Wrappers for external binaries

These modules provide convenience classes for calling various external binaries.

modpipe.cdhit – Wrapper for CD-HIT

class modpipe.cdhit.CDHit(seqfile)

Defines a CDHit object and methods.

cluster(outfile, sequence_identity=95, throw_away_seq_length=30, length_difference=10)

Take an input file in fasta format and cluster it at the given sequence identity threshold. It will return the stdout, stderr of the program and the name of the file containing the clusters.

parse_clusters()

Parse the entries in the cluster file.

modpipe.ce – Wrapper for CE

class modpipe.ce.CE(modenv, pdb0, chn0, pdb1, chn1)

Defines a CE object and methods.

calculate_superpositions()

Calculates superpositions using the current alignment and prints numbers.

fix_alignment()

Clean up the CE alignment and return a Modeller alignment object.

get_alignment()

Calculate CE alignment.

parse_output()

This parses the output from a CE run and returns the alignment and some details.

read_program_output(file)

This routine reads an existing file with CE output.

write_alignment(file, format='pir')

Write out the current alignment to file.

write_program_output(file)

This routine writes the raw output of the CE program to a specified file.

exception modpipe.ce.Error

An error raised by CE

modpipe.tmalign – Wrapper for TMAlign

class modpipe.tmalign.TMAlign(modenv, pdb0, chn0, pdb1, chn1)

Defines a TMAlign object and methods.

calculate_superpositions()

Calculates superpositions using the current alignment and prints numbers.

fix_alignment()

Clean up the TMalign alignment and return a Modeller alignment object.

get_alignment()

Calculate TMAlign alignment.

parse_output()

This parses the output from a TMAlign run and returns the alignment and some details.

read_program_output(file)

This routine reads an existing file with TMAlign output.

write_alignment(file, format='pir')

Write out the current alignment to file.

write_program_output(file)

This routine writes the raw output of the TMAlign program to a specified file.