reading and extracting data from file using python

Question

I am new to python , and I want to extract the data from this format

<seq id> <alignment start> <alignment end> <envelope start> <envelope end> <hmm acc> <hmm name> <type> <hmm start> <hmm end> <hmm length> <bit score> <E-value> <significance> <clan>

**FBpp0143497**      **5    151**      5    157 PF00339.22  **Arrestin_N**        Domain     1   135   149     83.4   **1.1e-23**   1 CL0135   
**FBpp0143497**    **183    323**    183    324 PF02752.15  Arrestin_C        Domain     1   137   138     58.5     **6e-16**   1 CL0135   
FBpp0131987     60    280     51    280 PF00089.19  Trypsin           Domain    14   219   219    127.7   3.7e-37   1 CL0124

to this format

>FBpp0143497
 5      151        Arrestin_N     1.1e-23

>FBpp0143497
 183    323        Arrestin_C     6e-16

Please show the code you have so far. This is not "Write Code For Me.COM" — S.Lott
– S.Lott, Commented May 19, 2010 at 9:59
possible duplicate of problem in extracting the data from text file — mmmmmm
– mmmmmm, Commented May 20, 2010 at 13:22

Marco Mariani · Accepted Answer · 2010-05-19 10:02:20Z

1

You could parse the file with the 'csv' module, using space as a delimiter. See the documentation for csv.reader

answered May 19, 2010 at 10:02

Marco Mariani

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joaquin · Accepted Answer · 2010-05-19 10:18:12Z

1

As this is proteomic data, probably you could find dedicated parsers in the BioPython package

answered May 19, 2010 at 10:18

joaquin

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jhocking · Accepted Answer · 2011-03-31 21:20:26Z

0

You can use split() to separate the items at spaces and then print out the values you want from the returned list.

answered Mar 31, 2011 at 21:20

jhocking

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