def geneTranslation(var):
"""Translates variants to genes
Arguments:
var {list} -- List of chromosome regions
"""
data = pyensembl.Genome(
reference_name='GRCh37',
annotation_name='my_genome_features',
gtf_path_or_url='../../data/datasets/Original/ensembl_v37.gtf')
data.index()
genes, variants = [], []
bar = Bar('Processing', max=len(var), suffix='%(percent)d%%')
for v in var:
locus = v.split(':')
chr, pos = locus[0][3:], int(float(locus[1]))
gene = data.genes_at_locus(chr, pos)
if len(gene) == 0:
genes.append('None')
variants.append(v)
elif gene[0].biotype == 'protein_coding':
genes.append(gene[0].gene_name)
variants.append(v)
else:
genes.append('None')
variants.append(v)
bar.next()
bar.finish()
result = zip(genes, variants) # Creates a list of (gene,variant region)
print('>>> Writing txt...')
with open('../../data/genes/geneList.csv', mode='w', newline='') as myfile:
wr = csv.writer(myfile)
wr.writerow(("Genes", "Variants"))
for row in result:
wr.writerow(list(row))
def load_ensembl_gene_ids(mouse_gtf=None):
data = pyensembl.Genome(
reference_name='GRCm38',
gtf_path_or_url=
'ftp://ftp.ensembl.org/pub/release-81/gtf/mus_musculus/Mus_musculus.GRCm38.81.gtf.gz',
transcript_fasta_path_or_url=
'ftp://ftp.ensembl.org/pub/release-81/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz',
protein_fasta_path_or_url=
'ftp://ftp.ensembl.org/pub/release-81/fasta/mus_musculus/pep/Mus_musculus.GRCm38.pep.all.fa.gz'
)
return data
def main():
sys.stderr = open(snakemake.log[0], "w")
data = pyensembl.Genome(
reference_name='GRCm38',
annotation_name='mus_musculus',
gtf_path_or_url=snakemake.params.gtf)
data.index()
df_cts = annotate(snakemake.input.counts, data)
df_dge = annotate(snakemake.input.dge, data)
df = df_dge.merge(df_cts, how='inner', left_index=True, right_index=True)
df = df.sort_values(by='padj')
df.to_csv(snakemake.output.table, sep='\t')
def get_genome(reference_name,
gtf,
transcript_fasta=None,
logging_args=None,
annotation_name='ensembl',
**kwargs):
""" Retrieve the pyensembl annotations associated with the given reference.
The script also creates the database (with the "index" method) if it does
not already exist.
This function is largely a wrapper around the pyensembl.Genome constructor,
so please see it for more details.
Parameters
----------
reference_name: string
The identifier for the reference
gtf: string
The path to the GTF annotation file
transcript_fasta: string (optional)
The path to the fasta file with transcript sequences. The fasta keys
must match the transcript_id in the GTF file
logging_args: argparse.Namespace
pyensembl appears to change several logging levels while opening the
annotation database (sometimes?). If the logging arguments are given,
then they will be restored after opening the database.
annotation_name, kwargs:
Other options to pass to the pyensembl constructor
"""
ensembl = pyensembl.Genome(reference_name=reference_name,
gtf_path_or_url=gtf,
transcript_fasta_paths_or_urls=transcript_fasta,
annotation_name=annotation_name,
**kwargs)
# this will create the database if needed
ensembl.index()
if logging_args is not None:
logging_utils.update_logging(logging_args)
return ensembl
def main(tsv_path):
"""
annotate.py
Manually annotate a file with gene symbols from Ensemble ID.
:param tsv_path: Path for TSV to annotate
"""
data = pyensembl.Genome(reference_name='GRCm38',
annotation_name='mus_musculus',
gtf_path_or_url='resources/genome.gtf')
data.index()
df = annotate(tsv_path, data)
parent_dir = os.path.dirname(tsv_path)
name, ext = os.path.splitext(os.path.basename(tsv_path))
out_dir = os.path.join(parent_dir, "{}_anno{}".format(name, ext))
df.to_csv(out_dir, sep='\t')
def main():
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description="Given a meme motif file, extract the gene names and map "
"them to ensembl identifiers using pyensembl. The pyensembl database "
"information can be given either in a yaml config file or as command "
"line options. The yaml config file values have precedence over the "
"command line options.")
parser.add_argument('meme', help="The meme file")
parser.add_argument('out', help="The output file")
parser.add_argument(
'-c',
'--config',
help="The yaml config file. If "
"given, this should include keys 'genome_name' and 'gtf'. Otherwise, "
"they may be specified using the respective command line options.",
default=None)
parser.add_argument('-n',
'--genome-name',
help="The genome_parameter for "
"retrieving the pyensembl database",
default=None)
parser.add_argument('-g',
'--gtf',
help="The gtf file for pyensembl",
default=None)
logging_utils.add_logging_options(parser)
args = parser.parse_args()
logging_utils.update_logging(args)
# if the config file was given, use any values in it to replace those
# passed on the command line
if args.config is not None:
msg = "Reading config file"
logger.info(msg)
config = yaml.load(open(args.config))
args.genome_name = config.get('genome_name', args.genome_name)
args.gtf = config.get('gtf', args.gtf)
msg = "genome_name: {}".format(args.genome_name)
logger.debug(msg)
msg = "gtf: {}".format(args.gtf)
logger.debug(msg)
msg = "Loading pyensembl database"
logger.info(msg)
ensembl = pyensembl.Genome(reference_name=args.genome_name,
annotation_name="ensembl",
gtf_path_or_url=args.gtf)
# this will create the database if needed
ensembl.index()
msg = "Parsing motif gene names"
logger.info(msg)
# a line from CISBP looks like:
# MOTIF M002_0.6 (Ankhd1)_(Homo_sapiens)_(RBD_1.00)
all_motifs = []
motif_re = ("\((?P<gene_name>[^\)]+)\)_\((?P<species>[^\)]+)\)_"
"\((?P<rbd_score>[^\)]+)\)")
motif_re = re.compile(motif_re)
with open(args.meme) as meme_f:
for line in meme_f:
if line.startswith("MOTIF"):
(key, motif_name, info) = line.split()
m = motif_re.match(info)
if m is None:
msg = ("Could not parse gene name. Guessing the entire "
"string is the gene name: '{}'.".format(info))
logger.warning(msg)
gene_name = info
else:
gene_name = m.group("gene_name")
try:
ensembl_ids = ensembl.gene_ids_of_gene_name(gene_name)
except ValueError:
msg = ("Could not find Ensembl identifier for gene_name: "
"'{}'".format(gene_name))
logger.warning(msg)
ensembl_ids = [gene_name]
for ensembl_id in ensembl_ids:
motif = {
"motif_name": motif_name,
"gene_name": gene_name,
"ensembl_id": ensembl_id
}
all_motifs.append(motif)
msg = "Joining motif gene names into large data frame"
logger.info(msg)
all_motifs_df = pd.DataFrame(all_motifs)
msg = "Writing motifs to disk"
logger.info(msg)
utils.write_df(all_motifs_df, args.out, index=False)
from __future__ import print_function
import sys
import pyensembl
myfile = open(sys.argv[1])
gtffile = sys.argv[2]
outfile = open(sys.argv[1][:-4] + '_geneanno.sam', 'w')
data = pyensembl.Genome(reference_name='GRCH37', annotation_name='my_genome_features', gtf_path_or_url=gtffile)
data.index()
with myfile:
for line in myfile:
if line[0] == '@':
continue
info = line.split('\t')
chr = info[2]
pos = int(info[3])
nameresult = data.gene_names_at_locus(contig=chr, position=pos)
k = 20
if nameresult == []:
nameresult = data.gene_names_at_locus(contig=chr, position=pos+k)
if nameresult == []:
nameresult = data.gene_names_at_locus(contig=chr, position=pos - k)
genename = ''
for item in nameresult:
genename += item + ';'
genename = genename[:-1]
outfile.write(genename + '\t' + line)
peak[2],
width=peak[1] - peak[0],
color='b',
edgecolor='none')
axes[8].set_xlim([start_pos, end_pos])
axes[8].set_title('RelA Lipid A 2h')
axes[8].set_yticks([0, 40])
axes[8].set_xticks([])
"""
Plot location of Ccl3 and Ccl4
"""
mouse_genome = pyensembl.Genome(
reference_name='NCBIM37',
gtf_path_or_url=
'ftp://ftp.ensembl.org/pub/release-67/gtf/mus_musculus/Mus_musculus.NCBIM37.67.gtf.gz',
transcript_fasta_path_or_url=
'ftp://ftp.ensembl.org/pub/release-67/fasta/mus_musculus/cdna/Mus_musculus.NCBIM37.67.cdna.all.fa.gz',
protein_fasta_path_or_url=
'ftp://ftp.ensembl.org/pub/release-67/fasta/mus_musculus/pep/Mus_musculus.NCBIM37.67.pep.all.fa.gz'
)
list_of_genes = ['Ccl3', 'Ccl4']
transcript_dict = {}
gene_object_dict = {}
for gene in list_of_genes:
transcript_dict[gene] = mouse_genome.transcript_ids_of_gene_name(gene)
for gene in list_of_genes:
gene_object_dict[gene] = mouse_genome.genes_by_name(gene)[0]
# Gene locations
def count_rsem_files(direc_name,
bammed_direc='aligned_star',
quant_direc='quant_rsem',
counted_direc='counted_rsem',
spikeids=[]):
quant_path = os.path.join(direc_name, quant_direc)
counted_path = os.path.join(direc_name, counted_direc)
bammed_path = os.path.join(direc_name, bammed_direc)
file_list = os.listdir(quant_path)
mouse_genome = pyensembl.Genome(
reference_name='GRCm38',
gtf_path_or_url=
'ftp://ftp.ensembl.org/pub/release-81/gtf/mus_musculus/Mus_musculus.GRCm38.81.gtf.gz',
transcript_fasta_path_or_url=
'ftp://ftp.ensembl.org/pub/release-81/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz',
protein_fasta_path_or_url=
'ftp://ftp.ensembl.org/pub/release-81/fasta/mus_musculus/pep/Mus_musculus.GRCm38.pep.all.fa.gz'
)
for seq_file_temp in file_list:
if fnmatch.fnmatch(seq_file_temp, r'*.isoforms.results'):
seq_file = seq_file_temp
gene_names = mouse_genome.gene_names()
transcript_dict = {}
counter = 0
for gene in gene_names:
transcript_dict[gene] = mouse_genome.transcript_ids_of_gene_name(gene)
counter += 1
print counter
for seq_file in file_list:
print seq_file, fnmatch.fnmatch(seq_file, r'*.isoforms.results')
if fnmatch.fnmatch(seq_file, r'*.isoforms.results'):
bfs = seq_file.split('.')
bam_file_sorted_by_loc = bfs[0] + '.transcript.sorted.bam'
num_mapped, num_unmapped = bam_read_count(
os.path.join(bammed_path, bam_file_sorted_by_loc))
transcripts, spikeins = load_sequence_counts_rsem(
rsem_file=os.path.join(quant_path, seq_file),
spikeids=spikeids)
filename_save = os.path.join(counted_path, seq_file + '.h5')
print 'Saving ' + filename_save
store = pd.HDFStore(filename_save)
d = {'num_mapped': num_mapped, 'num_unmapped': num_unmapped}
quality_control = pd.DataFrame(d, index=[0])
# Create a transcript table indexed by gene name - sum over all isoforms
counts_list = []
fpkm_list = []
tpm_list = []
for j in xrange(len(gene_names)):
gene = gene_names[j]
transcript_list = transcript_dict[gene]
counts = 0
fpkm = 0
tpm = 0
for transcript in transcript_list:
if transcript in transcripts.index:
counts += transcripts.loc[transcript]['est_counts']
fpkm += transcripts.loc[transcript]['fpkm']
tpm += transcripts.loc[transcript]['tpm']
counts_list += [counts]
fpkm_list += [fpkm]
tpm_list += [tpm]
d = {
'gene_name': gene_names,
'est_counts': counts_list,
'fpkm': fpkm_list,
'tpm': tpm_list
}
gene_counts = pd.DataFrame(d)
gene_counts.set_index('gene_name', inplace=True)
# Store data frames in HDF5 format
store['quality_control'] = quality_control
store['transcripts'] = transcripts
store['gene_counts'] = gene_counts
store['spikeins'] = spikeins
store.close()
def count_hdf5_files(direc_name,
bammed_direc='bammed',
aligned_direc='aligned',
counted_direc='counted',
spikeids=[]):
bammed_path = os.path.join(direc_name, bammed_direc)
aligned_path = os.path.join(direc_name, aligned_direc)
counted_path = os.path.join(direc_name, counted_direc)
file_list = os.listdir(aligned_path)
mouse_genome = pyensembl.Genome(
reference_name='GRCm38',
gtf_path_or_url=
'ftp://ftp.ensembl.org/pub/release-81/gtf/mus_musculus/Mus_musculus.GRCm38.81.gtf.gz',
transcript_fasta_path_or_url=
'ftp://ftp.ensembl.org/pub/release-81/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz',
protein_fasta_path_or_url=
'ftp://ftp.ensembl.org/pub/release-81/fasta/mus_musculus/pep/Mus_musculus.GRCm38.pep.all.fa.gz'
)
for seq_file_temp in file_list:
if fnmatch.fnmatch(seq_file_temp, r'*.h5'):
seq_file = seq_file_temp
transcripts, spikeins = load_sequence_counts_kallisto(
h5file_name=os.path.join(aligned_path, seq_file), spikeids=spikeids)
transcript_names = transcripts.index
gene_names = []
counter = 0
for transcript in transcript_names:
counter += 1
print counter
gene_names += [mouse_genome.gene_name_of_transcript_id(transcript)]
unique_gene_names = list(set(gene_names))
transcript_dict = {}
for gene in unique_gene_names:
transcript_dict[gene] = []
for transcript in transcript_names:
gene_name = mouse_genome.gene_name_of_transcript_id(transcript)
transcript_dict[gene_name] += [transcript]
for seq_file in file_list:
print seq_file, fnmatch.fnmatch(seq_file, r'*.h5')
if fnmatch.fnmatch(seq_file, r'*.h5'):
bfs = seq_file.split('.')
bam_file_sorted_by_loc = bfs[0] + '_sorted_by_location.bam'
num_mapped, num_unmapped = bam_read_count(
os.path.join(bammed_path, bam_file_sorted_by_loc))
transcripts, spikeins = load_sequence_counts_kallisto(
h5file_name=os.path.join(aligned_path, seq_file),
spikeids=spikeids)
filename_save = os.path.join(counted_path, seq_file[:-3] + '.h5')
print 'Saving ' + filename_save
store = pd.HDFStore(filename_save)
d = {'num_mapped': num_mapped, 'num_unmapped': num_unmapped}
quality_control = pd.DataFrame(d, index=[0])
# Create a transcript table indexed by gene name
counts_list = []
fpkm_list = []
tpm_list = []
length_list = []
for j in xrange(len(unique_gene_names)):
gene = unique_gene_names[j]
transcript_list = transcript_dict[gene]
counts = 0
fpkm = 0
tpm = 0
mean_eff_length = 0
for transcript in transcript_list:
counts += transcripts.loc[transcript]['est_counts']
fpkm += transcripts.loc[transcript]['fpkm']
tpm += transcripts.loc[transcript]['tpm']
mean_eff_length += transcripts.loc[transcript][
'eff_length'] / len(transcript_list)
counts_list += [counts]
fpkm_list += [fpkm]
tpm_list += [tpm]
length_list += [mean_eff_length]
d = {
'gene_name': unique_gene_names,
'est_counts': counts_list,
'fpkm': fpkm_list,
'tpm': tpm_list,
'mean_eff_length': length_list
}
gene_counts = pd.DataFrame(d)
gene_counts.set_index('gene_name', inplace=True)
# Store data frames in HDF5 format
store['quality_control'] = quality_control
store['transcripts'] = transcripts
store['gene_counts'] = gene_counts
store['spikeins'] = spikeins
store.close()
