Gene Selkov, Jr. > Finnigan > uf-trailer

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NAME ^

uf-trailer - examine the ScanEvent structures in a Finnigan raw file "trailer"

SYNOPSIS ^

uf-trailer [options] file

 Options:

  -a[ll]                         process all ScanEvent objects
  -c[oefficients]                print the table of conversion coefficients
  -n[unmber] <n:0+n>             extract ScanEvent number <n>
  -range <from:0+n> .. <to:0+n>  extract ScanEvent objects with numbers between <from> and <to>
  -d[ump]                        dump all data in each ScanEvent
  -h[tml]                        dump as html
  -w[iki]                        dump in wiki table format
  -r[elative]                    show relative addersess in dump
  -p[reamble]                    include the full listing of ScanEventPreamble
  <file>                         input file

OPTIONS ^

-help

Print a brief help message and exits.

-d[ump]

Prints a table listing all fields in ScanEvent entries, with their seek addresses, sizes, names and values. Individual entries can be selected with the -n[umber] option or with the -range option.

-n[umber]

Gives the number of a single ScanEvent to process

-r[ange]

Selects a range of the ScanEvent records to process

-h[tml]

Format the dump output as an html table. When multiple entries are specified, each will be rendered in its own table

-w[iki]

Format the dump output as a wiki table.

-r[elative]

Show relative addresses of all itmes in the dump. The default is to show the absolute seek address. (works with the -d[ump] option)

-a[ll]

Process all entries, including those that may lie outside the declared range. It appears as though it can be possible to find more index entries in the file than would fit between the first and the last scan numbers specified in RunHeader/SampleInfo. In that case, in the absence of the -all option, the entries will be enumerated according to ScanIndex, which will be treated as a linked list -- starting with the entry whose index matches the first scan number.

-p[reamble]

Show the translated scan event preamble for each scan on one line (useful for comparison and for spotting changes).

DESCRIPTION ^

uf-trailer can be used to list or dump the ScanEvent records in a Finnigan raw file. These records are stored in a stream Thermo calls a "trailer", which occurs near the end of the file. Now, the "trailer" containing scan event descriptions is not the only stream trailing the data; apparently, new ones were added as the format evolved, but the name stuck. The code in Thermo libraries refers to this stream as "TrailerScanEvent".

SEE ALSO ^

Finnigan::ScanEvent

Finnigan::ScanEventPreamble

Finnigan::FractionCollector

Finnigan::Reaction

EXAMPLES ^

List all scan events in the file using Thermo's short-hand notation known as "filter line":
  uf-trailer sample.raw
List the first five records:
  uf-trailer -range 1 .. 5 sample.raw
Dump the fifth ScanEvent with relative addresses:
  uf-trailer -drn 5 sample.raw
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