irefindex MS-Digest changes

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paulbodd@hfaistos.uio.no — Tue, 26 Mar 2013 17:13:31 -0000

A program which obtains results from the MS-Digest Web site, producing FASTA-like output.
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paulbodd@hfaistos.uio.no — Tue, 26 Mar 2013 17:13:31 -0000

Added a script which extracts sequences for certain organisms from a larger FASTA file, writing them to individual organism-related files.
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paulbodd@hfaistos.uio.no — Tue, 26 Mar 2013 17:13:31 -0000

Fixed the extraction script to actually record more than the first line of each sequence (since the FASTA format has sequences split into 80 columns over potentially many lines). Made the results be put in a directory called "FASTA".
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paulbodd@hfaistos.uio.no — Tue, 26 Mar 2013 17:13:31 -0000

Added a script which looks for certain names in a specified FASTA file and puts the records which contain such names in their headers into a results file in the "candidates" directory.
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paulbodd@hfaistos.uio.no — Tue, 26 Mar 2013 17:13:31 -0000

Added a list of names for the find.py script.
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paulbodd@hfaistos.uio.no — Tue, 26 Mar 2013 17:13:31 -0000

Added test for directory.
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paulbodd@hfaistos.uio.no — Tue, 26 Mar 2013 17:13:31 -0000

Removed names that are not worth looking for.
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paulbodd@hfaistos.uio.no — Tue, 26 Mar 2013 17:13:31 -0000

Made functions for non-program use.
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paulbodd@hfaistos.uio.no — Tue, 26 Mar 2013 17:13:31 -0000

Renamed find to proteinfind.
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paulbodd@hfaistos.uio.no — Tue, 26 Mar 2013 17:13:31 -0000

Fixed write_sequence signature. Renamed add_sequence to add_sequences. Made make_digest return the output filename. Added docstrings. Increased the pause between requests.
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