Package biana :: Package BianaObjects :: Module sequenceUtilities

Module sequenceUtilities

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Classes

[hide private]

BlastallParserIterator

Functions

[hide private]

get_clustalw_alignment(sequencesList)
Executes clustalw to get the multiple sequence alignment between the proteins in the list

source code

get_cd_hit_clusters(fasta_file, output_path='./', sequence_identity_threshold=0.95)
Executes CD-HIT with the sequences fasta file and saves the results in the ouput_path source code

blast_cd_hit_clusters(cd_hit_clusters_file, output_fd, dbaccess, length_blast_db=None, effective_length_space_search=None)
Performs a blast between all the proteins belonging to the same cd-hit cluster

source code

blast_sequence(blastDatabase, sequenceObject, temporalOutputPath=None)
Does a blast of sequence sequenceObject against database "blastDatabase"

source code

_calculate_similarities(dbaccess, length_blast_db=None, effective_length_space_search=None, sequenceID_list=[], fd_output_file=sys.stdout, representant=None)
Calculates the similarity between all proteins in the list "cluster_sequences". source code

self_blast_fasta_file(fasta_file, fd_output_file)
Does a blast within all sequences in a file

source code

parse_blastall_output(fd_blastall_output, temporalOutputFile_fd=None, return_only_ids=False, limit_to_sequenceIDs=Set([]))
"fd_blastall_output" is the output fd of the blast process (input for this method)

source code

parse_bl2seq_output(sequenceID_A, sequenceID_B, bl2seq_output=None, fd_output_file=None)

source code

Function Details

[hide private]

get_cd_hit_clusters(fasta_file, output_path=`'./'`, sequence_identity_threshold=0.95)

source code

Executes CD-HIT with the sequences fasta file and saves the results in the ouput_path

# TODO: Automate for executing in cluster (now it is done manually)

blast_sequence(blastDatabase, sequenceObject, temporalOutputPath=None)

source code

Does a blast of sequence sequenceObject against database "blastDatabase"

ATTENTION: "temporalOutputPath" is the temporal gzipped file where the blast results are stored. If it exists, blast is not calculated! If it is None, results are not saved.

_calculate_similarities(dbaccess, length_blast_db=None, effective_length_space_search=None, sequenceID_list=`[]`, fd_output_file=sys.stdout, representant=None)

source code

Calculates the similarity between all proteins in the list "cluster_sequences".

"cluster_sequences" must be a list of the sequenceIDs

It uses bl2seq or blastall to calculate them

Results are printed to "fd_output_file"

self_blast_fasta_file(fasta_file, fd_output_file)

source code

Does a blast within all sequences in a file

If file is very big, it won't work. It is intended for small sets

parse_blastall_output(fd_blastall_output, temporalOutputFile_fd=None, return_only_ids=False, limit_to_sequenceIDs=Set([]))

source code

"fd_blastall_output" is the output fd of the blast process (input for this method)

"temporalOutputFile" is a file where all the input of fd_blastall_output is saved

"return_only_ids" is used to store only ids, not complete blast results

"limit_to_sequenceIDs" is used to filter blast parsing to only those sequenceids

Module sequenceUtilities

get_cd_hit_clusters(fasta_file, output_path='./', sequence_identity_threshold=0.95)

blast_sequence(blastDatabase, sequenceObject, temporalOutputPath=None)

_calculate_similarities(dbaccess, length_blast_db=None, effective_length_space_search=None, sequenceID_list=[], fd_output_file=sys.stdout, representant=None)

self_blast_fasta_file(fasta_file, fd_output_file)

parse_blastall_output(fd_blastall_output, temporalOutputFile_fd=None, return_only_ids=False, limit_to_sequenceIDs=Set([]))

get_cd_hit_clusters(fasta_file, output_path=`'./'`, sequence_identity_threshold=0.95)

_calculate_similarities(dbaccess, length_blast_db=None, effective_length_space_search=None, sequenceID_list=`[]`, fd_output_file=sys.stdout, representant=None)