From 724550160a6440b1dabc53ebae0e3ad8905ac9ce Mon Sep 17 00:00:00 2001 From: martinahansen Date: Wed, 2 Jul 2008 05:10:42 +0000 Subject: [PATCH] even more wikis git-svn-id: http://biopieces.googlecode.com/svn/trunk@100 74ccb610-7750-0410-82ae-013aeee3265d --- bp_usage/complement_seq | 16 -------- bp_usage/complement_seq.wiki | 56 ++++++++++++++++++++++++++++ bp_usage/count_records | 19 ---------- bp_usage/count_records.wiki | 65 +++++++++++++++++++++++++++++++++ bp_usage/reverse_seq | 17 --------- bp_usage/reverse_seq.wiki | 71 ++++++++++++++++++++++++++++++++++++ bp_usage/uppercase_seq | 17 --------- bp_usage/uppercase_seq.wiki | 70 +++++++++++++++++++++++++++++++++++ 8 files changed, 262 insertions(+), 69 deletions(-) delete mode 100644 bp_usage/complement_seq create mode 100644 bp_usage/complement_seq.wiki delete mode 100644 bp_usage/count_records create mode 100644 bp_usage/count_records.wiki delete mode 100644 bp_usage/reverse_seq create mode 100644 bp_usage/reverse_seq.wiki delete mode 100644 bp_usage/uppercase_seq create mode 100644 bp_usage/uppercase_seq.wiki diff --git a/bp_usage/complement_seq b/bp_usage/complement_seq deleted file mode 100644 index c6d57c8..0000000 --- a/bp_usage/complement_seq +++ /dev/null @@ -1,16 +0,0 @@ -Author: Martin Asser Hansen - Copyright (C) - All rights reserved - -Contact: mail@maasha.dk - -Date: August 2007 - -License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html) - -Description: Complement sequences in stream. - -Usage: ... | $script [options] - -Options: [-I | --stream_in=] - Read input from stream file - Default=STDIN -Options: [-O | --stream_out=] - Write output to stream file - Default=STDOUT - -Examples: ... | $script - Complements all sequences in stream. diff --git a/bp_usage/complement_seq.wiki b/bp_usage/complement_seq.wiki new file mode 100644 index 0000000..fb573bc --- /dev/null +++ b/bp_usage/complement_seq.wiki @@ -0,0 +1,56 @@ +=Biopiece: complement_seq= + +==Synopsis== + +Complement nucleotide sequences in the stream. + +==Description== + +[complement_seq] complements nucleotide sequences in the stream which along with [reverse_seq] +results in reverse/complemented sequence. + +==Usage== + +{{{ +... | complement_seq [options] +}}} + +==Options== + +{{{ +[-I | --stream_in=] - Read input from stream file - Default=STDIN +[-O | --stream_out=] - Write output to stream file - Default=STDOUT +}}} + +==Examples== + +To reverse complement sequence first reverse the sequence with [reverse_seq] and then +complement it using [complement_seq] (or visa versa): + +{{{ +... | complement_seq | reverse_seq +}}} + +==See also== + +[reverse_seq] + +==Author== + +Martin Asser Hansen - Copyright (C) - All rights reserved. + +mail@maasha.dk + +August 2007 + +==License== + +GNU General Public License version 2 + +http://www.gnu.org/copyleft/gpl.html + +==Help== + +[complement_seq] is part of the Biopieces framework. + +http://code.google.com/p/biopieces/ diff --git a/bp_usage/count_records b/bp_usage/count_records deleted file mode 100644 index 8662a50..0000000 --- a/bp_usage/count_records +++ /dev/null @@ -1,19 +0,0 @@ -Author: Martin Asser Hansen - Copyright (C) - All rights reserved - -Contact: mail@maasha.dk - -Date: August 2007 - -License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html) - -Description: Count the number of records in stream. - -Usage: ... | count_records [options] - -Options: [-x | --no_stream] - Do not emit records. -Options: [-o | --data_out=] - Write result to file. -Options: [-I | --stream_in=] - Read input from stream file - Default=STDIN -Options: [-O | --stream_out=] - Write output to stream file - Default=STDOUT - -Examples: ... | count_records -x -o count.txt - Count records in stream and write result to 'count.txt' - diff --git a/bp_usage/count_records.wiki b/bp_usage/count_records.wiki new file mode 100644 index 0000000..53b802b --- /dev/null +++ b/bp_usage/count_records.wiki @@ -0,0 +1,65 @@ +=Biopiece: count_records= + +==Synopsis== + +Count the number of records in the stream. + +==Description== + +[count_records] count the number of records in the stream and outputs the count as a +record who's count is _not_ included. Using [count_recrods] with the `-x` switch is +a lot faster because this prevents the need for parsing and emitting the records. + +==Usage== + +{{{ +... | count_records [options] +}}} + +==Options== + +{{{ +[-x | --no_stream] - Do not emit records. +[-o | --data_out=] - Write result to file. +[-I | --stream_in=] - Read input from stream file - Default=STDIN +[-O | --stream_out=] - Write output to stream file - Default=STDOUT +}}} + +==Examples== + +To count the records in the stream and saving the result to file, do: + +{{{ +... | count_record -o +}}} + +The resulting file will then contain some thing like this: + +{{{ +count_records: 1234 +--- +}}} + +==See also== + +[count_vals] + +==Author== + +Martin Asser Hansen - Copyright (C) - All rights reserved. + +mail@maasha.dk + +August 2007 + +==License== + +GNU General Public License version 2 + +http://www.gnu.org/copyleft/gpl.html + +==Help== + +[count_records] is part of the Biopieces framework. + +http://code.google.com/p/biopieces/ diff --git a/bp_usage/reverse_seq b/bp_usage/reverse_seq deleted file mode 100644 index 594ec8b..0000000 --- a/bp_usage/reverse_seq +++ /dev/null @@ -1,17 +0,0 @@ -Author: Martin Asser Hansen - Copyright (C) - All rights reserved - -Contact: mail@maasha.dk - -Date: August 2007 - -License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html) - -Description: Reverse sequences in stream. - -Usage: ... | reverse_seq [options] - -Options: [-I | --stream_in=] - Read input from stream file - Default=STDIN -Options: [-O | --stream_out=] - Write output to stream file - Default=STDOUT - -Examples: ... | reverse_seq - Reverses all sequences in stream. - diff --git a/bp_usage/reverse_seq.wiki b/bp_usage/reverse_seq.wiki new file mode 100644 index 0000000..41d9225 --- /dev/null +++ b/bp_usage/reverse_seq.wiki @@ -0,0 +1,71 @@ +=Biopiece: reverse_seq= + +==Synopsis== + +Reverse sequences in the stream. + +==Description== + +[reverse_seq] reverses sequences in the stream which is useful for extracting subsequences +[extract_seq] or reverse complementing sequence [complement_seq]. + +==Usage== + +{{{ +... | reverse_seq [options] +}}} + +==Options== + +{{{ +[-I | --stream_in=] - Read input from stream file - Default=STDIN +[-O | --stream_out=] - Write output to stream file - Default=STDOUT +}}} + +==Examples== + +To reverse sequences simply pipe the stream through [reverse_seq]: + +{{{ +... | reverse_seq +}}} + +To reverse complement sequence first reverse the sequence with [reverse_seq] and then +complement it using [complement_seq] (or visa versa): + +{{{ +... | reverse_seq | complement_seq +}}} + +To obtain the last e.g. five residues from all sequences, first use [reverse_seq], then [extract_seq], +and then re-reverse with [reverse_seq]: + +{{{ +... | reverse_seq | extract_seq -l 5 | reverse_seq +}}} + +==See also== + +[complement_seq] + +[extract_seq] + +==Author== + +Martin Asser Hansen - Copyright (C) - All rights reserved. + +mail@maasha.dk + +August 2007 + +==License== + +GNU General Public License version 2 + +http://www.gnu.org/copyleft/gpl.html + +==Help== + +[reverse_seq] is part of the Biopieces framework. + +http://code.google.com/p/biopieces/ diff --git a/bp_usage/uppercase_seq b/bp_usage/uppercase_seq deleted file mode 100644 index bc7c441..0000000 --- a/bp_usage/uppercase_seq +++ /dev/null @@ -1,17 +0,0 @@ -Author: Martin Asser Hansen - Copyright (C) - All rights reserved - -Contact: mail@maasha.dk - -Date: August 2007 - -License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html) - -Description: Uppercases sequences in stream. - -Usage: ... | uppercase_seq [options] - -Options: [-I | --stream_in=] - Read input from stream file - Default=STDIN -Options: [-O | --stream_out=] - Write output to file - Default=STDOUT - -Examples: ... | uppercase_seq - Uppercases all sequences in stream. - diff --git a/bp_usage/uppercase_seq.wiki b/bp_usage/uppercase_seq.wiki new file mode 100644 index 0000000..4813153 --- /dev/null +++ b/bp_usage/uppercase_seq.wiki @@ -0,0 +1,70 @@ +=Biopiece: uppercase_seq= + +==Synopsis== + +Uppercases sequences in stream. + +==Description== + +[upppercase_seq] changes all lowercase letter in sequences to uppercase letters. + +==Usage== + +{{{ +... | uppercase_seq [options] +}}} + +==Options== + +{{{ +[-I | --stream_in=] - Read input from stream file - Default=STDIN +[-O | --stream_out=] - Write output to stream file - Default=STDOUT +}}} + +==Examples== + +Consider the following sequence entry in FASTA format in the file `test.fna`: + +{{{ +>test +ACGACGCATNNNNNNactgatcga +}}} + +To read in this sequence use [read_fasta] and then [uppercase_seq] to uppercase all letters: + +{{{ +read_fasta -i test.fna | uppercase_seq + +SEQ: ACGACGCATNNNNNNACTGATCGA +SEQ_NAME: test +SEQ_LEN: 24 +--- +}}} + +==See also== + +[read_fasta] + +[transliterate_seq] + +[transliterate_vals] + +==Author== + +Martin Asser Hansen - Copyright (C) - All rights reserved. + +mail@maasha.dk + +August 2007 + +==License== + +GNU General Public License version 2 + +http://www.gnu.org/copyleft/gpl.html + +==Help== + +[uppercase_seq] is part of the Biopieces framework. + +http://code.google.com/p/biopieces/ -- 2.39.5