def get_aligned_fasta(self):
r = []
for name, value in bio_helper.parse_fasta(text=self.alignment):
r.append(">" +
self.model.genes.by_legacy_accession(name).accession)
r.append(value)
return "\n".join(r)
def load(self, table: LookupTable, fasta: str):
sequences = list(bio_helper.parse_fasta(text=fasta))
self.max_len = max(len(x[1]) for x in sequences) if sequences else 0
self.genes = []
for i in range(len(sequences)):
self.genes.append(
(sequences[i][0], sequences[i][1].ljust(self.max_len)))
self.table = table
self.highlight_row = None
self.highlight_col = None
def colour_fasta_ansi(array: str,
site_type: Optional[ESiteType] = None,
model: Model = None,
x=1,
n=99999):
table = __table_from_type(site_type)
result = []
first = True
for name, sites in bio_helper.parse_fasta(text=array):
if first:
first = False
else:
result.append("\n")
if model is not None:
if Gene.is_legacy_accession(name):
name = model.genes.by_legacy_accession(name).accession
result.append(ansi.BACK_BRIGHT_BLACK + name.ljust(20) +
ansi.BACK_RESET + "\n")
result_line = []
s = (x - 1)
if s != 0:
result_line.append(ansi.FORE_WHITE + ansi.BACK_BLUE + "…" +
ansi.RESET)
e = s + n
for char in sites[s:e]:
result_line.append(table.get(char, ansi.FORE_BRIGHT_BLACK) + char)
if e < len(sites) - 1:
result_line.append(ansi.FORE_WHITE + ansi.BACK_BLUE + "…")
result.append("".join(result_line) + ansi.RESET)
return "".join(result)
def import_genes(file_name: str) -> EChanges:
"""
Imports a FASTA file into your model.
If data already exists in the model, only sequence data matching sequences already in the model is loaded.
:param file_name: File to import
"""
model = global_view.current_model()
model.get_status(STAGES.SEQUENCES_2).assert_import()
model.user_comments.append("IMPORT_FASTA \"{}\"".format(file_name))
with LOG("IMPORT FASTA FROM '{}'".format(file_name)):
obtain_only = model._has_data()
num_updates = 0
idle = 0
idle_counter = 10000
for name, sequence_data in bio_helper.parse_fasta(file=file_name):
sequence = _make_gene(model, str(name), obtain_only,
len(sequence_data), True)
if sequence:
LOG("FASTA UPDATES {} WITH ARRAY OF LENGTH {}".format(
sequence, len(sequence_data)))
num_updates += 1
sequence.site_array = str(sequence_data)
idle = 0
else:
idle += 1
if idle == idle_counter:
LOG("THIS FASTA IS BORING...")
idle_counter *= 2
idle = 0
pr.printx("<verbose>Imported Fasta from <file>{}</file>.</verbose>",
file_name)
return EChanges.MODEL_ENTITIES
def composite_search_fix( blast: isFilename[EFileMode.READ], fasta: isFilename[EFileMode.READ], output: isFilename[EFileMode.OUTPUT] ):
"""
Converts standard BLAST format 6 TSV to `Composite search` formatted BLAST.
Composite search [1] uses a custom input format.
If you already have standard BLAST this converts to that format, so you don't need to BLAST again.
[1] JS Pathmanathan, P Lopez, F-J Lapointe and E Bapteste
:param blast: BLAST file
:param fasta: FASTA file
:param output: Output
:return: BLAST file, suitable for use with composite searcher
"""
#
# CS: qseqid sseqid evalue pident bitscore qstart qend qlen* sstart send slen*
# ST: qseqid sseqid pident alignment length mismatches gapopens qstart qend sstart send evalue bitscore
lengths = { }
with pr.pr_action( "Reading FASTA" ) as action:
for accession, sequence in bio_helper.parse_fasta( file = fasta ):
if " " in accession:
accession = accession.split( " ", 1 )[0]
lengths[accession] = len( sequence )
action.increment()
pr.pr_verbose( "{} accessions".format( len( lengths ) ) )
count = 0
with io_helper.open_write( output ) as file_out:
with pr.pr_action( "Processing" ) as action:
with open( blast, "r" ) as file_in:
for row in file_in:
count += 1
action.increment()
elements = row.strip().split( "\t" )
qseqid = elements[0]
sseqid = elements[1]
pident = elements[2]
# length = elements[3]
# mismatches = elements[4]
# gapopens = elements[5]
qstart = elements[6]
qend = elements[7]
sstart = elements[8]
send = elements[9]
evalue = elements[10]
bitscore = elements[11]
try:
qlen = str( lengths[qseqid] )
slen = str( lengths[sseqid] )
except KeyError as ex:
raise ValueError( "Accession found in BLAST file but not in FASTA file. See internal error for details." ) from ex
file_out.write( "\t".join( [qseqid, sseqid, evalue, pident, bitscore, qstart, qend, qlen, sstart, send, slen] ) )
file_out.write( "\n" )
pr.pr_verbose( "{} BLASTs".format( count ) )