MaliIO.py -

Author:Andreas Heger Release:$Id$ Date:December 09, 2013 Tags:Python

Code

MaliIO.writeFasta(outfile, mali, line_width=60, identifiers=None, skip_first=0, gap_char=None)

print multiple alignment in fasta format.

MaliIO.WriteMODELLER(outfile, mali, line_width=60, identifiers=None, skip_first=0, gap_char=None)

print multiple alignment in PIR (MODELLER) format. example:

>P1;5fd1 structureX:5fd1:1 : :106 : :ferredoxin:Azotobacter vinelandii: 1.90: 0.19 AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELA EVWPNITEKKDPLPDAEDWDGVKGKLQHLER*

MaliIO.writeClustalW(outfile, mali, line_width=60, identifiers=None)

print alignment in ClustalW format. (have to still look up the format, dsc can read it.)

MaliIO.readPicasso(infile)

read alignment in the non-defined picasso format.

MaliIO.compressAlignment(alignment, gap_character='-', ignore_beginning=0)

compress an alignment string. Lower-case characters at the beginning are ignored if so wished. –xxabBCDEfgHI becomes: -6+4

This was necessary for radar output (e.g., 46497)

MaliIO.readFasta(infile, pattern_identifier='\\S+')

read alignment in fasta format.

MaliIO.convertGaps(mali, old_gap='.', new_gap='-')

convert gaps characters in mali.

MaliIO.removeGappedColumns(mali, gap_char='-')

remove all gapped columns in mali.

MaliIO.getSubset(mali, identifiers, not_in_set=False)

return subset of mali which only contains identifiers.

MaliIO.getFrameColumnsForMaster(mali, master, gap_char='-')

get columns in frame according to master.

MaliIO.getFrameColumnsForMasterPattern(mali, identifiers, master_pattern, gap_char='-')

get columns in frame for all masters matching the pattern.

MaliIO.getMapFromMali(seq1, seq2, gap_char='-')

build map of positions between mali.

MaliIO.getCodonSequence(sequence, frame_columns, gap_char='-', remove_stops=True)

return a pruned sequence given frame columns.

everything not in frame is deleted, only complete codons are kept.

MaliIO.getPercentIdentity(seq1, seq2, gap_char='-')

get number of identical residues between seq1 and seq2.