--- name: "Bio::SeqIO::msout" section: "3pm" platform: "linux" package: "libbio-perl-perl" version: "1.7.8-1" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/Bio::SeqIO::msout" --- # Bio::SeqIO::msout(3pm) input stream for output by Hudson's ms ## NAME Bio::SeqIO::msout - input stream for output by Hudson's ms ## SYNOPSIS Do not use this module directly. Use it via the Bio::SeqIO class. ## DESCRIPTION ms ( Hudson, R. R. (2002) Generating samples under a Wright-Fisher neutral model. Bioinformatics 18:337-8 ) can be found at http://home.uchicago.edu/~rhudson1/source/mksamples.html. Currently, this object can be used to read output from ms into seq objects. However, because bioperl has no support for haplotypes created using an infinite sites model (where '1' identifies a derived allele and '0' identifies an ancestral allele), the sequences returned by msout are coded using A, T, C and G. To decode the bases, use the sequence conversion table (a hash) returned by **get\_base\_conversion\_table()**. In the table, 4 and 5 are used when the ancestry is unclear. This should not ever happen when creating files with ms, but it will be used when creating msOUT files from a collection of seq objects ( To be added later ). Alternatively, use **get\_next\_hap()** to get a string with 1's and 0's instead of a seq object. ### Mapping to Finite Sites This object can now also be used to map haplotypes created using an infinite sites model to sequences of arbitrary finite length. See **set\_n\_sites()** for more detail. Thanks to Filipe G. Vieira \ for the idea and code. ## FEEDBACK ### Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. ``` bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists ``` ### Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: ``` https://github.com/bioperl/bioperl-live/issues ``` ## AUTHOR - Warren Kretzschmar This module was written by Warren Kretzschmar email: wkretzsch@gmail.com This module grew out of a parser written by Aida Andres. ## COPYRIGHT ### Public Domain Notice This software/database is \`\`United States Government Work'' under the terms of the United States Copyright Act. It was written as part of the authors' official duties for the United States Government and thus cannot be copyrighted. This software/database is freely available to the public for use without a copyright notice. Restrictions cannot be placed on its present or future use. Although all reasonable efforts have been taken to ensure the accuracy and reliability of the software and data, the National Human Genome Research Institute (NHGRI) and the U.S. Government does not and cannot warrant the performance or results that may be obtained by using this software or data. NHGRI and the U.S. Government disclaims all warranties as to performance, merchantability or fitness for any particular purpose. ## METHODS ### Methods for Internal Use *\_initialize* Title : \_initialize Usage : `$stream` = Bio::SeqIO::msOUT-\>new($infile) Function: extracts basic information about the file. Returns : Bio::SeqIO object Args : no\_og, gunzip, gzip, n\_sites Details :\ \- include 'no\_og' flag if the last population of an msout file contains\ only one haplotype and you don't want the last haplotype to be\ treated as the outgroup ( suggested when reading data created by ms ).\ \- including 'n\_sites' (positive integer) causes all output haplotypes to be\ mapped to a sequence of length 'n\_sites'. See **set\_n\_sites()** for more details. *\_read\_start* Title : \_read\_start Usage : `$stream`-\>**\_read\_start()** Function: reads from the filehandle `$stream`-\>{\_filehandle} all information up to the first haplotype (sequence). Closes the filehandle if all lines have been read. Returns : void Args : none ### Methods to Access Data *get\_segsites* Title : get\_segsites Usage : `$segsites` = `$stream`-\>**get\_segsites()** Function: returns the number of segsites in the msOUT file (according to the msOUT header line's -s option), or the current run's segsites if -s was not specified in the command line (in this case the number of segsites varies from run to run). Returns : scalar Args : NONE *get\_current\_run\_segsites* Title : get\_current\_run\_segsites Usage : `$segsites` = `$stream`-\>**get\_current\_run\_segsites()** Function: returns the number of segsites in the run of the last read\ haplotype (sequence). Returns : scalar Args : NONE *get\_n\_sites* Title : get\_n\_sites Usage : `$n_sites` = `$stream`-\>**get\_n\_sites()** Function: Gets the number of total sites (variable or not) to be output. Returns : scalar if n\_sites option is defined at call time of **new()** Args : NONE Note :\ WARNING: Final sequence length might not be equal to n\_sites if n\_sites is\ too close to number of segregating sites in the msout file. *set\_n\_sites* Title : set\_n\_sites Usage : `$n_sites` = `$stream`-\>set\_n\_sites($value) Function: Sets the number of total sites (variable or not) to be output. Returns : 1 on success; throws an error if `$value` is not a positive integer or undef Args : positive integer Note :\ WARNING: Final sequence length might not be equal to n\_sites if it is\ too close to number of segregating sites.\ \- n\_sites needs to be at least as large as the number of segsites of\ the next haplotype returned\ \- n\_sites may also be set to undef, in which case haplotypes are returned\ under the infinite sites model assumptions. *get\_runs* Title : get\_runs Usage : `$runs` = `$stream`-\>**get\_runs()** Function: returns the number of runs in the msOUT file (according to the\ msinfo line) Returns : scalar Args : NONE *get\_Seeds* Title : get\_Seeds Usage : `@seeds` = `$stream`-\>**get\_Seeds()** Function: returns an array of the seeds used in the creation of the msOUT file. Returns : array Args : NONE Details : In older versions, ms used three seeds. Newer versions of ms seem to\ use only one (longer) seed. This function will return all the seeds\ found. *get\_Positions* Title : get\_Positions Usage : `@positions` = `$stream`-\>**get\_Positions()** Function: returns an array of the names of each segsite of the run of the last\ read hap. Returns : array Args : NONE Details : The Positions may or may not vary from run to run depending on the\ options used with ms. *get\_tot\_run\_haps* Title : get\_tot\_run\_haps Usage : `$number_of_haps_per_run` = `$stream`-\>**get\_tot\_run\_haps()** Function: returns the number of haplotypes (sequences) in each run of the msOUT\ file ( according to the msinfo line ). Returns : scalar \>= 0 Args : NONE Details : This number should not vary from run to run. *get\_ms\_info\_line* Title : get\_ms\_info\_line Usage : `$ms_info_line` = `$stream`-\>**get\_ms\_info\_line()** Function: returns the header line of the msOUT file. Returns : scalar Args : NONE *tot\_haps* Title : tot\_haps Usage : `$number_of_haplotypes_in_file` = `$stream`-\>**tot\_haps()** Function: returns the number of haplotypes (sequences) in the msOUT file.\ Information gathered from msOUT header line. Returns : scalar Args : NONE *get\_Pops* Title : get\_Pops Usage : `@pops` = `$stream`-\>**pops()** Function: returns an array of population sizes (order taken from the -I flag in\ the msOUT header line). This array will include the last hap even if\ it looks like an outgroup. Returns : array of scalars \> 0 Args : NONE *get\_next\_run\_num* Title : get\_next\_run\_num Usage : `$next_run_number` = `$stream`-\>**next\_run\_num()** Function: returns the number of the ms run that the next haplotype (sequence)\ will be taken from (starting at 1). Returns undef if the complete\ file has been read. Returns : scalar \> 0 or undef Args : NONE *get\_last\_haps\_run\_num* Title : get\_last\_haps\_run\_num Usage : `$last_haps_run_number` = `$stream`-\>**get\_last\_haps\_run\_num()** Function: returns the number of the ms run that the last haplotype (sequence)\ was taken from (starting at 1). Returns undef if no hap has been\ read yet. Returns : scalar \> 0 or undef Args : NONE *get\_last\_read\_hap\_num* Title : get\_last\_read\_hap\_num Usage : `$last_read_hap_num` = `$stream`-\>**get\_last\_read\_hap\_num()** Function: returns the number (starting with 1) of the last haplotype read from\ the ms file Returns : scalar \>= 0 Args : NONE Details : 0 means that no haplotype has been read yet. Is reset to 0 every run. *outgroup* Title : outgroup Usage : `$outgroup` = `$stream`-\>**outgroup()** Function: returns '1' if the msOUT stream has an outgroup. Returns '0'\ otherwise. Returns : '1' or '0' Args : NONE Details : This method will return '1' only if the last population in the msOUT\ file contains only one haplotype. If the last population is not an\ outgroup then create the msOUT object using 'no\_og' as input flag.\ Also, return 0, if the run has only one population. *get\_next\_haps\_pop\_num* Title : get\_next\_haps\_pop\_num Usage : ($next\_haps\_pop\_num, `$num_haps_left_in_pop`) = `$stream`-\>**get\_next\_haps\_pop\_num()** Function: First return value is the population number (starting with 1) the\ next hap will come from. The second return value is the number of haps\ left to read in the population from which the next hap will come. Returns : (scalar \> 0, scalar \> 0) Args : NONE *get\_next\_seq* Title : get\_next\_seq Usage : `$seq` = `$stream`-\>**get\_next\_seq()** Function: reads and returns the next sequence (haplotype) in the stream Returns : Bio::Seq object or void if end of file Args : NONE Note : This function is included only to conform to convention. The\ returned Bio::Seq object holds a halpotype in coded form. Use the hash\ returned by **get\_base\_conversion\_table()** to convert 'A', 'T', 'C', 'G'\ back into 1,2,4 and 5. Use **get\_next\_hap()** to retrieve the halptoype as\ a string of 1,2,4 and 5s instead. *next\_seq* Title : next\_seq Usage : `$seq` = `$stream`-\>**next\_seq()** Function: Alias to **get\_next\_seq()** Returns : Bio::Seq object or void if end of file Args : NONE Note : This function is only included for convention. It calls **get\_next\_seq()**.\ See **get\_next\_seq()** for details. *get\_next\_hap* Title : get\_next\_hap Usage : `$hap` = `$stream`-\>**next\_hap()** Function: reads and returns the next sequence (haplotype) in the stream.\ Returns undef if all sequences in stream have been read. Returns : Haplotype string (e.g. '110110000101101045454000101' Args : NONE Note : Use **get\_next\_seq()** if you want the halpotype returned as a\ Bio::Seq object. *get\_next\_pop* Title : get\_next\_pop Usage : `@seqs` = `$stream`-\>**next\_pop()** Function: reads and returns all the remaining sequences (haplotypes) in the\ population of the next sequence. Returns an empty list if no more\ haps remain to be read in the stream Returns : array of Bio::Seq objects Args : NONE *next\_run* Title : next\_run Usage : `@seqs` = `$stream`-\>**next\_run()** Function: reads and returns all the remaining sequences (haplotypes) in the ms\ run of the next sequence. Returns an empty list if all haps have been\ read from the stream. Returns : array of Bio::Seq objects Args : NONE ### Methods to Retrieve Constants *base\_conversion\_table* Title : get\_base\_conversion\_table Usage : `$table_hash_ref` = `$stream`-\>**get\_base\_conversion\_table()** Function: returns a reference to a hash. The keys of the hash are the letters '\ A','T','G','C'. The values associated with each key are the value that\ each letter in the sequence of a seq object returned by a\ Bio::SeqIO::msout stream should be translated to. Returns : reference to a hash Args : NONE Synopsis: ``` # retrieve the Bio::Seq object's sequence my $haplotype = $seq->seq; # need to convert all letters to their corresponding numbers. foreach my $base (keys %{$rh_base_conversion_table}){ $haplotype =~ s/($base)/$rh_base_conversion_table->{$base}/g; } # $haplotype is now an ms style haplotype. (e.g. '100101101455') ```