Contents

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.\" http://github.com/rtomayko/ronn/tree/0.7.3
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.TH "MAF_TO_FASTA" "1" "July 2012" "BioRuby" "BioRuby Manual"
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.SH "NAME"
\fBmaf_to_fasta\fR \- convert MAF file to FASTA
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.SH "SYNOPSIS"
\fBmaf_to_fasta\fR [\fIoptions\fR\.\.\.] \fImaf\fR \fIfasta\fR
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.SH "DESCRIPTION"
\fBmaf_to_fasta\fR, part of the bioruby\-maf library, converts Multiple Alignment Format (MAF) files to FASTA format\. It does not attempt to combine alignment blocks, but simply writes out each sequence in order\.
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.SH "FILES"
The \fImaf\fR input file must be a valid MAF file of any length\.
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.P
The \fIfasta\fR output file will be written in FASTA format\.
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.SH "OPTIONS"
The options are only useful for performance measurement\.
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.SH "EXAMPLES"
Convert a MAF file to FASTA:
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.IP "" 4
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.nf

$ maf_to_fasta chrY\.maf chrY\.fa
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.fi
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.IP "" 0
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.SH "ENVIRONMENT"
\fBmaf_to_fasta\fR is a Ruby program and relies on ordinary Ruby environment variables\.
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.SH "BUGS"
\fBmaf_to_fasta\fR should provide flexibility in selecting the alignment blocks and sequences to convert, and perhaps allow alignment blocks to be spliced together\.
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.SH "COPYRIGHT"
\fBmaf_to_fasta\fR is copyright (C) 2012 Clayton Wheeler\.
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.SH "SEE ALSO"
ruby(1)
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.IP "\(bu" 4
\fIhttps://github\.com/csw/bioruby\-maf/\fR
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.IP "" 0

Version data entries

5 entries across 5 versions & 1 rubygems

Version	Path
bio-maf-0.3.2-java	man/maf_to_fasta.1
bio-maf-0.3.2	man/maf_to_fasta.1
bio-maf-0.3.1	man/maf_to_fasta.1
bio-maf-0.3.0-java	man/maf_to_fasta.1
bio-maf-0.3.0	man/maf_to_fasta.1