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Shell Programming and Scripting
Perl to parse
Post 302939340 by cmccabe on Tuesday 24th of March 2015 07:00:37 PM
03-24-2015
In the attached file the lastline:
NM_004004.5:c.35delG NC_000013.10:g.20763686delC NM_004004.5:c.35delG XM_005266354.1:c.35delG XM_005266355.1:c.35delG XM_005266356.1:c.35delG and the third column (the header row is skipped) NC_000013.10:g.20763686delC is the column/field to be parsed into the desired output: 13 20763686 20763686 C -
there is no "-" in the file the only indicator is in $5 there is a "-" to signify a deletion.
The code in the post seems to work for the first and second case (where there is a >), but not for the third (del).
Thank you
.
NM_004004.5:c.35delG NC_000013.10:g.20763686delC NM_004004.5:c.35delG XM_005266354.1:c.35delG XM_005266355.1:c.35delG XM_005266356.1:c.35delG and the third column (the header row is skipped) NC_000013.10:g.20763686delC is the column/field to be parsed into the desired output: 13 20763686 20763686 C -
there is no "-" in the file the only indicator is in $5 there is a "-" to signify a deletion.
The code in the post seems to work for the first and second case (where there is a >), but not for the third (del).
Thank you
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LEARN ABOUT LINUX
psc
PSC(1) General Commands Manual PSC(1) NAME
psc - prepare sc files SYNOPSIS
psc [-fLkrSPv] [-s cell] [-R n] [-C n] [-n n] [-d c] DESCRIPTION
Psc is used to prepare data for input to the spreadsheet calculator sc(1). It accepts normal ascii data on standard input. Standard out- put is a sc file. With no options, psc starts the spreadsheet in cell A0. Strings are right justified. All data on a line is entered on the same row; new input lines cause the output row number to increment by one. The default delimiters are tab and space. The column for- mats are set to one larger than the number of columns required to hold the largest value in the column. OPTIONS
-f Omit column width calculations. This option is for preparing data to be merged with an existing spreadsheet. If the option is not specified, the column widths calculated for the data read by psc will override those already set in the existing spreadsheet. -L Left justify strings. -k Keep all delimiters. This option causes the output cell to change on each new delimiter encountered in the input stream. The default action is to condense multiple delimiters to one, so that the cell only changes once per input data item. -r Output the data by row first then column. For input consisting of a single column, this option will result in output of one row with multiple columns instead of a single column spreadsheet. -s cell Start the top left corner of the spreadsheet in cell. For example, -s B33 will arrange the output data so that the spreadsheet starts in column B, row 33. -R n Increment by n on each new output row. -C n Increment by n on each new output column. -n n Output n rows before advancing to the next column. This option is used when the input is arranged in a single column and the spreadsheet is to have multiple columns, each of which is to be length n. -d c Use the single character c as the delimiter between input fields. -P Plain numbers only. A field is a number only when there is no imbedded [-+eE]. -S All numbers are strings. -v Print the version of psc SEE ALSO
sc(1) AUTHOR
Robert Bond PSC 7.16 19 September 2002 PSC(1)