| ''' |
| Created on Dec 6, 2012 |
| |
| @author: jonathanfriedman |
| ''' |
| import numpy as np |
| from pandas.io.parsers import read_table |
| from Lineages import Lineages |
| |
|
|
|
|
|
|
| |
| def read_txt(file, T=True, lin=None, lin_label='lineage', |
| format='QIIME', verbose=True, **kwargs): |
| ''' |
| Read general delimited file into DataFrame. |
| |
| This a wrapper around pandas' read_table function which adds |
| optional parsing of lineage information, and sets some default |
| parameter values. |
| |
| Note: |
| By default the data is transposed! |
| To avoid this behavior set the parameter 'T' to False. |
| |
| Parameters |
| ---------- |
| file : string |
| Path to input file. |
| T : bool (default True) |
| Indicated whether the produced DataFrame will be transposed. |
| lin : bool/None (default None) |
| Indicated whether lineage information is given in the input file. |
| If None, read_txt tries to infer the presence of |
| lineage information automatically |
| lin_label : string (default 'lineage') |
| Label of the column containing the lineage information. |
| format : string (default 'QIIME') |
| Format of the lineage information. |
| This argument is passed to the Lineage object constructor. |
| verbose : bool (default True) |
| Indicated whether to print to screen the parsed table stats. |
| |
| Returns |
| ------- |
| table : DataFrame |
| Parsed table. |
| lins : Lineages (optional) |
| Parsed Lineages object. |
| Returned only if lineage information was parsed. |
| ''' |
| kwargs.setdefault('index_col',0) |
| temp = read_table(file, engine='python', **kwargs) |
| |
| if lin is None: |
| lin = False |
| lin_labels = ('lin','lins','lineage','lineages', |
| 'taxon','taxa','rdp') |
| for c in temp.columns: |
| if hasattr(c, 'lower'): |
| if c.lower() in lin_labels: |
| lin = True |
| lin_label = c |
| if lin: |
| lins = Lineages.from_dict(temp[lin_label], format=format) |
| temp = temp.drop(lin_label,axis=1) |
| if T: |
| temp = temp.T |
| |
| s = ['Finished parsing table.', |
| 'Table dimensions: (%d,%d)' %temp.shape] |
| if T: |
| s += ['**** Data has been transposed! ****'] |
| ncol = min(temp.shape[1],3) |
| nrow = min(temp.shape[0],3) |
| scol = tuple([ncol] + list(temp.columns[:ncol])) |
| srow = tuple([nrow] + list(temp.index[:nrow])) |
| s += [('First %d column labels are :' |
| + ' ,'.join(['%s']*ncol)) %scol, |
| ('First %d row labels are :' |
| + ' ,'.join(['%s']*nrow)) %srow] |
| |
| table = temp |
| if lin: |
| if verbose: print '\n'.join(s), '\n' |
| return table, lins |
| else: |
| if verbose: print '\n'.join(s), '\n' |
| return table |
|
|
| def write_txt(frame, file, T=True, lin=None, lin_label='lineage', **kwargs): |
| ''' |
| Write frame to txt file. |
| |
| This a wrapper around pandas' to_csv function which adds |
| optional writing of lineage information, and sets some default |
| parameter values. |
| |
| Note: |
| By default the data is transposed! |
| To avoid this behavior set the parameter 'T' to False. |
| |
| Parameters |
| ---------- |
| file : string |
| Path to input file. |
| T : bool (default True) |
| Indicated whether the produced DataFrame will be transposed. |
| lin : None/None (default None) |
| Lineages object to be included in the output file. |
| lin_label : string (default 'lineage') |
| Label of the column containing the lineage information. |
| ''' |
| from pandas import Series |
| kwargs.setdefault('sep','\t') |
| if T: data = frame.T |
| else: data = frame |
| if lin is not None: |
| d = {} |
| for i in data.index: |
| if i in lin: |
| d[i] = lin[i].lin_str |
| else: |
| d[i] = None |
| t = Series(d, name=lin_label) |
| data = data.join(t) |
| data.to_csv(file,**kwargs) |
|
|
| |
| if __name__ == '__main__': |
| file = 'demo/data/fake_data_lin.counts' |
| t, lin = read_txt(file) |
| |
| |
| |
| |
|
|
