def blast_to_df_iter(fn, delimiter='\t', chunksize=10000, remap=True):
'''Iterator of DataFrames of length chunksize parsed from an
NCBI BLAST+ `-outfmt6` file.
Native BLAST+ uses an interval of the form [start,end), start >= 1. This
changes to [end,start) when on the negative strand, apparently solely
to make other bioinformaticians suffer.
We convert to proper 0-based, half-open intervals.
Args:
fn (str): The results file.
chunksize (int): Hits per iteration.
Yields:
DataFrame: Pandas DataFrme with the BLAST+ hits.
'''
for group in pd.read_table(fn,
header=None,
skipinitialspace=True,
names=[k for k, _ in blast_cols],
delimiter=delimiter,
chunksize=chunksize):
convert_dtypes(group, dict(blast_cols))
if remap:
remap_blast(group)
yield group
def crb_to_df_iter(fn, chunksize=10000, remap=False):
'''Iterator of DataFrames of length chunksize parsed from
the results from CRBB version crb-blast 0.6.6.
Args:
fn (str): The results file.
chunksize (int): Hits per iteration.
Yields:
DataFrame: Pandas DataFrame with the CRBB hits.
'''
for group in pd.read_table(fn,
header=None,
names=[k for k, _ in crb_cols],
delimiter='\t',
chunksize=chunksize):
convert_dtypes(group, dict(crb_cols))
qrange = group.qrange.str.partition('..')
group['qstart'] = qrange[0].astype(int)
group['qend'] = qrange[2].astype(int)
del group['qrange']
srange = group.srange.str.partition('..')
group['sstart'] = srange[0].astype(int)
group['send'] = srange[2].astype(int)
del group['srange']
if remap:
remap_blast(group)
yield group
def crb_to_df_iter(fn, chunksize=10000, remap=False):
'''Iterator of DataFrames of length chunksize parsed from
the results from CRBB version crb-blast 0.6.6.
Args:
fn (str): The results file.
chunksize (int): Hits per iteration.
Yields:
DataFrame: Pandas DataFrame with the CRBB hits.
'''
for group in pd.read_table(fn, header=None, names=[k for k, _ in crb_cols],
delimiter='\t', chunksize=chunksize):
convert_dtypes(group, dict(crb_cols))
qrange = group.qrange.str.partition('..')
group['qstart'] = qrange[0].astype(int)
group['qend'] = qrange[2].astype(int)
del group['qrange']
srange = group.srange.str.partition('..')
group['sstart'] = srange[0].astype(int)
group['send'] = srange[2].astype(int)
del group['srange']
if remap:
remap_blast(group)
yield group
def crb_to_df_iter(fn, chunksize=10000, remap=True):
'''Iterator of DataFrames of length chunksize parsed from
the results from CRBB version crb-blast 0.6.6.
crb-blast is given the same treatment as BLAST+, as that's what
it uses under the hood.
We convert to proper 0-based, half-open intervals.
Args:
fn (str): The results file.
chunksize (int): Hits per iteration.
Yields:
DataFrame: Pandas DataFrame with the CRBB hits.
'''
for group in pd.read_table(fn, header=None, names=[k for k, _ in crb_cols],
delimiter='\t', chunksize=chunksize):
convert_dtypes(group, dict(crb_cols))
qrange = group.qrange.str.partition('..')
group['qstart'] = qrange[0].astype(int)
group['qend'] = qrange[2].astype(int)
del group['qrange']
srange = group.srange.str.partition('..')
group['sstart'] = srange[0].astype(int)
group['send'] = srange[2].astype(int)
del group['srange']
if remap:
remap_blast(group)
yield group
def blast_to_df_iter(fn, delimiter='\t', chunksize=10000, remap=False):
'''Iterator of DataFrames of length chunksize parsed from an
NCBI BLAST+ `-outfmt6` file.
Args:
fn (str): The results file.
chunksize (int): Hits per iteration.
Yields:
DataFrame: Pandas DataFrme with the BLAST+ hits.
'''
for group in pd.read_table(fn, header=None, skipinitialspace=True,
names=[k for k, _ in blast_cols],
delimiter=delimiter, chunksize=chunksize):
convert_dtypes(group, dict(blast_cols))
if remap:
remap_blast(group)
yield group
def blast_to_df_iter(fn, delimiter='\t', chunksize=10000, remap=False):
'''Iterator of DataFrames of length chunksize parsed from an
NCBI BLAST+ `-outfmt6` file.
Args:
fn (str): The results file.
chunksize (int): Hits per iteration.
Yields:
DataFrame: Pandas DataFrme with the BLAST+ hits.
'''
for group in pd.read_table(fn,
header=None,
skipinitialspace=True,
names=[k for k, _ in blast_cols],
delimiter=delimiter,
chunksize=chunksize):
convert_dtypes(group, dict(blast_cols))
if remap:
remap_blast(group)
yield group
def crb_to_df_iter(fn, chunksize=10000, remap=True):
'''Iterator of DataFrames of length chunksize parsed from
the results from CRBB version crb-blast 0.6.6.
crb-blast is given the same treatment as BLAST+, as that's what
it uses under the hood.
We convert to proper 0-based, half-open intervals.
Args:
fn (str): The results file.
chunksize (int): Hits per iteration.
Yields:
DataFrame: Pandas DataFrame with the CRBB hits.
'''
for group in pd.read_table(fn,
header=None,
names=[k for k, _ in crb_cols],
delimiter='\t',
chunksize=chunksize):
convert_dtypes(group, dict(crb_cols))
qrange = group.qrange.str.partition('..')
group['qstart'] = qrange[0].astype(int)
group['qend'] = qrange[2].astype(int)
del group['qrange']
srange = group.srange.str.partition('..')
group['sstart'] = srange[0].astype(int)
group['send'] = srange[2].astype(int)
del group['srange']
if remap:
remap_blast(group)
yield group
def blast_to_df_iter(fn, delimiter='\t', chunksize=10000, remap=True):
'''Iterator of DataFrames of length chunksize parsed from an
NCBI BLAST+ `-outfmt6` file.
Native BLAST+ uses an interval of the form [start,end), start >= 1. This
changes to [end,start) when on the negative strand, apparently solely
to make other bioinformaticians suffer.
We convert to proper 0-based, half-open intervals.
Args:
fn (str): The results file.
chunksize (int): Hits per iteration.
Yields:
DataFrame: Pandas DataFrme with the BLAST+ hits.
'''
for group in pd.read_table(fn, header=None, skipinitialspace=True,
names=[k for k, _ in blast_cols],
delimiter=delimiter, chunksize=chunksize):
convert_dtypes(group, dict(blast_cols))
if remap:
remap_blast(group)
yield group
