labblouin.pfam module

labblouin.pfam.decompressGzipFile(gzip_file_name, destfolder, file_ext='ann')

Takes in GZIP file from PFAM or PDB and decompresses it to an .ann or specified file extension.

labblouin.pfam.doSequenceSearch(seq_file)

Performs the PFAM search for a sequence file.

labblouin.pfam.downloadFamilySequences(pfam_family_id, dest_folder, atype='seed')

Takes in PFAM family ID and acquires the gzipped flat file filled with seed or full sequence allignments.

labblouin.pfam.extractPDBChain(pdb_file, ch, dest_file)

Extracts a PDB file from another that has only information for a single chain.

labblouin.pfam.extractPDBSequences(pdb_file)

Extracts the Amino Acid sequences for a protein structure defined by a PDB file and returns as a dictionary.

labblouin.pfam.grabNCBIAccessionMetadata(accession_id)

Takes in an accession ID and returns NCBI metadata from GenBank.

labblouin.pfam.grabPDBFile(pdb_code, dest_folder)

Takes in a PDB code and acquires the PDB file from the PDB database, placing it in the specified destination folder.

labblouin.pfam.list2txttable(list_in, title)

Converts a list to a string table.

class labblouin.pfam.pfamFile(filepath)

cluster()

parse()

labblouin.pfam.printListToFile(list_in, dest)

Prints a list to a file.

labblouin.pfam.processSequenceSearch(search_results)

Takes in a XML result returned from a sequence search and parses it in order to determine what the most significant results are for related families. Returns a list of the family PFAM IDs.

labblouin.pfam.readPfamFile(file_name)

Takes in PFAM Stockholm file and reads it, returning a pfamFile object.

labblouin.pfam.removeListDuplicates(list_in)

Removes all duplicates in a list.

labblouin.pfam.writeSequenceToFasta(seq, seq_id, targetpath)

Creates FASTA file from given sequence string.

labblouin.pfam.writeSequencesToFasta(seq_list, dest_file)

Creates single FASTA file from given sequence tuple list where first item is sequence ID, second item is the sequence.

labblouin.pfam.writeSequencesToFile(seq_list, targetfolder, fasta=True)

Takes in a dictionary of sequences and writes them to seperate .seq or .fasta files.