From 02d89fb067b8e4072a7d54902e643e808afc3628 Mon Sep 17 00:00:00 2001 From: Henning Schumann Date: Tue, 31 Mar 2015 11:58:10 +0200 Subject: [PATCH] nicer formatting for mafft functions in documentary --- docs/mafft.md | 60 +++++++++++++++++++++++++++++++++------------------ 1 file changed, 39 insertions(+), 21 deletions(-) diff --git a/docs/mafft.md b/docs/mafft.md index 7762e38..45f2115 100644 --- a/docs/mafft.md +++ b/docs/mafft.md @@ -9,29 +9,13 @@ Tested with MAFFT v7.215 (2014/12/17) ## Dependencies * MAFFT has to be installed - * FastaIO - -## Usage - -```julia -mafft("examples/fasta/il4.fasta") -``` - -Runs mafft with the provided fasta file and returns the alignment in FastaIO dataformat. By default mafft is called with the `--auto` option. - - -```julia -mafft("examples/fasta/il4.fasta", ["--localpair", "--maxiterate", "1000"]) -``` - -Calling mafft with custom arguments. Arguments have to be a array of strings. This call is also equivalent to calling: - -```julia - mafft("examples/fasta/il4.fasta", :linsi) -``` + * Julia Packages + * FastaIO ## Exported functions +### mafft + ```julia mafft(fasta_in::String, preconfiguration=:default) ``` @@ -42,6 +26,8 @@ Runs mafft with the provided fasta file and returns the alignment in FastaIO dat *preconfiguration*: optional commandline arguments for MAFFT (array of strings) +### mafft_from_string + ```julia mafft_from_string(fasta_in::String, preconfiguration=:default) ``` @@ -52,6 +38,8 @@ Calls MAFFT with the given FASTA string as input and returns aligned FASTA in th **preconfiguration**: optional commandline arguments for MAFFT (array of strings) +### mafft_from_fasta + ```julia mafft_from_fasta(fasta_in, preconfiguration=:default) ``` @@ -62,6 +50,8 @@ Calls MAFFT with the given FASTA in FastaIO format *preconfiguration*: optional commandline arguments for MAFFT (array of strings) +### mafft_profile + ```julia mafft_profile(group1::String, group2::String) ``` @@ -69,6 +59,8 @@ Group-to-group alignments **group1** and **group2** have to be files with alignments. Returns aligned FASTA in the FastaIO dataformat. +### mafft_profile_from_string + ```julia mafft_profile_from_string(group1::String, group2::String) ``` @@ -76,6 +68,8 @@ Group-to-group alignments with input strings in FASTA format. **group1** and **group2** have to be strings with alignments in FASTA format. + ### mafft_profile_from_fasta + ```julia mafft_profile_from_fasta(group1, group2) ``` @@ -87,6 +81,8 @@ Group-to-group alignments with input in FastaIO format ### Helper functions for aligned FASTA This module also includes a few helper functions for the FastaIO dataformat (which is returned by the mafft functions of this module). +#### alignment_length + ```julia alignment_length(fasta) ``` @@ -94,6 +90,8 @@ Returns the length of the alignment. **fasta**: A FastaIO dataformat object +#### to_aminoacids + ```julia to_aminoacids(fasta) ``` @@ -101,6 +99,8 @@ Converts a FastaIO-formatted array into an array of BioSeq AminoAcid. **fasta**: A FastaIO dataformat object +#### print_fasta + ```julia print_fasta(fasta) ``` @@ -108,7 +108,6 @@ Prints a FastaIO object in a nicely formatted way to the screen. **fasta**: A FastaIO dataformat object - ## Supported pre-configurations (strategies) The following mafft strategies are supported by built-in preconfigurations which can be used by supplying the function calls with the corresponding symbol (in the parentheses). @@ -121,6 +120,25 @@ The following mafft strategies are supported by built-in preconfigurations which * NW-NS-i (``:nwnsi``) * NW-NS-2 (``:nwns``) +## Usage + +```julia +mafft("examples/fasta/il4.fasta") +``` + +Runs mafft with the provided fasta file and returns the alignment in FastaIO dataformat. By default mafft is called with the `--auto` option. + + +```julia +mafft("examples/fasta/il4.fasta", ["--localpair", "--maxiterate", "1000"]) +``` + +Calling mafft with custom arguments. Arguments have to be a array of strings. This call is also equivalent to calling: + +```julia + mafft("examples/fasta/il4.fasta", :linsi) +``` + ## References