DELETION
cataataat/cat
CATAATAat/Cat
HNN17H
HNN17H


Pf3D7_01_v3
190616
A
[G]
SYNONYMOUS_CODING
acA/acG
acA/acG
T116
T116T


Pf3D7_01_v3
190862
CAATAAT
[C]
CODON_DELETION
aataat/-
aaCAATAAT/aaC
NN199-
NNN198N


Pf3D7_01_v3
190944
G
[GATAGTATTAATAATAGTATTAATA]
CODON_INSERTION
gat/gATAGTATTAATAATAGTATTAATAat
Gat/GATAGTATTAATAATAGTATTAATAat
D226DSINNSINN
D226DSINNSINN


Pf3D7_01_v3
191685
TATA
[T]
CODON_DELETION
tataat/tat
TATAat/Tat
YN473Y
YN473Y


Pf3D7_01_v3
192111
T
[C]
NON_SYNONYMOUS_CODING
Tat/Cat
Tat/Cat
Y615H
Y615H


Pf3D7_01_v3
192605
A
[T]
NON_SYNONYMOUS_CODING
aaA/aaT
aaA/aaT
K779N
K779N


Pf3D7_01_v3
192608
GGGT
[A]
CODON_DELETION
ggt/-
aaGGGT/aaA
G781-
KG780K


Pf3D7_01_v3
192617
T
[C]
SYNONYMOUS_CODING
gaT/gaC
gaT/gaC
D783
D783D


Pf3D7_01_v3
192618
A
[G]
NON_SYNONYMOUS_CODING
Aat/Gat
Aat/Gat
N784D
N784D


Pf3D7_01_v3
192621
A
[G]
NON_SYNONYMOUS_CODING
Aaa/Gaa
Aaa/Gaa
K785E
K785E


Pf3D7_01_v3
192623
A
[AGATGACGATGAC]
CODON_INSERTION
-/GATGACGATGAC
aaA/aaAGATGACGATGAC
-786DDDD
K785KDDDD


Pf3D7_01_v3
193667
G
[C]
NON_SYNONYMOUS_CODING
agG/agC
agG/agC
R1133S
R1133S


Pf3D7_01_v3
194117
T
[C]
SYNONYMOUS_CODING
ttT/ttC
ttT/ttC
F1283
F1283F


Pf3D7_01_v3
194843
CAAATATGAA
[C]
CODON_DELETION
aaatatgaa/-
gaCAAATATGAA/gaC
KYE1526-
DKYE1525D


Pf3D7_01_v3
195383
A
[AAAC]
CODON_INSERTION
-/AAC
aaA/aaAAAC
-1706N
K1705KN


Pf3D7_01_v3
196010
A
[C]
NON_SYNONYMOUS_CODING
aaA/aaC
aaA/aaC
K1914N
K1914N


Pf3D7_01_v3
196011
G
[A]
NON_SYNONYMOUS_CODING
Gaa/Aaa
Gaa/Aaa
E1915K
E1915K


Pf3D7_01_v3
196981
G
[A]
NON_SYNONYMOUS_CODING
aGa/aAa
aGa/aAa
R2238K
R2238K


Pf3D7_01_v3
199812
G
[C]
NON_SYNONYMOUS_CODING
cGt/cCt
cGt/cCt
R3104P
R3104P


Pf3D7_01_v3
199847
C
[G]
NON_SYNONYMOUS_CODING
Cat/Gat
Cat/Gat
H3116D
H3116D


Pf3D7_01_v3
199848
A
[G]
NON_SYNONYMOUS_CODING
cAt/cGt
cAt/cGt
H3116R
H3116R


Pf3D7_01_v3
199851
C
[T]
NON_SYNONYMOUS_CODING
gCa/gTa
gCa/gTa
A3117V
A3117V


Pf3D7_01_v3
199855
C
[T]
SYNONYMOUS_CODING
aaC/aaT
aaC/aaT
N3118
N3118N


Pf3D7_01_v3
199863
G
[A]
NON_SYNONYMOUS_CODING
aGt/aAt
aGt/aAt
S3121N
S3121N


Pf3D7_01_v3
205066
G
[A]
SYNONYMOUS_CODING
ttC/ttT
ttC/ttT
F108
F108F


Pf3D7_01_v3
206406
A
[AAAAGATGAT]
CODON_INSERTION
-/AAAGATGAT
gaA/gaAAAAGATGAT
-80KDD
E79EKDD


Pf3D7_01_v3
207421
A
[AATGATAATTATGATAATAATAATTATGATAATTATGATAATAATAATTATGATAATT]
CODON_INSERTION
aat/aATGATAATTATGATAATAATAATTATGATAATTATGATAATAATAATTATGATAATTat
Aat/AATGATAATTATGATAATAATAATTATGATAATTATGATAATAATAATTATGATAATTat
N418NDNYDNNNYDNYDNNNYDNY
N418NDNYDNNNYDNYDNNNYDNY


Pf3D7_01_v3
207736
T
[C]
NON_SYNONYMOUS_CODING
Tat/Cat
Tat/Cat
Y523H
Y523H


Pf3D7_01_v3
207960
A
[C]
NON_SYNONYMOUS_CODING
aaA/aaC
aaA/aaC
K597N
K597N


Pf3D7_01_v3
207962
T
[A]
NON_SYNONYMOUS_CODING
aTt/aAt
aTt/aAt
I598N
I598N


Pf3D7_01_v3
208014
A
[T]
NON_SYNONYMOUS_CODING
aaA/aaT
aaA/aaT
K615N
K615N


Pf3D7_01_v3
216754
T
[G]
NON_SYNONYMOUS_CODING
Tac/Gac
Tac/Gac
Y327D
Y327D


Pf3D7_01_v3
216756
C
[CAATAATAATAATAAT]
CODON_INSERTION
-/AATAATAATAATAAT
taC/taCAATAATAATAATAAT
-328NNNNN
Y327YNNNNN


Pf3D7_01_v3
227206
C
[T]
NON_SYNONYMOUS_CODING
aGa/aAa
aGa/aAa
R27K
R27K


Pf3D7_01_v3
233811
G
[A]
NON_SYNONYMOUS_CODING
tCa/tTa
tCa/tTa
S134L
S134L


Pf3D7_01_v3
239206
T
[TATAATAATA]
CODON_INSERTION
tat/tATAATAATAat
Tat/TATAATAATAat
Y181YNNN
Y181YNNN


Pf3D7_01_v3
239511
G
[GACAAATGATGTGAAA]
CODON_INSERTION
-/ACAAATGATGTGAAA
aaG/aaGACAAATGATGTGAAA
-283TNDVK
K282KTNDVK


Pf3D7_01_v3
241843
C
[G]
NON_SYNONYMOUS_CODING
Caa/Gaa
Caa/Gaa
Q1060E
Q1060E


Pf3D7_01_v3
242535
TAATATTCAA
[T]
CODON_DELETION
aatattcaa/-
caTAATATTCAA/caT
NIQ1291-
HNIQ1290H


Pf3D7_01_v3
243925
A
[G]
NON_SYNONYMOUS_CODING
Aat/Gat
Aat/Gat
N1754D
N1754D


Pf3D7_01_v3
244758
C
[CAATAATAATAATAATAATAATAAT]
CODON_INSERTION
-/AATAATAATAATAATAATAATAAT
gaC/gaCAATAATAATAATAATAATAATAAT
-2032NNNNNNNN
D2031DNNNNNNNN


Pf3D7_01_v3
246384
CAAT
[C]
CODON_DELETION
aat/-
aaCAAT/aaC
N2574-
NN2573N


Pf3D7_01_v3
247606
T
[TATAATA]
CODON_INSERTION
tat/tATAATAat
Tat/TATAATAat
Y2981YNN
Y2981YNN


Pf3D7_01_v3
247675
TATACAAATC
[T]
CODON_DELETION
tatacaaatcat/tat
TATACAAATCat/Tat
YTNH3004Y
YTNH3004Y


Pf3D7_01_v3
257826
G
[GATTATTATTATTATT]
CODON_CHANGE_PLUS_CODON_INSERTION
aat/aaAATAATAATAATAATt
Caa/AATAATAATAATAATCaa
N239KIIIII
Q240NNNNNQ


Pf3D7_01_v3
263684
A
[C]
NON_SYNONYMOUS_CODING
Tat/Gat
Tat/Gat
Y102D
Y102D


Pf3D7_01_v3
266480
A
[T]
SYNONYMOUS_CODING
atT/atA
atT/atA
I898
I898I


Pf3D7_01_v3
266640
TCTC
[T]
CODON_CHANGE_PLUS_CODON_DELETION
ggagat/gat
gGAGAt/gAt
GD844D
GD844D


Pf3D7_01_v3
267777
C
[T]
NON_SYNONYMOUS_CODING
aGt/aAt
aGt/aAt
S466N
S466N


Pf3D7_01_v3
269132
C
[T]
SYNONYMOUS_CODING
gaG/gaA
gaG/gaA
E14
E14E


Pf3D7_01_v3
274550
C
[A]
NON_SYNONYMOUS_CODING
aCc/aAc
aCc/aAc
T79N
T79N


Pf3D7_01_v3
275206
C
[G]
NON_SYNONYMOUS_CODING
Cat/Gat
Cat/Gat
H298D
H298D


Pf3D7_01_v3
275655
T
[C]
SYNONYMOUS_CODING
aaT/aaC
aaT/aaC
N447
N447N


Pf3D7_01_v3
276134
A
[C]
NON_SYNONYMOUS_CODING
aAt/aCt
aAt/aCt
N607T
N607T


Pf3D7_01_v3
276137
A
[C]
NON_SYNONYMOUS_CODING
aAt/aCt
aAt/aCt
N608T
N608T


Pf3D7_01_v3
276845
G
[A]
NON_SYNONYMOUS_CODING
aGt/aAt
aGt/aAt
S844N
S844N


Pf3D7_01_v3
281975
A
[T]
NON_SYNONYMOUS_CODING
cAt/cTt
cAt/cTt
H274L
H274L


Pf3D7_01_v3
282004
G
[A]
NON_SYNONYMOUS_CODING
Gca/Aca
Gca/Aca
A284T
A284T


Pf3D7_01_v3
282010
TATGATA
[T]
CODON_DELETION
tatgataat/tat
TATGATAat/Tat
YDN286Y
YDN286Y


Pf3D7_01_v3
282425
GTGATGGAGATGATGACGATGATGATGTAGGTGATGATAACGTTGA
[G]
CODON_DELETION
ggtgatggagatgatgacgatgatgatgtaggtgatgataacgttgat/ggt
gGTGATGGAGATGATGACGATGATGATGTAGGTGATGATAACGTTGAt/gGt
GDGDDDDDDVGDDNVD424G
GDGDDDDDDVGDDNVD424G


Pf3D7_01_v3
282546
TGATAAC
[T]
CODON_DELETION
gataac/-
gaTGATAAC/gaT
DN465-
DDN464D


Pf3D7_01_v3
282549
TAAC
[T]
CODON_DELETION
aac/-
gaTAAC/gaT
N466-
DN465D


Pf3D7_01_v3
282555
TGAC
[T]
CODON_DELETION
gac/-
gaTGAC/gaT
D468-
DD467D


Pf3D7_01_v3
282558
C
[T]
SYNONYMOUS_CODING
gaC/gaT
gaC/gaT
D468
D468D


Pf3D7_01_v3
282597
CGATGACGATGAT
[C]
CODON_DELETION
gatgacgatgat/-
aaCGATGACGATGAT/aaC
DDDD482-
NDDDD481N


Pf3D7_01_v3
282609
T
[TAAC]
CODON_INSERTION
-/AAC
gaT/gaTAAC
-486N
D485DN


Pf3D7_01_v3
283144
C
[G]
NON_SYNONYMOUS_CODING
Cac/Gac
Cac/Gac
H664D
H664D


Pf3D7_01_v3
283203
G
[GAT]
FRAME_SHIFT
-/AT
gaG/gaGATg
-684?
E683EM


Pf3D7_01_v3
283273
A
[AATGATGATGATGATGATGATG]
CODON_INSERTION
aat/aATGATGATGATGATGATGATGat
Aat/AATGATGATGATGATGATGATGat
N707NDDDDDDD
N707NDDDDDDD


Pf3D7_01_v3
283356
C
[CGATGATGATGAAAATGAT]
CODON_INSERTION
-/GATGATGATGAAAATGAT
ggC/ggCGATGATGATGAAAATGAT
-735DDDEND
G734GDDDEND


Pf3D7_01_v3
283406
T
[TTGA]
CODON_INSERTION
att/atTGAt
aTt/aTTGAt
I751ID
I751ID


Pf3D7_01_v3
288303
AATATATATATAT
[AATATATATAT, A]
None
None
None
None
None


Pf3D7_01_v3
291547
G
[A]
NON_SYNONYMOUS_CODING
Gat/Aat
Gat/Aat
D388N
D388N


Pf3D7_01_v3
306237
C
[A]
SYNONYMOUS_CODING
acG/acT
acG/acT
T1007
T1007T


Pf3D7_01_v3
307173
G
[A]
SYNONYMOUS_CODING
gaC/gaT
gaC/gaT
D695
D695D


Pf3D7_01_v3
308600
C
[T]
NON_SYNONYMOUS_CODING
Gat/Aat
Gat/Aat
D220N
D220N


Pf3D7_01_v3
308617
TCCTC
[T]
FRAME_SHIFT
-
GAGGAt/Atg
-213
ED213M


Pf3D7_01_v3
314881
A
[T]
NON_SYNONYMOUS_CODING
aaA/aaT
aaA/aaT
K88N
K88N


Pf3D7_01_v3
315518
TATA
[T]
CODON_DELETION
tataat/tat
TATAat/Tat
YN301Y
YN301Y


Pf3D7_01_v3
316004
GAAAATGTAA
[G]
CODON_DELETION
gaaaatgtaaaa/gaa
GAAAATGTAAaa/Gaa
ENVK463E
ENVK463E


Pf3D7_01_v3
316513
T
[G]
NON_SYNONYMOUS_CODING
aaT/aaG
aaT/aaG
N632K
N632K


Pf3D7_01_v3
318006
ATATCATGTT
[A]
CODON_DELETION
aatatcatgttt/aat
aATATCATGTTt/aAt
NIMF1130N
NIMF1130N


Pf3D7_01_v3
318011
ATGTT
[A]
FRAME_SHIFT
-
ATGTTt/Ata
-1132
MF1132I


Pf3D7_01_v3
320629
CAATAAT
[C, CAATAATAATAATAATAATAAT]
CODON_DELETION
aataat/-
aaCAATAAT/aaC
NN155-
NNN154N


Pf3D7_01_v3
322875
A
[AATAATATTTATC]
CODON_INSERTION
aat/aATAATATTTATCat
Aat/AATAATATTTATCat
N169NNIYH
N169NNIYH


Pf3D7_01_v3
323333
TGAA
[T]
CODON_DELETION
gaa/-
aaTGAA/aaT
E322-
NE321N


Pf3D7_01_v3
324213
G
[GATA]
CODON_INSERTION
gat/gATAat
Gat/GATAat
D615DN
D615DN


Pf3D7_01_v3
325302
G
[A]
NON_SYNONYMOUS_CODING
Gaa/Aaa
Gaa/Aaa
E978K
E978K


Pf3D7_01_v3
335111
CATATATATATATAT
[C]
FRAME_SHIFT
-
None
-83
None


Pf3D7_01_v3
335390
ATT
[A]
FRAME_SHIFT
-
None
-176
None


Pf3D7_01_v3
338214
TGATGAAGATGATGATGATGATGAA
[T]
CODON_DELETION
gatgaagatgatgatgatgatgaa/-
gaTGATGAAGATGATGATGATGATGAA/gaT
DEDDDDDE350-
DDEDDDDDE349D


Pf3D7_01_v3
338340
A
[AGATGACGAGGATTATGACGATGATGAT]
CODON_INSERTION
-/GATGACGAGGATTATGACGATGATGAT
gaA/gaAGATGACGAGGATTATGACGATGATGAT
-392DDEDYDDDD
E391EDDEDYDDDD


Pf3D7_01_v3
338598
C
[CAAT]
CODON_INSERTION
-/AAT
atC/atCAAT
-478N
I477IN


Pf3D7_01_v3
339060
T
[TAAC]
CODON_INSERTION
-/AAC
aaT/aaTAAC
-632N
N631NN


Pf3D7_01_v3
339074
G
[A]
NON_SYNONYMOUS_CODING
aGt/aAt
aGt/aAt
S636N
S636N


Pf3D7_01_v3
339436
A
[G]
NON_SYNONYMOUS_CODING
Att/Gtt
Att/Gtt
I757V
I757V


Pf3D7_01_v3
339504
A
[C]
SYNONYMOUS_CODING
acA/acC
acA/acC
T779
T779T


Pf3D7_01_v3
340513
ATTC
[A]
CODON_CHANGE_PLUS_CODON_DELETION
attcat/aat
ATTCat/Aat
IH1116N
IH1116N


Pf3D7_01_v3
341173
A
[G]
NON_SYNONYMOUS_CODING
Atg/Gtg
Atg/Gtg
M1336V
M1336V


Pf3D7_01_v3
341176
A
[G]
NON_SYNONYMOUS_CODING
Aac/Gac
Aac/Gac
N1337D
N1337D


Pf3D7_01_v3
341183
A
[C]
NON_SYNONYMOUS_CODING
aAc/aCc
aAc/aCc
N1339T
N1339T


Pf3D7_01_v3
342021
A
[AAAT]
CODON_INSERTION
-/AAT
aaA/aaAAAT
-1619N
K1618KN


Pf3D7_01_v3
342450
CAAT
[C]
CODON_DELETION
aat/-
agCAAT/agC
N1762-
SN1761S


Pf3D7_01_v3
342833
T
[TTAATAA]
CODON_INSERTION
att/atTAATAAt
aTt/aTTAATAAt
I1889INN
I1889INN


Pf3D7_01_v3
343374
CAAT
[C]
CODON_DELETION
aat/-
aaCAAT/aaC
N2070-
NN2069N


Pf3D7_01_v3
343596
A
[AAATAAT]
CODON_INSERTION
-/AATAAT
gaA/gaAAATAAT
-2144NN
E2143ENN


Pf3D7_01_v3
345060
C
[CAT]
INTRAGENIC

None

None


Pf3D7_01_v3
345066
C
[T]
INTRAGENIC

None

None


Pf3D7_01_v3
345730
A
[G]
NON_SYNONYMOUS_CODING
Tca/Cca
Tca/Cca
S130P
S130P


Pf3D7_01_v3
349247
C
[T]
SYNONYMOUS_CODING
gaC/gaT
gaC/gaT
D26
D26D



...

In [200]:

    

eff._tbl_features.eq('type', 'gene').display(20)


    

    








seqid
source
type
start
end
score
strand
phase
feature_id
parent_id




Pf3D7_01_v3
chado
gene
29510
37126
.
+
.
PF3D7_0100100
None


Pf3D7_01_v3
chado
gene
38982
40207
.
-
.
PF3D7_0100200
None


Pf3D7_01_v3
chado
gene
42367
46507
.
-
.
PF3D7_0100300
None


Pf3D7_01_v3
chado
gene
50363
51636
.
+
.
PF3D7_0100400
None


Pf3D7_01_v3
chado
gene
53778
55006
.
-
.
PF3D7_0100600
None


Pf3D7_01_v3
chado
gene
56690
56893
.
-
.
PF3D7_0100700
None


Pf3D7_01_v3
chado
gene
59772
61003
.
+
.
PF3D7_0100800
None


Pf3D7_01_v3
chado
gene
62187
63400
.
-
.
PF3D7_0100900
None


Pf3D7_01_v3
chado
gene
65817
66989
.
-
.
PF3D7_0101000
None


Pf3D7_01_v3
chado
gene
69304
70417
.
-
.
PF3D7_0101100
None


Pf3D7_01_v3
chado
gene
71624
72426
.
+
.
PF3D7_0101200
None


Pf3D7_01_v3
chado
gene
74563
75366
.
+
.
PF3D7_0101300
None


Pf3D7_01_v3
chado
gene
81765
83106
.
-
.
PF3D7_0101600
None


Pf3D7_01_v3
chado
gene
87203
88177
.
-
.
PF3D7_0101800
None


Pf3D7_01_v3
chado
gene
90242
91420
.
-
.
PF3D7_0101900
None


Pf3D7_01_v3
chado
gene
98819
102282
.
+
.
PF3D7_0102200
None


Pf3D7_01_v3
chado
gene
104704
105209
.
+
.
PF3D7_0102300
None


Pf3D7_01_v3
chado
gene
110750
115799
.
-
.
PF3D7_0102500
None


Pf3D7_01_v3
chado
gene
119041
121249
.
-
.
PF3D7_0102600
None


Pf3D7_01_v3
chado
gene
124517
125484
.
+
.
PF3D7_0102700
None



...

In [201]:

    

Seq(eff._fasta['Pf3D7_01_v3'][115793:115802])


    

    
Out[201]:





Seq(u'tttcatatt', Alphabet())

In [202]:

    

Seq(eff._fasta['Pf3D7_01_v3'][115793:115802]).reverse_complement()


    

    
Out[202]:





Seq('aatatgaaa', Alphabet())

In [206]:

    

dbg(eff.get_coding_positions('Pf3D7_01_v3', 115799, 'T'))


    

    




[[('gene_id', 'PF3D7_0102500'),
  ('gene_start', 110750),
  ('gene_stop', 115799),
  ('transcript_id', 'PF3D7_0102500.1'),
  ('transcript_start', 110750),
  ('transcript_stop', 115799),
  ('exon_id', 'PF3D7_0102500.1:exon:4'),
  ('exon_start', 111338),
  ('exon_stop', 115799),
  ('strand', '-'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 115799),
  ('ref', 'T'),
  ('ref_start', 115799),
  ('ref_stop', 115799),
  ('ref_cds_start', 0),
  ('ref_cds_stop', 0)]]

In [208]:

    

dbg(eff.get_coding_positions('Pf3D7_01_v3', 115798, 'A'))


    

    




[[('gene_id', 'PF3D7_0102500'),
  ('gene_start', 110750),
  ('gene_stop', 115799),
  ('transcript_id', 'PF3D7_0102500.1'),
  ('transcript_start', 110750),
  ('transcript_stop', 115799),
  ('exon_id', 'PF3D7_0102500.1:exon:4'),
  ('exon_start', 111338),
  ('exon_stop', 115799),
  ('strand', '-'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 115798),
  ('ref', 'A'),
  ('ref_start', 115798),
  ('ref_stop', 115798),
  ('ref_cds_start', 1),
  ('ref_cds_stop', 1)]]

In [209]:

    

dbg(eff.get_coding_positions('Pf3D7_01_v3', 115797, 'C'))


    

    




[[('gene_id', 'PF3D7_0102500'),
  ('gene_start', 110750),
  ('gene_stop', 115799),
  ('transcript_id', 'PF3D7_0102500.1'),
  ('transcript_start', 110750),
  ('transcript_stop', 115799),
  ('exon_id', 'PF3D7_0102500.1:exon:4'),
  ('exon_start', 111338),
  ('exon_stop', 115799),
  ('strand', '-'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 115797),
  ('ref', 'C'),
  ('ref_start', 115797),
  ('ref_stop', 115797),
  ('ref_cds_start', 2),
  ('ref_cds_stop', 2)]]

In [212]:

    

dbg(eff.get_amino_acid_changes('Pf3D7_01_v3', 115799, 'T', 'C'))


    

    




[[('gene_id', 'PF3D7_0102500'),
  ('gene_start', 110750),
  ('gene_stop', 115799),
  ('transcript_id', 'PF3D7_0102500.1'),
  ('transcript_start', 110750),
  ('transcript_stop', 115799),
  ('exon_id', 'PF3D7_0102500.1:exon:4'),
  ('exon_start', 111338),
  ('exon_stop', 115799),
  ('strand', '-'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 115799),
  ('ref', 'T'),
  ('ref_start', 115799),
  ('ref_stop', 115799),
  ('ref_cds_start', 0),
  ('ref_cds_stop', 0),
  ('alt', 'C'),
  ('ref_codon', 'Atg'),
  ('alt_codon', 'Gtg'),
  ('codon_change', 'Atg/Gtg'),
  ('aa_pos', 1),
  ('ref_aa', 'M'),
  ('alt_aa', 'V'),
  ('aa_change', 'M1V')]]

In [213]:

    

dbg(eff.get_amino_acid_changes('Pf3D7_01_v3', 115798, 'A', 'X'))


    

    




[[('gene_id', 'PF3D7_0102500'),
  ('gene_start', 110750),
  ('gene_stop', 115799),
  ('transcript_id', 'PF3D7_0102500.1'),
  ('transcript_start', 110750),
  ('transcript_stop', 115799),
  ('exon_id', 'PF3D7_0102500.1:exon:4'),
  ('exon_start', 111338),
  ('exon_stop', 115799),
  ('strand', '-'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 115798),
  ('ref', 'A'),
  ('ref_start', 115798),
  ('ref_stop', 115798),
  ('ref_cds_start', 1),
  ('ref_cds_stop', 1),
  ('alt', 'X'),
  ('ref_codon', 'aTg'),
  ('alt_codon', 'aXg'),
  ('codon_change', 'aTg/aXg'),
  ('aa_pos', 1),
  ('ref_aa', 'M'),
  ('alt_aa', 'X'),
  ('aa_change', 'M1X')]]

In [214]:

    

dbg(eff.get_amino_acid_changes('Pf3D7_01_v3', 115797, 'C', 'X'))


    

    




[[('gene_id', 'PF3D7_0102500'),
  ('gene_start', 110750),
  ('gene_stop', 115799),
  ('transcript_id', 'PF3D7_0102500.1'),
  ('transcript_start', 110750),
  ('transcript_stop', 115799),
  ('exon_id', 'PF3D7_0102500.1:exon:4'),
  ('exon_start', 111338),
  ('exon_stop', 115799),
  ('strand', '-'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 115797),
  ('ref', 'C'),
  ('ref_start', 115797),
  ('ref_stop', 115797),
  ('ref_cds_start', 2),
  ('ref_cds_stop', 2),
  ('alt', 'X'),
  ('ref_codon', 'atG'),
  ('alt_codon', 'atX'),
  ('codon_change', 'atG/atX'),
  ('aa_pos', 1),
  ('ref_aa', 'M'),
  ('alt_aa', 'X'),
  ('aa_change', 'M1X')]]

In [216]:

    

dbg(eff.get_amino_acid_changes('Pf3D7_01_v3', 115796, 'T', 'C'))


    

    




[[('gene_id', 'PF3D7_0102500'),
  ('gene_start', 110750),
  ('gene_stop', 115799),
  ('transcript_id', 'PF3D7_0102500.1'),
  ('transcript_start', 110750),
  ('transcript_stop', 115799),
  ('exon_id', 'PF3D7_0102500.1:exon:4'),
  ('exon_start', 111338),
  ('exon_stop', 115799),
  ('strand', '-'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 115796),
  ('ref', 'T'),
  ('ref_start', 115796),
  ('ref_stop', 115796),
  ('ref_cds_start', 3),
  ('ref_cds_stop', 3),
  ('alt', 'C'),
  ('ref_codon', 'Aaa'),
  ('alt_codon', 'Gaa'),
  ('codon_change', 'Aaa/Gaa'),
  ('aa_pos', 2),
  ('ref_aa', 'K'),
  ('alt_aa', 'E'),
  ('aa_change', 'K2E')]]

In [218]:

    

dbg(eff.get_amino_acid_changes('Pf3D7_01_v3', 115799, 'T', 'TCGG'))


    

    




[[('gene_id', 'PF3D7_0102500'),
  ('gene_start', 110750),
  ('gene_stop', 115799),
  ('transcript_id', 'PF3D7_0102500.1'),
  ('transcript_start', 110750),
  ('transcript_stop', 115799),
  ('exon_id', 'PF3D7_0102500.1:exon:4'),
  ('exon_start', 111338),
  ('exon_stop', 115799),
  ('strand', '-'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 115799),
  ('ref', 'T'),
  ('ref_start', 115799),
  ('ref_stop', 115799),
  ('ref_cds_start', 0),
  ('ref_cds_stop', 0),
  ('alt', 'TCGG'),
  ('ref_codon', 'Atg'),
  ('alt_codon', 'CCGAtg'),
  ('codon_change', 'Atg/CCGAtg'),
  ('aa_pos', 1),
  ('ref_aa', 'M'),
  ('alt_aa', 'PM'),
  ('aa_change', 'M1PM')]]

In [219]:

    

dbg(eff.get_amino_acid_changes('Pf3D7_01_v3', 115798, 'A', 'AN'))


    

    




[[('gene_id', 'PF3D7_0102500'),
  ('gene_start', 110750),
  ('gene_stop', 115799),
  ('transcript_id', 'PF3D7_0102500.1'),
  ('transcript_start', 110750),
  ('transcript_stop', 115799),
  ('exon_id', 'PF3D7_0102500.1:exon:4'),
  ('exon_start', 111338),
  ('exon_stop', 115799),
  ('strand', '-'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 115798),
  ('ref', 'A'),
  ('ref_start', 115798),
  ('ref_stop', 115798),
  ('ref_cds_start', 1),
  ('ref_cds_stop', 1),
  ('alt', 'AN'),
  ('ref_codon', 'aTg'),
  ('alt_codon', 'aNT'),
  ('codon_change', 'aTg/aNT'),
  ('aa_pos', 1),
  ('ref_aa', 'M'),
  ('alt_aa', 'X'),
  ('aa_change', 'M1X')]]

In [220]:

    

dbg(eff.get_amino_acid_changes('Pf3D7_01_v3', 115798, 'A', 'AXX'))


    

    




[[('gene_id', 'PF3D7_0102500'),
  ('gene_start', 110750),
  ('gene_stop', 115799),
  ('transcript_id', 'PF3D7_0102500.1'),
  ('transcript_start', 110750),
  ('transcript_stop', 115799),
  ('exon_id', 'PF3D7_0102500.1:exon:4'),
  ('exon_start', 111338),
  ('exon_stop', 115799),
  ('strand', '-'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 115798),
  ('ref', 'A'),
  ('ref_start', 115798),
  ('ref_stop', 115798),
  ('ref_cds_start', 1),
  ('ref_cds_stop', 1),
  ('alt', 'AXX'),
  ('ref_codon', 'aTg'),
  ('alt_codon', 'aXXTga'),
  ('codon_change', 'aTg/aXXTga'),
  ('aa_pos', 1),
  ('ref_aa', 'M'),
  ('alt_aa', 'X*'),
  ('aa_change', 'M1X*')]]

In [221]:

    

dbg(eff.get_amino_acid_changes('Pf3D7_01_v3', 115798, 'A', 'AXXX'))


    

    




[[('gene_id', 'PF3D7_0102500'),
  ('gene_start', 110750),
  ('gene_stop', 115799),
  ('transcript_id', 'PF3D7_0102500.1'),
  ('transcript_start', 110750),
  ('transcript_stop', 115799),
  ('exon_id', 'PF3D7_0102500.1:exon:4'),
  ('exon_start', 111338),
  ('exon_stop', 115799),
  ('strand', '-'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 115798),
  ('ref', 'A'),
  ('ref_start', 115798),
  ('ref_stop', 115798),
  ('ref_cds_start', 1),
  ('ref_cds_stop', 1),
  ('alt', 'AXXX'),
  ('ref_codon', 'aTg'),
  ('alt_codon', 'aXXXTg'),
  ('codon_change', 'aTg/aXXXTg'),
  ('aa_pos', 1),
  ('ref_aa', 'M'),
  ('alt_aa', 'XX'),
  ('aa_change', 'M1XX')]]

In [222]:

    

dbg(eff.get_amino_acid_changes('Pf3D7_01_v3', 115796, 'TCAT', 'T'))


    

    




[[('gene_id', 'PF3D7_0102500'),
  ('gene_start', 110750),
  ('gene_stop', 115799),
  ('transcript_id', 'PF3D7_0102500.1'),
  ('transcript_start', 110750),
  ('transcript_stop', 115799),
  ('exon_id', 'PF3D7_0102500.1:exon:4'),
  ('exon_start', 111338),
  ('exon_stop', 115799),
  ('strand', '-'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 115796),
  ('ref', 'TCAT'),
  ('ref_start', 115796),
  ('ref_stop', 115799),
  ('ref_cds_start', 0),
  ('ref_cds_stop', 3),
  ('alt', 'T'),
  ('ref_codon', 'ATGAaa'),
  ('alt_codon', 'Aaa'),
  ('codon_change', 'ATGAaa/Aaa'),
  ('aa_pos', 1),
  ('ref_aa', 'MK'),
  ('alt_aa', 'K'),
  ('aa_change', 'MK1K')]]

In [223]:

    

dbg(eff.get_amino_acid_changes('Pf3D7_01_v3', 115796, 'TCAT', 'TCA'))


    

    




[[('gene_id', 'PF3D7_0102500'),
  ('gene_start', 110750),
  ('gene_stop', 115799),
  ('transcript_id', 'PF3D7_0102500.1'),
  ('transcript_start', 110750),
  ('transcript_stop', 115799),
  ('exon_id', 'PF3D7_0102500.1:exon:4'),
  ('exon_start', 111338),
  ('exon_stop', 115799),
  ('strand', '-'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 115796),
  ('ref', 'TCAT'),
  ('ref_start', 115796),
  ('ref_stop', 115799),
  ('ref_cds_start', 0),
  ('ref_cds_stop', 3),
  ('alt', 'TCA'),
  ('ref_codon', 'ATGAaa'),
  ('alt_codon', 'TGA'),
  ('codon_change', 'ATGAaa/TGA'),
  ('aa_pos', 1),
  ('ref_aa', 'MK'),
  ('alt_aa', '*'),
  ('aa_change', 'MK1*')]]

In [224]:

    

dbg(eff.get_amino_acid_changes('Pf3D7_01_v3', 115796, 'TCAT', 'TC'))


    

    




[[('gene_id', 'PF3D7_0102500'),
  ('gene_start', 110750),
  ('gene_stop', 115799),
  ('transcript_id', 'PF3D7_0102500.1'),
  ('transcript_start', 110750),
  ('transcript_stop', 115799),
  ('exon_id', 'PF3D7_0102500.1:exon:4'),
  ('exon_start', 111338),
  ('exon_stop', 115799),
  ('strand', '-'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 115796),
  ('ref', 'TCAT'),
  ('ref_start', 115796),
  ('ref_stop', 115799),
  ('ref_cds_start', 0),
  ('ref_cds_stop', 3),
  ('alt', 'TC'),
  ('ref_codon', 'ATGAaa'),
  ('alt_codon', 'GAa'),
  ('codon_change', 'ATGAaa/GAa'),
  ('aa_pos', 1),
  ('ref_aa', 'MK'),
  ('alt_aa', 'E'),
  ('aa_change', 'MK1E')]]

In [225]:

    

dbg(eff.get_amino_acid_changes('Pf3D7_01_v3', 115796, 'TCA', 'T'))


    

    




[[('gene_id', 'PF3D7_0102500'),
  ('gene_start', 110750),
  ('gene_stop', 115799),
  ('transcript_id', 'PF3D7_0102500.1'),
  ('transcript_start', 110750),
  ('transcript_stop', 115799),
  ('exon_id', 'PF3D7_0102500.1:exon:4'),
  ('exon_start', 111338),
  ('exon_stop', 115799),
  ('strand', '-'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 115796),
  ('ref', 'TCA'),
  ('ref_start', 115796),
  ('ref_stop', 115798),
  ('ref_cds_start', 1),
  ('ref_cds_stop', 3),
  ('alt', 'T'),
  ('ref_codon', 'aTGAaa'),
  ('alt_codon', 'aAa'),
  ('codon_change', 'aTGAaa/aAa'),
  ('aa_pos', 1),
  ('ref_aa', 'MK'),
  ('alt_aa', 'K'),
  ('aa_change', 'MK1K')]]

In [226]:

    

dbg(eff.get_amino_acid_changes('Pf3D7_01_v3', 115796, 'TC', 'T'))


    

    




[[('gene_id', 'PF3D7_0102500'),
  ('gene_start', 110750),
  ('gene_stop', 115799),
  ('transcript_id', 'PF3D7_0102500.1'),
  ('transcript_start', 110750),
  ('transcript_stop', 115799),
  ('exon_id', 'PF3D7_0102500.1:exon:4'),
  ('exon_start', 111338),
  ('exon_stop', 115799),
  ('strand', '-'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 115796),
  ('ref', 'TC'),
  ('ref_start', 115796),
  ('ref_stop', 115797),
  ('ref_cds_start', 2),
  ('ref_cds_stop', 3),
  ('alt', 'T'),
  ('ref_codon', 'atGAaa'),
  ('alt_codon', 'atA'),
  ('codon_change', 'atGAaa/atA'),
  ('aa_pos', 1),
  ('ref_aa', 'MK'),
  ('alt_aa', 'I'),
  ('aa_change', 'MK1I')]]

In [227]:

    

dbg(eff.get_amino_acid_changes('Pf3D7_01_v3', 115795, 'TTCA', 'T'))


    

    




[[('gene_id', 'PF3D7_0102500'),
  ('gene_start', 110750),
  ('gene_stop', 115799),
  ('transcript_id', 'PF3D7_0102500.1'),
  ('transcript_start', 110750),
  ('transcript_stop', 115799),
  ('exon_id', 'PF3D7_0102500.1:exon:4'),
  ('exon_start', 111338),
  ('exon_stop', 115799),
  ('strand', '-'),
  ('chrom', 'Pf3D7_01_v3'),
  ('pos', 115795),
  ('ref', 'TTCA'),
  ('ref_start', 115795),
  ('ref_stop', 115798),
  ('ref_cds_start', 1),
  ('ref_cds_stop', 4),
  ('alt', 'T'),
  ('ref_codon', 'aTGAAa'),
  ('alt_codon', 'aAa'),
  ('codon_change', 'aTGAAa/aAa'),
  ('aa_pos', 1),
  ('ref_aa', 'MK'),
  ('alt_aa', 'K'),
  ('aa_change', 'MK1K')]]