Example #1
0
    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()
Example #2
0
    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()
Example #3
0
    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()
Example #4
0
    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()