phylogenetics/project.py
def compute_gblocks(self, **kwargs):

        """Run Gblocks on a phylopandas dataframe.

        Full docs for software are here:
        http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_documentation.html#Installation

        As of this writing (August 2019), Gblocks can be installed using
        bioconda (https://bioconda.github.io/).

        sequence_type: type of sequence
                       default: protein
                       allowed: ("protein","dna","codon")
                       gblock flag: -t
        min_conserved: minimum number of sequences for conserved position
                       default: num_seqs*0.5 + 1
                       allowed: (num_seqs*0.5 + 1,num_seqs)
                       gblock flag: -b1
        min_flank: minimum number of sequences for a flank position
                       default: 0.85*num_seqs
                       allowed: (min_conserved,num_seqs)
                       gblock flag: -b2
        max_contig_noncon: maximum number of contiguous non-conserved positions
                       default: 8
                       allowed: any integer > 0
                       gblock flag: -b3
        min_block_length: minimum length of a block
                       default: 10
                       allowed: any integer > 2
                       gblock flag: -b4
        allowed_gap: allowed gap positions
                       default: "no"
                       allowed: ("no","half","all")
                       gblock flag: -b5
        use_sim_matrix: use similarity matrix
                       default: True
                       allowed: True,False (True only allowed for proteins)
                       gblock flag: -b6
        min_initial_block: minimum length of an initial block
                       default: min_block_length
                       allowed: any integer > 2
                       gblock flag: -b0
        keep_tmp: keep temporary files and write out reports
                       default: False
                       allowed: False,True
        """

        print("Computing gblocks...")
        output = "/3_gblocks_alignment_output.csv"

        new_df = phylogenetics.tools.gblocks.run(self.data, **kwargs)
        self.data = new_df

        new_df.to_csv(self.project_dir + output)

        print("Writing gblocks results to " + self.project_dir + output + "...Done.\n")
Run Gblocks on a phylopandas dataframe.

        Full docs for software are here:
        http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_documentation.html#Installation

        As of this writing (August 2019), Gblocks can be installed using
        bioconda (https://bioconda.github.io/).

        sequence_type: type of sequence
                       default: protein
                       allowed: ("protein","dna","codon")
                       gblock flag: -t
        min_conserved: minimum number of sequences for conserved position
                       default: num_seqs*0.5 + 1
                       allowed: (num_seqs*0.5 + 1,num_seqs)
                       gblock flag: -b1
        min_flank: minimum number of sequences for a flank position
                       default: 0.85*num_seqs
                       allowed: (min_conserved,num_seqs)
                       gblock flag: -b2
        max_contig_noncon: maximum number of contiguous non-conserved positions
                       default: 8
                       allowed: any integer > 0
                       gblock flag: -b3
        min_block_length: minimum length of a block
                       default: 10
                       allowed: any integer > 2
                       gblock flag: -b4
        allowed_gap: allowed gap positions
                       default: "no"
                       allowed: ("no","half","all")
                       gblock flag: -b5
        use_sim_matrix: use similarity matrix
                       default: True
                       allowed: True,False (True only allowed for proteins)
                       gblock flag: -b6
        min_initial_block: minimum length of an initial block
                       default: min_block_length
                       allowed: any integer > 2
                       gblock flag: -b0
        keep_tmp: keep temporary files and write out reports
                       default: False
                       allowed: False,True
        
Run Gblocks on a phylopandas dataframe.

As of this writing (August 2019), Gblocks can be installed using
bioconda .


Run Gblocks on a phylopandas dataframe . As of this writing ( August 2019 ) Gblocks can be installed using bioconda .
def compute_gblocks(self, **kwargs):
        print("Computing gblocks...")
        output = "/3_gblocks_alignment_output.csv"
        new_df = phylogenetics.tools.gblocks.run(self.data, **kwargs)
        self.data = new_df
        new_df.to_csv(self.project_dir + output)
        print("Writing gblocks results to " + self.project_dir + output + "...Done.\n")
def compute_gblocks ( self , ** kwargs ) : print ( "Computing gblocks..." ) output = "/3_gblocks_alignment_output.csv" new_df = phylogenetics . tools . gblocks . run ( self . data , ** kwargs ) self . data = new_df new_df . to_csv ( self . project_dir + output ) print ( "Writing gblocks results to " + self . project_dir + output + "...Done.\n" )
Run Gblocks on a phylopandas dataframe.
Run Gblocks on a phylopandas dataframe .
"""Run Gblocks on a phylopandas dataframe.

        Full docs for software are here:
        http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_documentation.html#Installation

        As of this writing (August 2019), Gblocks can be installed using
        bioconda (https://bioconda.github.io/).

        sequence_type: type of sequence
                       default: protein
                       allowed: ("protein","dna","codon")
                       gblock flag: -t
        min_conserved: minimum number of sequences for conserved position
                       default: num_seqs*0.5 + 1
                       allowed: (num_seqs*0.5 + 1,num_seqs)
                       gblock flag: -b1
        min_flank: minimum number of sequences for a flank position
                       default: 0.85*num_seqs
                       allowed: (min_conserved,num_seqs)
                       gblock flag: -b2
        max_contig_noncon: maximum number of contiguous non-conserved positions
                       default: 8
                       allowed: any integer > 0
                       gblock flag: -b3
        min_block_length: minimum length of a block
                       default: 10
                       allowed: any integer > 2
                       gblock flag: -b4
        allowed_gap: allowed gap positions
                       default: "no"
                       allowed: ("no","half","all")
                       gblock flag: -b5
        use_sim_matrix: use similarity matrix
                       default: True
                       allowed: True,False (True only allowed for proteins)
                       gblock flag: -b6
        min_initial_block: minimum length of an initial block
                       default: min_block_length
                       allowed: any integer > 2
                       gblock flag: -b0
        keep_tmp: keep temporary files and write out reports
                       default: False
                       allowed: False,True
        """
self