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Last update on 28. Nov 2017 .
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How to define new import formats

OCCURRENCE

ARB_NT

 

BRIEF DESCRIPTION

Import filters delivered together with ARB are located in the directory '$ARBHOME/lib/import'. Their file extension has to be '.ift'!

To customize your own import filters, click on the 'Test'-button in the import window (see ´Test import filter´).

Note: If multiple users should be able to use a customized filter, you need to copy that filter from '~/.arb_prop/filter' into '$ARBHOME/lib/import'.

Each of the import filters describes how to analyze and read files of one specific format.

A basic import description file (.ift) looks like this:

[AUTODETECT     "Matchpattern"]
BEGIN           "Matchpattern"
[KEYWIDTH       #Columnnumber]
[AUTOTAG        ["TAGNAME"]]
[IFNOTSET       x "Reason why x is not set"]+
[SETGLOBAL      x "global value"]+
[INCLUDE        "file"]+
[DESCRIPTION    "text describing import filter"]+
[MATCH          "Matchpattern"
        [SRT            "SRT_STRING"]
        [ACI            "ACI_STRING"]
        [TAG            "TAGNAME"]
        [WRITE          "DB_FIELD_NAME"]
        [WRITE_INT      "DB_FIELD_NAME"]
        [WRITE_FLOAT    "DB_FIELD_NAME"]
        [APPEND         "DB_FIELD_NAME"]
        [SETVAR         x]
]*
SEQUENCESTART   "Matchpattern"
SEQUENCECOLUMN  #Columnnumber
[SEQUENCESRT    "SRT_STRING"]
[SEQUENCEACI    "ACI_STRING"]
SEQUENCEEND     "STRING"
[CREATE_ACC_FROM_SEQUENCE]
[DONT_GEN_NAMES]
END             "STRING"

or it can pipe the data through any external program PROGRAM to convert it to an already existing format 'exformat' using the following basic design:

[AUTODETECT     "Matchpattern"]
SYSTEM          "PROGRAM $< $>"
NEW_FORMAT      "lib/import/exformat.ift"

$< will be replaced by the input file name $> will ve replaced by the intermediate file name

 

DESCRIPTION

First of all the converter appends all import files maching
the filepattern into one file. The files are separated by the
string defined with the keyword  SEQUENCEEND.
  1. Search the first line matching the pattern defined by BEGIN
  2. Try to match all MATCH_patterns.
    For all lines that match do:
    • append all following lines, which start after column KEYWIDTH
    • run commands with the concatenated lines

    Known commands are (they are executed in the order listed here):
    • SRT "SRT_STRING"
      start the string replace tool on the current result and set the output as current result (see ´Search and Replace Tool (SRT)´).
    • ACI "ACI_STRING"
      run the arb command interpreter to change the current result (see ´ARB Command Interpreter (ACI)´).
    • TAG "TAGNAME"
      tag information (i.e. "[EBI] 1997 [RDP] 1998")
    • WRITE "DB_FIELD_NAME"
      write the current result into DB_FIELD_NAME
    • WRITE_INT "DB_FIELD_NAME"
      like WRITE, but expect integer target field
    • WRITE_FLOAT "DB_FIELD_NAME"
      like WRITE, but expect floating-point target field
    • APPEND "DB_FIELD_NAME"
      append the current result to DB_FIELD_NAME
    • SETVAR x
      store the current result in the variable x, where x may be any character. After it was set this variable can be referenced by using $x in any command expression (SRT_STRING,ACI_STRING,TAGNAME,DB_FIELD_NAME).
      For each used variable there has to be defined an error reason describing, what's wrong if the variable has NOT been set. Define error reasons using
      IFNOTSET x "Reason why x is not set"
      Note: use '$$' to insert a single '$'.
      Allowed variable names are 'a' to 'z'.

    Note: Every of these commands may only occur once in one MATCH rule.
          To run some of them multiple, create multiple MATCH rules.
  3. If the line matches SEQUENCESTART_pattern, assume that all following lines to and except the line matching SEQUENCEEND_pattern contain the sequence data.
  4. GOTO 1

Postprocesses:

CREATE_ACC_FROM_SEQUENCE:
Generate a checksum for all sequences with no accession entry ('acc' -field) and write it as the accession number
DONT_GEN_NAMES:
Do not try to generate unique identifiers (shortnames) for the species using the full_name field.

General commands:

INCLUDE "filename"
Simply inserts the contents of "filename" at the current position.
It's possible to declare variables in the file where the INCLUDE happens and to use them in the included file. (Example: longebi.ift, longgenbank.ift and feature_table.ift in subdir nonformats)
SETGLOBAL x "value"
Sets global variable 'x' to 'value'.
AUTOTAG ["TAGNAME"]
If set, act like each MATCH rule has a
   TAG "TAGNAME"
entry. Use AUTOTAG w/o parameter to reset
to default behavior.
 

EXAMPLES

Look at the files in '$ARBHOME/lib/import'

 

WARNINGS

Format detection does not always work