def write_as_fasta(self, fh, n=None):
"""-----------------------------------------------------------------------------------------
Write to a file in fasta format, if n is defined, write only the specified ORF in the list
:param fh, open filehandle for writing
:param n: integer, index of ORF to write, write all if not specified
:return: n
-----------------------------------------------------------------------------------------"""
fasta = Fasta()
nwritten = 0
if n is None:
# print all ORFS
for orf in self.orf:
fasta.id = orf['id']
fasta.doc = 'len={} strand={} frame={} begin={} end={}'. \
format(orf['length'], orf['direction'], orf['frame'], orf['begin'], orf['end'])
fasta.seq = orf['sequence']
fh.write(fasta.format(linelen=60))
fh.write('\n')
nwritten += 1
elif n < len(self.orf):
# print the selected ORF
orf = self.orf[n]
fasta.id = orf['id']
fasta.doc = 'len={} strand={} frame={} begin={} end={}'. \
format(orf['length'], orf['direction'], orf['frame'], orf['begin'], orf['end'])
fasta.seq = orf['sequence']
fh.write(fasta.format(linelen=60))
fh.write('\n')
nwritten = 1
return nwritten
def getSequence():
sequence = None
if request.method == 'POST':
if 'file1' in request.files:
f = request.files['file1']
sequence = 0
state['seq'][1]['status'] = 'next'
elif 'file2' in request.files:
f = request.files['file2']
sequence = 1
fasta = Fasta(fh=f)
fasta.read()
print(fasta.format())
seq = state['seq'][sequence]
seq['fasta'] = fasta
seq['status'] = 'loaded'
# if both sequences have been selected, check whether the sequences are DNA or protein
state['params']['seqtype'] = 'protein'
if state['seq'][0]['status'] is 'loaded' and state['seq'][1][
'status'] is 'loaded':
if state['seq'][0]['fasta'].isACGT(
) and state['seq'][1]['fasta'].isACGT():
state['params']['seqtype'] = 'DNA'
return render_template('dashboard.html', state=state)
n_notmatch[fastafile] = 0
n_file += 1
while fasta.next():
n_sequence[fastafile] += 1
n_total += 1
if fasta.id in idlist or not idlist:
# desired selected sequences
fasta.trimDocByRegex(trim)
seqlen = len(fasta.seq)
if args.minlen and seqlen < args.minlen:
# skip sequences shorter than minimum length, if specified
continue
out.write('{}\n'.format(fasta.format(linelen=args.linelen)))
n_written += 1
n_match[fastafile] += 1
if fasta.id in n_found:
n_found[fasta.id] += 1
else:
n_found[fasta.id] = 1
else:
# not selected sequence
n_notmatch[fastafile] += 1
sys.stderr.write('files read: {}\n'.format(n_file))
sys.stderr.write('total sequences read: {}\n'.format(n_total))
sys.stderr.write('total sequences written: {}\n'.format(n_written))
"""---------------------------------------------------------------------------------------------------------------------
Remove the Trinity path information from the id line
usage
fasta_reformat.py *.fasta
---------------------------------------------------------------------------------------------------------------------"""
import glob
import sys
import re
from sequence.fasta import Fasta
linelen = 60
# default target file name
target = '*.fasta'
if len(sys.argv) > 1:
target = sys.argv[1]
print(' target file:', target)
for fastafile in glob.glob(target):
# output file
outfile = fastafile + '.reformatted'
out = open(outfile, 'w')
print(' input file:', fastafile, ' output file:', outfile)
fasta = Fasta()
fasta.open(fastafile)
while fasta.next():
fasta.doc = re.sub(r' path=\[[^]]+\]', '', fasta.doc)
out.write(fasta.format(linelen=linelen))
n_uniqueperfile = 0
n_total = 0
n_unique_total = 0
sys.stderr.write('{}\t{}\t\t{}\n'.format('file', 'per file', 'total'))
for fastafile in glob.glob(target):
fasta = Fasta()
fasta.open(fastafile)
n_file += 1
n_perfile = 0
while fasta.next():
n_perfile += 1
if fasta.id in unique_seq:
continue
else:
n_uniqueperfile += 1
unique_seq[fasta.id] = fasta.format(linelen=100)
n_total += n_perfile
n_unique_total += n_uniqueperfile
sys.stderr.write('{}\t{}\t{}\t{}\t{}\t{}\n'.format(n_file, fastafile,
n_perfile,
n_uniqueperfile,
n_total,
n_unique_total))
# write out sequences
for seq in unique_seq:
sys.stdout.write(unique_seq[seq])
exit(0)
diagonal[d] = filtered
return nmatch
# --------------------------------------------------------------------------------------------------
# Testing
# --------------------------------------------------------------------------------------------------
if __name__ == '__main__':
print('\ntest 0: identity matching')
print('\texpect 7 matches\n')
fasta = Fasta()
fasta.id = 'test0'
fasta.doc = '5 letter DNA test'
fasta.seq = 'ACAGT'
print('{}\n'.format(fasta.format()))
match = Match()
match.s1 = fasta
match.s2 = fasta
nmatch = match.identityPos()
print('matches: {}'.format(nmatch))
print('\ntest 1: identity matching, unequal length sequences')
print('\texpect 11 matches\n')
match = Match()
fasta1 = Fasta()
fasta1.id = 'test1.1'
fasta1.doc = '5 letter DNA test'
fasta1.seq = 'ACAGT'
print('in', n_current, 'sequences', end=' ')
print('written to', outfilename)
except NameError:
pass
n_out += 1
n_current = 0
base_current = 0
outfilename = '{0}.{1}.{2}'.format(outbase, n_out, outsuffix)
outfile = open(outfilename, 'w')
n_seq += 1
base_total += fasta.length()
n_current += 1
base_current += fasta.length()
outfile.write(fasta.format())
# report statistics for last file
outfile.close()
print(' ', base_current, 'bases/amino acids', end=' ')
print('in', n_current, 'sequences', end=' ')
print('written to', outfilename)
# report overall statistics
print('\n')
print(base_total, 'characters from', n_seq, 'sequences written to', n_out,
'files\n')
nfeature += 1
elif info['Parent'] in flist:
for k in info:
if k not in flist[info['Parent']]:
flist[info['Parent']][k] = info[k]
else:
# flist[info['ID']] = info
sys.stderr.write('unknown feature {}\n'.format(info['feature']))
# write out sequences
for gene in flist:
thisgene = flist[gene]
f = Fasta()
f.id = thisgene['ID']
f.doc = ''
for k in save:
if k in thisgene:
f.doc += ' {}:{}'.format(k, thisgene[k])
f.seq = seq[thisgene['seqname']][thisgene['begin'] - 1:thisgene['end']]
if (thisgene['end'] - thisgene['begin'] > 100000):
# coordinates cross origin
f.seq = seq[thisgene['seqname']][thisgene['end'] - 1:] + seq[
thisgene['seqname']][:thisgene['begin']]
if thisgene['strand'] == '-':
f.seq = complement(f.seq)
sys.stdout.write(f.format(linelen=100))
exit(0)
"phams":["56154"],
"Start":15822,
"Stop":16230,
"Length":408,
"Name":"24",
"translation":"MTNVFTLDAMREETRKKYQPVKIGLSEDVTVELKPLLKLGKKAREAVADAVKEIEALPDEIDEDDEDSDELMDEVAEKICESIAKVFKLIATSPRKLLAELDTEEEPQIRAELYGAVLRTWMRET QLGEAAPSPN",
"Orientation":"F",
"Notes":"b'tail assembly chaperone'"} ...
Michael Gribskov 10 April 2021
================================================================================================="""
import sys
import json
from sequence.fasta import Fasta
# --------------------------------------------------------------------------------------------------
# main program
# --------------------------------------------------------------------------------------------------
if __name__ == '__main__':
fp = open(sys.argv[1], 'r')
phage = json.load(fp)
for gene in phage['results']:
f = Fasta()
f.id = gene['GeneID']
f.seq = gene['translation']
f.doc = gene['Notes'][2:-1]
print(f.format(linelen=100))
exit(0)
base = base.replace('.seq', '')
sys.stdout.write('\n\tExpanded file: {}\n\tbasename: {}\n'.format(
infilename, base))
outfilename = base + '.fasta'
outfile = None
try:
outfile = open(outfilename, 'w')
except:
sys.stderr.write(
'Unable to open output file ({})\n'.format(outfilename))
exit(2)
# process all sequences in the file
n = 0
for seq in infile:
fasta = Fasta()
fasta.id = base + '_{}'.format(n)
fasta.seq = seq.rstrip().upper()
fasta.doc = 'length={}'.format(fasta.length())
outfile.write(fasta.format(linelen=100))
n += 1
infile.close()
outfile.close()
sys.stdout.write('\t{} sequences written to {}\n'.format(
n, outfilename))
# end of loop over files
exit(0)