def get_best_hits():
print('--- Calculating best hits...')
store = get_store()
for i, (name, target) in enumerate(best_hits_files):
print('\t...working on {}'.format(target))
df = blasttools.blast_to_df(target)
blasttools.remap_blast_coords_df(df)
#store[target] = df
tmp = pd.merge(pd.DataFrame(index=store['annot_df'].index),
df,
left_index=True,
right_index=True,
how='left')
blasttools.best_hits(tmp)
if i == 0:
best_hits_panel = pd.Panel({name: tmp})
else:
best_hits_panel[name] = tmp
store['best_hits_panel'] = best_hits_panel
best_hits = best_hits_panel.minor_xs('sseqid')
store['best_hits_df'] = best_hits
#store['blast_filter_df'] = best_hits.minor_xs('evalue') >= 0
store.close()
def get_orthologies():
print('--- Calculating recipricol best hits...')
store = get_store()
for i, (name, A_fn, B_fn) in enumerate(ortho_files):
print('\t...working on {}, {}'.format(A_fn, B_fn))
A = blasttools.blast_to_df(A_fn)
B = blasttools.blast_to_df(B_fn)
blasttools.remap_blast_coords_df(A)
blasttools.remap_blast_coords_df(B)
X = blasttools.get_orthologies(A, B, store['annot_df'].index)
if i == 0:
ortho_panel = pd.Panel({name: X})
else:
ortho_panel[name] = X
store['ortho_panel'] = ortho_panel
orthos = ortho_panel.minor_xs('sseqid')
store['ortho_df'] = orthos
#store['ortho_filter_df'] = orthos.minor_xs('evalue') >= 0
store.close()
def get_orthologies():
print('--- Calculating recipricol best hits...')
store = get_store()
for i, (name, A_fn, B_fn) in enumerate(ortho_files):
print('\t...working on {}, {}'.format(A_fn, B_fn))
A = blasttools.blast_to_df(A_fn)
B = blasttools.blast_to_df(B_fn)
blasttools.remap_blast_coords_df(A)
blasttools.remap_blast_coords_df(B)
X = blasttools.get_orthologies(A, B, store['annot_df'].index)
if i == 0:
ortho_panel = pd.Panel({name: X})
else:
ortho_panel[name] = X
store['ortho_panel'] = ortho_panel
orthos = ortho_panel.minor_xs('sseqid')
store['ortho_df'] = orthos
#store['ortho_filter_df'] = orthos.minor_xs('evalue') >= 0
store.close()
def get_best_hits():
print('--- Calculating best hits...')
store = get_store()
for i, (name, target) in enumerate(best_hits_files):
print('\t...working on {}'.format(target))
df = blasttools.blast_to_df(target)
blasttools.remap_blast_coords_df(df)
#store[target] = df
tmp = pd.merge(pd.DataFrame(index=store['annot_df'].index), df,
left_index=True, right_index=True, how='left')
blasttools.best_hits(tmp)
if i == 0:
best_hits_panel = pd.Panel({name: tmp})
else:
best_hits_panel[name] = tmp
store['best_hits_panel'] = best_hits_panel
best_hits = best_hits_panel.minor_xs('sseqid')
store['best_hits_df'] = best_hits
#store['blast_filter_df'] = best_hits.minor_xs('evalue') >= 0
store.close()
