[med-svn] [kmer-tools] 04/12: Add manpage for leaff
Afif Elghraoui
afif-guest at moszumanska.debian.org
Sun Jan 3 00:54:25 UTC 2016
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afif-guest pushed a commit to branch master
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commit b16659624c45a0bce2f5c5c3334e38e8ca841d15
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Sat Jan 2 15:35:10 2016 -0800
Add manpage for leaff
---
debian/leaff.manpages | 1 +
debian/man/leaff/leaff.1 | 159 +++++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 160 insertions(+)
diff --git a/debian/leaff.manpages b/debian/leaff.manpages
new file mode 100644
index 0000000..d8b5032
--- /dev/null
+++ b/debian/leaff.manpages
@@ -0,0 +1 @@
+debian/man/leaff/*.1
diff --git a/debian/man/leaff/leaff.1 b/debian/man/leaff/leaff.1
new file mode 100644
index 0000000..7263cd7
--- /dev/null
+++ b/debian/man/leaff/leaff.1
@@ -0,0 +1,159 @@
+.TH LEAFF 1 "January 2016"
+.SH NAME
+leaff \- sequence library utilities and applications
+.SH SYNOPSIS
+.B leaff
+[-f fasta-file] [options]
+.SH DESCRIPTION
+LEAFF (Let's Extract Anything From Fasta) is a utility program for
+working with multi-fasta files. In addition to providing random access
+to the base level, it includes several analysis functions.
+.SH OPTIONS
+SOURCE FILES
+ -f file: use sequence in 'file' (-F is also allowed for historical reasons)
+ -A file: read actions from 'file'
+
+SOURCE FILE EXAMINATION
+ -d: print the number of sequences in the fasta
+ -i name: print an index, labelling the source 'name'
+
+OUTPUT OPTIONS
+ -6 <#>: insert a newline every 60 letters
+ (if the next arg is a number, newlines are inserted every
+ n letters, e.g., -6 80. Disable line breaks with -6 0,
+ or just don't use -6!)
+ -e beg end: Print only the bases from position 'beg' to position 'end'
+ (space based, relative to the FORWARD sequence!) If
+ beg == end, then the entire sequence is printed. It is an
+ error to specify beg > end, or beg > len, or end > len.
+ -ends n Print n bases from each end of the sequence. One input
+ sequence generates two output sequences, with '_5' or '_3'
+ appended to the ID. If 2n >= length of the sequence, the
+ sequence itself is printed, no ends are extracted (they
+ overlap).
+ -C: complement the sequences
+ -H: DON'T print the defline
+ -h: Use the next word as the defline ("-H -H" will reset to the
+ original defline
+ -R: reverse the sequences
+ -u: uppercase all bases
+
+SEQUENCE SELECTION
+ -G n s l: print n randomly generated sequences, 0 < s <= length <= l
+ -L s l: print all sequences such that s <= length < l
+ -N l h: print all sequences such that l <= % N composition < h
+ (NOTE 0.0 <= l < h < 100.0)
+ (NOTE that you cannot print sequences with 100% N
+ This is a useful bug).
+ -q file: print sequences from the seqid list in 'file'
+ -r num: print 'num' randomly picked sequences
+ -s seqid: print the single sequence 'seqid'
+ -S f l: print all the sequences from ID 'f' to 'l' (inclusive)
+ -W: print all sequences (do the whole file)
+
+LONGER HELP
+ -help analysis
+ -help examples
+
+ANALYSIS FUNCTIONS
+ --findduplicates a.fasta
+ Reports sequences that are present more than once. Output
+ is a list of pairs of deflines, separated by a newline.
+
+ --mapduplicates a.fasta b.fasta
+ Builds a map of IIDs from a.fasta and b.fasta that have
+ identical sequences. Format is "IIDa <-> IIDb"
+
+ --md5 a.fasta:
+ Don't print the sequence, but print the md5 checksum
+ (of the entire sequence) followed by the entire defline.
+
+ --partition prefix [ n[gmk]bp | n ] a.fasta
+ --partitionmap [ n[gmk]bp | n ] a.fasta
+ Partition the sequences into roughly equal size pieces of
+ size nbp, nkbp, nmbp or ngbp; or into n roughly equal sized
+ parititions. Sequences larger that the partition size are
+ in a partition by themself. --partitionmap writes a
+ description of the partition to stdout; --partiton creates
+ a fasta file 'prefix-###.fasta' for each partition.
+ Example: -F some.fasta --partition parts 130mbp
+ -F some.fasta --partition parts 16
+
+ --segment prefix n a.fasta
+ Splits the sequences into n files, prefix-###.fasta.
+ Sequences are not reordered; the first n sequences are in
+ the first file, the next n in the second file, etc.
+
+ --gccontent a.fasta
+ Reports the GC content over a sliding window of
+ 3, 5, 11, 51, 101, 201, 501, 1001, 2001 bp.
+
+ --testindex a.fasta
+ Test the index of 'file'. If index is up-to-date, leaff
+ exits successfully, else, leaff exits with code 1. If an
+ index file is supplied, that one is tested, otherwise, the
+ default index file name is used.
+
+ --dumpblocks a.fasta
+ Generates a list of the blocks of N and non-N. Output
+ format is 'base seq# beg end len'. 'N 84 483 485 2' means
+ that a block of 2 N's starts at space-based position 483
+ in sequence ordinal 84. A '.' is the end of sequence
+ marker.
+
+ --errors L N C P a.fasta
+ For every sequence in the input file, generate new
+ sequences including simulated sequencing errors.
+ L -- length of the new sequence. If zero, the length
+ of the original sequence will be used.
+ N -- number of subsequences to generate. If L=0, all
+ subsequences will be the same, and you should use
+ C instead.
+ C -- number of copies to generate. Each of the N
+ subsequences will have C copies, each with different
+ errors.
+ P -- probability of an error.
+
+ HINT: to simulate ESTs from genes, use L=500, N=10, C=10
+ -- make C=10 sequencer runs of N=10 EST sequences
+ of length 500bp each.
+ to simulate mRNA from genes, use L=0, N=10, C=10
+ to simulate reads from genomes, use L=800, N=10, C=1
+ -- of course, N= should be increased to give the
+ appropriate depth of coverage
+
+ --stats a.fasta
+ Reports size statistics; number, N50, sum, largest.
+
+ --seqstore out.seqStore
+ Converts the input file (-f) to a seqStore file (for instance,
+ for use with the Celera assembler or sim4db).
+.SH NOTES
+Please note that options are ORDER DEPENDENT. Sequences are printed
+whenever a SEQUENCE SELECTION option occurs on the command line. OUTPUT
+OPTIONS are not reset when a sequence is printed.
+.PP
+SEQUENCES are numbered starting at ZERO, not one!
+.SH EXAMPLES
+1. Print the first 10 bases of the fourth sequence in file 'genes':
+.br
+ leaff -f genes -e 0 10 -s 3
+
+2. Print the first 10 bases of the fourth and fifth sequences:
+.br
+ leaff -f genes -e 0 10 -s 3 -s 4
+
+3. Print the fourth and fifth sequences reverse complemented, and the sixth
+ sequence forward. The second set of -R -C toggle off reverse-complement:
+.br
+ leaff -f genes -R -C -s 3 -s 4 -R -C -s 5
+
+4. Convert file 'genes' to a seqStore 'genes.seqStore'.
+.br
+ leaff -f genes --seqstore genes.seqStore
+.SH SEE ALSO
+README.leaff
+.br
+http://kmer.sourceforge.net/wiki/index.php/LEAFF_User%27s_Guide
+.br
+http://kmer.sourceforge.net/wiki/index.php/LEAFF_Programming_Example
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