def msafilesgen(inpath_a3m):
"""
Convert a3m format alignment to "jones" format (.aln) and print msa coverage graph
Parameters
----------
inpath_a3m : str
Multiple Sequence Alignment (.a3m) path
Returns
-------
parsemsa : msa
ConKit parsed MSA.
outpath_aln : str
MSA (jones format) file path.
"""
outpath_aln = os.path.join(os.path.splitext(inpath_a3m)[0] + ".aln")
biotag = os.path.splitext(os.path.splitext(inpath_a3m)[0])[1]
msacoveragefile = pdbid(
) + biotag + ".msa.coverage.png" if biotag == ".bio" else pdbid(
) + ".msa.coverage.png"
msacoveragepath = os.path.join(output_dir(), msacoveragefile)
parsemsa = ckio.read(inpath_a3m, 'a3m')
ckio.write(outpath_aln, 'jones', parsemsa)
ckplot.SequenceCoverageFigure(parsemsa, file_name=msacoveragepath)
return parsemsa, outpath_aln
def write(infile, ftype, indata, ck=False):
"""
:param infile: Path to input file.
:type infile: str
:param ftype: One of 'psicov', 'ccmpred', 'fasta', 'pdb', 'a3m', 'jones', 'xml'.
:type ftype: str
:param ck: Open alternative conkit version instead of default, defaults to False.
:type ck: bool, optional
:return: Parsed file (and, for 'pdb', list of filenames).
:rtype: One or two of list[str], :class:`~crops.elements.sequences.sequence`, :class:`~conkit.core.sequence.Sequence`,
"""
if (ftype.lower() not in _ftypelist() or
isinstance(ftype, str) is not True):
logging.critical('Specified type not valid.')
raise ValueError
if ck is True and ftype.lower() != 'xml':
output = ckio.write(infile, ftype.lower(), hyerarchy=indata)
else:
if ftype.lower() == 'psicov':
pass
if ftype.lower() == 'ccmpred':
pass
elif ftype.lower() == 'fasta':
output = cps.parseseqfile(infile)
elif ftype.lower() == 'pdb':
output1, output2 = cps.parsestrfile(infile)
return output1, output2
elif ftype.lower() == 'a3m' or 'jones':
output = ckio.read(infile, ftype.lower())
elif ftype.lower() == 'xml':
output = ET.parse(infile)
return output
def msafilesgen(inpath_a3m):
"""Convert a3m format alignment to "jones" format (.aln) and print msa coverage graph.
:param inpath_a3m: Multiple Sequence Alignment (.a3m) path
:type inpath_a3m: str
:return: ConKit parsed MSA
:rtype: :obj:`~conkit.core.sequencefile.SequenceFile`
"""
parsedmsa = ckio.read(inpath_a3m, 'a3m')
# Convert to 'jones' format
outpath_aln = os.path.join(os.path.splitext(inpath_a3m)[0], ".aln")
ckio.write(outpath_aln, 'jones', parsedmsa)
# Plot Coverage
msacoveragepath = os.path.join(
os.path.splitext(inpath_a3m)[0], ".coverage.png")
fig = ckplot.SequenceCoverageFigure(parsedmsa)
fig.savefig(msacoveragepath, overwrite=True)
neff = parsedmsa.meff
return neff
def crop_fasta(fastaseq, outdir=output_tmpdir()):
"""
FASTA SEQUENCE CROPPING
Parameters
----------
seqpath : ConKit Sequence
Source fasta sequence
outdir : str, optional
Directory where results biological sequence will be printed out. The default is output_tmpdir().
Returns
-------
bioseq : ConKit Sequence
Cropped (biological) sequence
newseqpath : str
Sequence path (bio.fasta file)
"""
# Obtain new chain ends (residue number)
fastaends = biochain_ends('fasta')
# Check that the sequence is consistent with the limits retrieved from the database
if fastaends[1] - fastaends[0] + 1 > fastaseq.seq_len:
isitbio = False
printout(
'WARNING: The biological sequence limits include a section greater than the input sequence.',
errorlog=True)
printout(' Skipping cropping. Returning input values.',
errorlog=True,
extraline=True)
bioseq = fastaseq
newseqfile = pdbid() + '.fasta'
newseqpath = os.path.join(outdir, newseqfile)
elif fastaends[1] - fastaends[0] + 1 == fastaseq.seq_len:
isitbio = True
printout(
' Biological and input sequences have the same length. Skipping cropping. Returning input values.',
extraline=True)
bioseq = fastaseq
newseqfile = pdbid() + '.bio.fasta'
newseqpath = os.path.join(outdir, newseqfile)
ckio.write(newseqpath, "fasta", hierarchy=bioseq)
else:
if fastaends[0] > fastaseq.seq_len:
isitbio = False
printout(
'WARNING: The sequence upper limit imported from the database is higher than the upper limit from the fasta file.',
errorlog=True) #LOGGING
printout(' Skipping cropping. Returning input values.',
errorlog=True,
extraline=True)
bioseq = fastaseq
newseqfile = pdbid() + '.fasta'
newseqpath = os.path.join(outdir, newseqfile)
else:
isitbio = True
# Append new info to sequence
newid = fastaseq.id
newid = newid + "|NO_CLONING_ARTIFACTS"
# Create new sequence
newseq = fastaseq.seq[fastaends[0] - 1:fastaends[1] - 1]
bioseq = ckc.Sequence(newid, newseq)
# Write new sequence to file
#locpdbid=os.path.splitext(os.path.basename(PDB_PATH))[0]
#outdir = os.path.join(OUTPUT_DIR, locpdbid,"")
newseqfile = pdbid() + '.bio.fasta'
newseqpath = os.path.join(outdir, newseqfile)
ckio.write(newseqpath, "fasta", hierarchy=bioseq)
return bioseq, newseqpath, isitbio