Display basic information about sequences Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequence] seqall (Gapped) sequence(s) filename and optional format, or reference (input USA) Additional (Optional) qualifiers: -outfile outfile [stdout] If you enter the name of a file here then this program will write the sequence details into that file. -html boolean [N] Format output as an HTML table Advanced (Unprompted) qualifiers: -[no]columns boolean [Y] Set this option on (Y) to print the sequence information into neat, aligned columns in the output file. Alternatively, leave it unset (N), in which case the information records will be delimited by a character, which you may specify by using the -delimiter option. In other words, if -columns is set on, the -delimiter option is overriden. -delimiter string [|] This string, which is usually a single character only, is used to delimit individual records in the text output file. It could be a space character, a tab character, a pipe character or any other character or string. (Any string) -only boolean [N] This is a way of shortening the command line if you only want a few things to be displayed. Instead of specifying: '-nohead -noname -noacc -notype -nopgc -nodesc' to get only the length output, you can specify '-only -length' -[no]heading boolean [Y] Display column headings -usa boolean [@(!$(only))] Display the USA of the sequence -database boolean [@(!$(only))] Display 'database' column -name boolean [@(!$(only))] Display 'name' column -accession boolean [@(!$(only))] Display 'accession' column -gi boolean [N] Display 'GI' column -seqversion boolean [N] Display 'version' column -type boolean [@(!$(only))] Display 'type' column -length boolean [@(!$(only))] Display 'length' column -pgc boolean [@(!$(only))] Display 'percent GC content' column -organism boolean [@(!$(only))] Display 'organism' column -description boolean [@(!$(only))] Display 'description' column Associated qualifiers: "-sequence" associated qualifiers -sbegin1 integer Start of each sequence to be used -send1 integer End of each sequence to be used -sreverse1 boolean Reverse (if DNA) -sask1 boolean Ask for begin/end/reverse -snucleotide1 boolean Sequence is nucleotide -sprotein1 boolean Sequence is protein -slower1 boolean Make lower case -supper1 boolean Make upper case -sformat1 string Input sequence format -sdbname1 string Database name -sid1 string Entryname -ufo1 string UFO features -fformat1 string Features format -fopenfile1 string Features file name "-outfile" associated qualifiers -odirectory string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit maleevacobalt@kodomo:~/term2/block1/pr1$ less infoseq_help.txt maleevacobalt@kodomo:~/term2/block1/pr1$ infoseq -help -verbose >infoseq_help.txt Display basic information about sequences Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequence] seqall (Gapped) sequence(s) filename and optional format, or reference (input USA) Additional (Optional) qualifiers: -outfile outfile [stdout] If you enter the name of a file here then this program will write the sequence details into that file. -html boolean [N] Format output as an HTML table Advanced (Unprompted) qualifiers: -[no]columns boolean [Y] Set this option on (Y) to print the sequence information into neat, aligned columns in the output file. Alternatively, leave it unset (N), in which case the information records will be delimited by a character, which you may specify by using the -delimiter option. In other words, if -columns is set on, the -delimiter option is overriden. -delimiter string [|] This string, which is usually a single character only, is used to delimit individual records in the text output file. It could be a space character, a tab character, a pipe character or any other character or string. (Any string) -only boolean [N] This is a way of shortening the command line if you only want a few things to be displayed. Instead of specifying: '-nohead -noname -noacc -notype -nopgc -nodesc' to get only the length output, you can specify '-only -length' -[no]heading boolean [Y] Display column headings -usa boolean [@(!$(only))] Display the USA of the sequence -database boolean [@(!$(only))] Display 'database' column -name boolean [@(!$(only))] Display 'name' column -accession boolean [@(!$(only))] Display 'accession' column -gi boolean [N] Display 'GI' column -seqversion boolean [N] Display 'version' column -type boolean [@(!$(only))] Display 'type' column -length boolean [@(!$(only))] Display 'length' column -pgc boolean [@(!$(only))] Display 'percent GC content' column -organism boolean [@(!$(only))] Display 'organism' column -description boolean [@(!$(only))] Display 'description' column Associated qualifiers: "-sequence" associated qualifiers -sbegin1 integer Start of each sequence to be used -send1 integer End of each sequence to be used -sreverse1 boolean Reverse (if DNA) -sask1 boolean Ask for begin/end/reverse -snucleotide1 boolean Sequence is nucleotide -sprotein1 boolean Sequence is protein -slower1 boolean Make lower case -supper1 boolean Make upper case -sformat1 string Input sequence format -sdbname1 string Database name -sid1 string Entryname -ufo1 string UFO features -fformat1 string Features format -fopenfile1 string Features file name "-outfile" associated qualifiers -odirectory string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit