154 lines
4.6 KiB
Text
154 lines
4.6 KiB
Text
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Wed Feb 17 11:30:28 GMT 1993
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----------------------------
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freetext.c
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PIR 35.0. Changes to format
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One field identifier has changed in the PIR-International
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databases. All "#Title" tags for submitted citations have been
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converted to the new tag "#Description" which will not be
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standardized. This information may be considered free text.
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Changed code to reflect this.
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access4.c
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The record size stored in acnum.hit header was 18. It should be
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4.
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piraccession.script
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emblaccession.script
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genbaccession.script
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The name of the accession number index files are now acnum.hit and
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acnum.trg.
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Thu Jan 21 15:32:26 GMT 1993
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----------------------------
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genbentryname1.c
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pirentryname1.c
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These programs now give the offset of the FIRST base in the
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sequence. The entryname index previously being created was not
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in accordance with the standard specification. This change
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corresponds to changes to programs in the Staden package,
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which are included in release 1993.0 of the package.
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Thu Jan 21 15:29:56 GMT 1993
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----------------------------
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genbentryname1.c
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The sequence offsets created in the entryname index were
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calculated wrongly. With the use with the Staden package
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it caused the first line of the entry to be omitted.
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genbaccession.script
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genbauthor.script
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genbdivision.script
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genbentryname.script
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genbfreetext.script
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genbtitle.script
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Genbank has 13 divisions
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division.c
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genbdivision.script
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pirdivision.script
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Routines and scripts to create division lookup files.
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Thu Jul 16 17:27:43 BST 1992
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----------------------------
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freetext.c
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Look for words in "OG" (EMBL/SWISSPROT) and "GN" (SWISSPROT)
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lines.
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Tue Jun 16 16:56:09 BST 1992
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----------------------------
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freetext4.c
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hitNtrg.c
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Creation of author and freetext indexes was in error. Each
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occurrance of author/word in the final sorted list was being written
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to the target file, rather than just once as it should have been.
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This bug did not affect the functionality but only the performance
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of the Staden programs that use the indexes.
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Wed May 20 10:43:56 BST 1992
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----------------------------
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title2.c
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entryname2.c
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In the embl updates it is possible that an entry appears more
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than once. These programs have been modified so that they ignore
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all but the first occurrence of the entry name, so that the brief
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and entryname index have the correct number of entries. This is
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not a clean solution, as words, authors, and accession numbers
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for the more recent entry won't appear in the annotation of the
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entry.
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Wed May 13 17:22:09 BST 1992
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----------------------------
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author.c
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hitNtrg.c
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emblauthor.script
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pirauthor.script
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genbauthor.script
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swissauthor.script
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Programs and scripts to create the new author indexes have been
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written. They are based closely on the freetext index. The program
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hitNtrg.c is almost identical to freetext4.c but takes the string
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length to be written to the target file from the command line.
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It is possible to write the accession number creation routines
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in the same fashion.
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Wed Apr 1 16:33:11 BST 1992
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----------------------------
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freetext4.c Version 1.1
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Words that were longer than target file field width were not being
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truncated, thus corrupting the index. Fixed.
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embltitle1.c Version 1.1
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pirtitle1.c Version 1.1
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pirtitle2.c Version 1.1
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genbtitle1.c Version 1.1
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From some sources, the sequence libraries end each line with a
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carriage return followed by a new line character. The programs
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were changed to filter out non-printable characters in the title
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lines.
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Wed Apr 1 18:48:12 BST 1992
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----------------------------
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genbaccession.script Version 1.1
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piraccession.script Version 1.1
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The second sort in these scripts was in error, causing the file
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access.sorted2 to in fact no be sorted on accession number. The
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command "${SORT} +1 +0..." should have been "${SORT} -b +1...".
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Wed Apr 22 1992
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---------------
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freetext.c Version 1.1
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The line offset for PIR should be 16 not 15. This would only affect
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libraries where the 10th character of the entry name is significant
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and excluding it would result in a different sort order.
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author.c Version 1.0
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A new program for extracting author names from sequence libraries.
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We have yet to see the EMBL CR-ROM author indexes, so this program
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may change. No scripts written yet. Subsequence processing of output
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file will include:
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1) Sorting on entry name, removing duplicate entry-name/author
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entries. (sort -u ...)
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2) Assigning entry numbers, using freetext2.c
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3) Sorting on author name. (sort -b +1 ...)
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4) Creation of indexes with program similar to freetext4 (differing
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only by the fact that the target string will be a different size.)
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