Commit 6235bcc95712f661684228f27e3270220716ac40
1 parent
e7acfec9
Exists in
stable-0.3
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1 other branch
merge fall back to simple implementation
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1 changed file
with
7 additions
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17 deletions
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merge.py
... | ... | @@ -135,30 +135,20 @@ def merge_g4rna(df, window=60, step=10, |
135 | 135 | overlap = window-step |
136 | 136 | pd.set_option('display.max_colwidth', -1) |
137 | 137 | if 'sequence' in df.columns: |
138 | - for ite in [0,1,2,3,4]: | |
139 | - print -(overlap+step*ite) | |
138 | + for ite in range(0,len(df)): | |
139 | + print any(df.sequence.str[:(overlap+step*ite)].eq( | |
140 | + df.sequence.str[step:].shift(1))) | |
141 | + if any(df.sequence.str[:(overlap+step*ite)].eq( | |
142 | + df.sequence.str[step:].shift(1))) is False: | |
143 | + break | |
140 | 144 | df.loc[ |
141 | 145 | df.sequence.str[:(overlap+step*ite)].eq( |
142 | 146 | df.sequence.str[step:].shift(1)) |
143 | 147 | , 'sequence'] = df.sequence.str[:step].shift(1) + \ |
144 | 148 | df.sequence.str[:] |
145 | - | |
146 | -# df.sequence.str[-(overlap+step*ite):].eq( | |
147 | -# df.sequence.str[:(overlap+step*ite)].shift(-1)) | |
148 | -# & | |
149 | -# df.sequence.str.len().shift(1) <= window) | |
150 | -# , 'sequence'] = df.sequence.str[:] + \ | |
151 | -# df.sequence.str[(overlap+step*ite):].shift(-1) | |
152 | - # df.loc[ | |
153 | - # df.sequence.str[-overlap:].eq( | |
154 | - # df.sequence.str[:overlap].shift(-6)) | |
155 | -# , 'sequence'] = df.sequence.str[:df.sequence.str.len().shift(-6).fillna(60)] | |
156 | - # , 'sequence'] = df.sequence.str.len().shift(-6).fillna(0) | |
157 | - print df | |
158 | - #print pd.DataFrame(df.sequence,df.sequence.str.len()) | |
159 | 149 | if 'description' in df.columns: |
160 | 150 | df_grouped = df.groupby( |
161 | - [df.description,df.sequence.str[-overlap:]], | |
151 | + [df.description,df.sequence.str[:overlap]], | |
162 | 152 | sort=False, |
163 | 153 | as_index=False) |
164 | 154 | print "******",{k:agg_fct[k] for k in df.columns.drop(['description'])} | ... | ... |