NAME
App::Sandy::Command::Custom - simulate command class. Simulate a custom sequencing
VERSION
version 0.17
SYNOPSIS
sandy custom [options] <fasta-file>
Arguments:
a fasta-file
Options:
-h, --help brief help message
-M, --man full documentation
-v, --verbose print log messages
-p, --prefix prefix output [default:"out"]
-o, --output-dir output directory [default:"."]
-i, --append-id append to the defined template id [Format]
-I, --id overlap the default template id [Format]
-j, --jobs number of jobs [default:"1"; Integer]
-z, --gzip compress output file
-s, --seed set the seed of the base generator
[default:"time()"; Integer]
-c, --coverage fastq-file coverage [default:"8", Number]
-n, --number-of-reads directly set the number of reads [Integer]
-t, --sequencing-type single-end or paired-end reads
[default:"paired-end"]
-q, --quality-profile sequencing system profiles from quality
database [default:"poisson"]
-e, --sequencing-error sequencing error rate
[default:"0.005"; Number]
-r, --read-size the read size [default:"100"; Integer]
the quality_profile from database overrides
this value
-m, --fragment-mean the mean size fragments for paired-end reads
[default:"300"; Integer]
-d, --fragment-stdd the standard deviation for fragment sizes
[default:"50"; Integer]
-b, --strand-bias which strand to be used: plus, minus and random
[default:"random"]
-w, --seqid-weight seqid raffle type: length, same, count
[default: "length"]
-f, --expression-matrix an expression-matrix entry from database,
when seqid-weight=countDESCRIPTION
Simulate a custom sequencing.
OPTIONS
- --help
-
Print a brief help message and exits.
- --man
-
Prints the manual page and exits.
- --verbose
-
Prints log information to standard error
- --prefix
-
Concatenates the prefix to the output-file name.
- --output-dir
-
Creates output-file inside output-dir. If output-dir does not exist, it is created recursively
- --append-id
-
Append string template to the defined template id. See Format
- --id
-
Overlap the default defined template id: single-end %i.%U %U and paired-end %i.%U %U e.g. SR123.1 1 See Format
- Format
-
A string Format is a combination of literal and escape characters similar to the way printf works. That way, the user has the freedom to customize the fastq sequence identifier to fit her needs. Valid escape characteres are:
Common escape characters
Escape Meaning ------ ------------------------------------------ %i instrument id composed by SR + PID %I job slot number %q quality profile %e sequencing error %x sequencing error position %R read 1, or 2 if it is the paired-end mate %U read number %r read size %c sequence id as chromossome, ref %s read or fragment strand %t read start position %n read end positionPaired-end specific escape characters
Escape Meaning ------ ------------------------------------------ %T mate read start position %N mate read end position %D distance between the paired-reads %m fragment mean %d fragment standard deviation %f fragment size %S fragment start position %E fragment end position - --jobs
-
Sets the number of child jobs to be created
- --gzip
-
Compress the output-file with gzip algorithm. It is possible to pass --no-gzip if one wants uncompressed output-file
- --seed
-
Sets the seed of the base generator. The ability to set the seed is useful for those who want reproducible simulations. Pay attention to the number of jobs (--jobs) set, because each job receives a different seed calculated from the main seed. So, for reproducibility, the same seed set before needs the same number of jobs set before as well.
- --read-size
-
Sets the read size, if quality-profile is equal to 'poisson'. The quality-profile from database overrides the read-size
- --coverage
-
Calculates the number of reads based on the sequence coverage: number_of_reads = (sequence_size * coverage) / read_size
- --number-of-reads
-
Sets directly the number of reads desired. It overrides coverage, in case the two options are given
- --sequencing-type
-
Sets the sequencing type to single-end or paired-end
- --fragment-mean
-
If the sequencing-type is set to paired-end, it sets the fragment mean
- --fragment-stdd
-
If the sequencing-type is set to paired-end, it sets the fragment standard deviation
- --sequencing-error
-
Sets the sequencing error rate. Valid values are between zero and one
- --quality-profile
-
Sets the sequencing system profile for quality. The default value is a poisson distribution, but the user can choose among several profiles stored into the database or import his own data. See quality command for more details
- --strand-bias
-
Sets which strand to use to make a read. Valid options are plus, minus and random - if you want to randomly calculte the strand for each read
- --seqid-weight
-
Sets the seqid (e.g. chromossome, ensembl id) raffle behavior. Valid options are length, same and count. If it is set to 'same', all seqid receives the same weight when raffling. If it is set to 'length', the seqid weight is calculated based on the seqid sequence length. And finally, if it is set to 'count', the user must set the option --expression-matrix. For details, see --expression-matrix
- --expression-matrix
-
If --seqid-weight is set to count, then this option becomes mandatory. The expression-matrix entries are found into the database. See expression command for more details
AUTHORS
Thiago L. A. Miller <tmiller@mochsl.org.br>
Gabriela Guardia <gguardia@mochsl.org.br>
J. Leonel Buzzo <lbuzzo@mochsl.org.br>
Fernanda Orpinelli <forpinelli@mochsl.org.br>
Pedro A. F. Galante <pgalante@mochsl.org.br>
COPYRIGHT AND LICENSE
This software is Copyright (c) 2018 by Teaching and Research Institute from Sírio-Libanês Hospital.
This is free software, licensed under:
The GNU General Public License, Version 3, June 2007