FETCH

Table of Contents

FUNCTION

DESCRIPTION

EXAMPLE

FUNCTION

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Fetch copies GCG sequences or data files from the GCG database into your directory or displays them on your terminal screen.

DESCRIPTION

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The related program of Fetch is: Fetch+, which copies GCG sequences or data files from the GCG database into your directory or displays them on your terminal screen.

The expression%fetch *bov* will retrieve every GCG data file or sequence entry whose name contains the string bov. Sequence specification is described in detail in Section 2, Using Sequence Files and Databases of the User's Guide.

When copying a sequence from a database, Fetch creates a file in GCG format whose name is the entry name and whose extension is the database logical name. For example,%fetch GenBank:Hsrep2 copies the requested sequence into a file called hsrep2.gb_pr. The filename extension is taken from the logical name for the database. In this example, the extension .gb_pr indicates that the sequence was copied from the Primate division of the GenBank nucleotide sequence database. (See "Using Database Sequences" in Section 2, Using Sequence Files and Databases of the User's Guide for a complete listing of logical names for all GCG databases.) If the file being copied is not from a sequence database, for example enzyme.dat, then its name is not changed.

If your sequence specification contains no logical name, Fetch looks in all the databases and in all the GCG data directories to find all possible entry names. For example, % fetch hum* would do almost the same thing as % fetch GenBank:hum*, except that if any sequences beginning with hum were present in databases other than GenBank or in any GCG data directories, they would also be retrieved.

Special Considerations for Searching

Keep in mind that filenames are case sensitive and database entry names are case insensitive. Because this program searches for both filenames and database entry names, you must take care when you enter the character pattern that makes up your specification.

For example, if you entered Gamma* as a file specification, this program would find all entries in the databases whose names begin with Gamma but no Accelrys GCG (GCG) supplied files would be found. This is because all the files in GCG are named using lowercase letters. Conversely, if you entered gamma*, this program would find all of the entries in the databases and all GCG supplied files whose names begin with gamma.

(Note that it is often convenient to add -OUTfile=term to the command line so the data are displayed on your terminal screen.)

EXAMPLE

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Here is a session using Fetch to retrieve local copies of most of the GenBank human beta globin sequences:

% fetch

 FETCH what sequence(s) ?  GenBank:HumHb*

 humhb16aa.gb_pr

 humhb1az.gb_pr

 humhb24.gb_pr

 ////////////////

 humhbp68.gb_pr

INPUT FILES

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Except for the exceptions listed below, Fetch accepts valid single file specifications. You can also specify multiple files by using a list file, for example @project.list, or by using an ambiguous specification with an asterisk (*) wildcard, for exampleGenBank:*. You can use Fetch to obtain copies of multiple sequence format (MSF) or rich sequence format (RSF) files, for example GenDocData:*.msf, but you cannot use specifications such as hsp70.msf{hsp_yeast} to extract sequences from such files into individual sequence files. (To accomplish this task, use the Reformat program.)

COMMAND-LINE SUMMARY

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All parameters for this program may be added to the command line. Use -CHEck to view the summary below and to specify parameters before the program executes. In the summary below, the capitalized letters in the parameter names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose parameter values that are optional.

Minimal Syntax: % fetch [-INfile=]GenBank:humhb*

Prompted Parameters: None

Local Data Files: None

Optional Parameters:

-DOCLines=6         copies only the first 6 lines of documentation

-OUTfile=filename   copies file(s)/sequence(s) into one file

-REFerence          copies only the documentation

-NOMONitor          suppresses the screen monitor

LOCAL DATA FILES

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None.

PARAMETER REFERENCE

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You can set the parameters listed below from the command line.

-DOCLines=6

Sets an individual GCG program to copy only six non-blank lines of documentation from input data files into the output files. Use the % doclines global switch to set this value for your whole session. Usually, Fetch copies all of the documentation from each sequence entry into your new files exactly as it appeared in the original entry.

-OUTfile=filename

Copies the sequence(s) and/or data file(s) into one file which you can name. If you leave out the name of the file, Fetch prompts you for one. (GCG programs will not read files containing more than one sequence unless they are in an MSF (multiple sequence format) or RSF (rich sequence format) file.)

It is often useful to use term for the filename so that the data are displayed on your terminal screen.

-MONitor

This program normally monitors its progress on your screen. However, when you use -Default to suppress all program interaction, you also suppress the monitor. You can turn it back on with this parameter. If you are running the program in batch, the monitor will appear in the log file.

-REFerence

Copies only the documentation for the sequence or data file. Unless specified, the name of the output file is the entry name concatenated with _ref, followed by the database logical name as the extension.

Printed: May 27, 2005 12:16

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