def format_oligos(oligos, options):
'''for output'''
oligo_list = []
for oligo in oligos:
id = oligo['id']
seq = oligo['seq'].upper()
size = oligo['size']
GC = chilli.cal_GC_content(seq, size)
Tm = TmDeltaG.calTm(seq, Seq.complement(seq), mono_conc=options.mono_conc, diva_conc=options.diva_conc, dntp_conc=options.dntp_conc, oligo_conc=options.oligo_conc)
GC = '%.1f' % GC
Tm = '%.1f' % Tm
oligo_list.append((id, seq, size, GC, Tm))
return oligo_list
def tab_out(amp_list, oligos, options, start_time, session_dir):
'''Format output in primer task'''
# amp_id, fp_id, rp_id, ppc, size, gc, fp_tm, fp_dg, rp_tm, rp_dg, seq, hit_id
options.outfile.write(
"AmpID\tFpID\tRpID\tHitID\tPPC\tSize\tAmpGC\tFpTm\tRpTm\tFpDg\tRpDg\tBindingStart\tBindingStop\tAmpSeq\n"
)
sn = 0
amp_list.sort(key=itemgetter(1, 2), reverse=True)
for ave_Tm, ppc, amp_len, amp in amp_list:
sn = sn + 1
amp_len = amp['size']
# p for plus, m for minus primer # History reason
p_qid = amp['pid']
f_3_pos = amp['f3_pos']
p_qseq = amp['p_qseq']
p_aseq = amp['p_aseq']
p_tail = amp['p_tail']
p_Tm = amp['p_Tm']
p_DeltaG = amp['p_DeltaG']
p_sb = f_3_pos - len(p_aseq) + 1
m_qid = amp['mid']
r_3_pos = amp['r3_pos']
m_qseq = amp['m_qseq']
m_aseq = amp['m_aseq']
m_tail = amp['m_tail']
m_Tm = amp['m_Tm']
m_DeltaG = amp['m_DeltaG']
m_se = r_3_pos + len(m_aseq)
mid_seq = amp['mid_seq']
real_hid = amp['real_hid']
amp_seq = p_tail + p_qseq + mid_seq + m_qseq + m_tail
amp_GC = chilli.cal_GC_content(amp_seq, +amp_len)
if p_qid == m_qid:
ppc = '-%.1f' % ppc
else:
ppc = '%.1f' % ppc
options.outfile.write(
"%d\t%s\t%s\t%s\t%s\t%d\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%d\t%d\t%s\n"
% (sn, p_qid, m_qid, real_hid, ppc, amp_len, amp_GC, p_Tm, m_Tm,
p_DeltaG, m_DeltaG, p_sb, m_se, amp_seq))
def tab_out(amp_list, oligos, options, start_time, session_dir):
'''Format output in primer task'''
# amp_id, fp_id, rp_id, ppc, size, gc, fp_tm, fp_dg, rp_tm, rp_dg, seq, hit_id
options.outfile.write("AmpID\tFpID\tRpID\tHitID\tPPC\tSize\tAmpGC\tFpTm\tRpTm\tFpDg\tRpDg\tBindingStart\tBindingStop\tAmpSeq\n")
sn = 0
amp_list.sort(key=itemgetter(1, 2), reverse=True)
for ave_Tm, ppc, amp_len, amp in amp_list:
sn = sn + 1
amp_len = amp['size']
# p for plus, m for minus primer # History reason
p_qid = amp['pid']
f_3_pos = amp['f3_pos']
p_qseq = amp['p_qseq']
p_aseq = amp['p_aseq']
p_tail = amp['p_tail']
p_Tm = amp['p_Tm']
p_DeltaG = amp['p_DeltaG']
p_sb = f_3_pos - len(p_aseq) + 1
m_qid = amp['mid']
r_3_pos = amp['r3_pos']
m_qseq = amp['m_qseq']
m_aseq = amp['m_aseq']
m_tail = amp['m_tail']
m_Tm = amp['m_Tm']
m_DeltaG = amp['m_DeltaG']
m_se = r_3_pos + len(m_aseq)
mid_seq = amp['mid_seq']
real_hid = amp['real_hid']
amp_seq = p_tail + p_qseq + mid_seq + m_qseq + m_tail
amp_GC = chilli.cal_GC_content(amp_seq, + amp_len)
if p_qid == m_qid:
ppc = '-%.1f' % ppc
else:
ppc = '%.1f' % ppc
options.outfile.write("%d\t%s\t%s\t%s\t%s\t%d\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%d\t%d\t%s\n" % (sn, p_qid, m_qid, real_hid, ppc, amp_len, amp_GC, p_Tm, m_Tm, p_DeltaG, m_DeltaG, p_sb, m_se, amp_seq))
def format_output_primer(amp_list, oligos, options, start_time, session_dir):
'''Format output in primer task'''
linesep = os.linesep
out = []
out = print_head(out, options)
ID_list = []
for i in xrange(len(oligos)):
ID_list.append(oligos[i]['id'])
query_line = textwrap.fill('Query = %s' % ('; '.join(ID_list)), 80)
out.append(query_line)
out.append(' %s primer sequences' % (len(oligos)))
out.append(linesep)
out.append('Database = %s' % textwrap.fill(', '.join([os.path.basename(db) for db in options.database]), 80))
#out.append(' %s sequences' % (len(fcdict)))
out.append(linesep)
out.append('Reports Beginning'.ljust(80, '.'))
out.append(linesep * 2)
amp_num = len(amp_list)
if amp_num > 1:
out.append('Distribution of %s potential PCR amplicons predicted by MFEprimer-2.0 on the query primers' % amp_num)
else:
out.append('Distribution of %s potential PCR amplicon predicted by MFEprimer-2.0 on the query primers' % amp_num)
out.append(linesep)
out.append('[Sorted by average Tm in descending order]')
out.append('FP '.rjust(69) + 'RP '.rjust(8) + 'FP '.rjust(8) + 'RP '.rjust(8) + 'FP '.rjust(8) + 'RP '.rjust(8))
# Δ takes two characters position
out.append('Size'.rjust(53) + 'PPC '.rjust(8) + 'Tm '.rjust(8) + 'Tm '.rjust(8) + ('%sG' % u'\u0394').rjust(7) + ('%sG' % u'\u0394').rjust(7) + ('3\'%sG' % u'\u0394').rjust(8) + ('3\'%sG' % u'\u0394').rjust(7))
out.append('Primers producing potential PCR products:'.ljust(42) + '(bp)'.rjust(11) + '(%) '.rjust(8) + u'\u2103'.rjust(6) + u'\u2103'.rjust(7) + '(kcal/mol)'.center(22) + '(kcal/mol)'.center(14))
out.append(linesep)
detail_line = []
fa_file = []
sn = 0
#amp_list.append([amp_len, ave_Tm, p, m, ppc, amp_graphic, mid_seq, real_hid, hdesc])
amp_list.sort(key=itemgetter(1, 2), reverse=True)
for ave_Tm, ppc, amp_len, amp in amp_list:
sn = sn + 1
hid = amp['real_hid']
desc = '%s: %s' % (sn, hid)
amp_len = amp['size']
p_qid = amp['pid']
f_len = amp['plen']
pseq = amp['pseq']
f_3_pos = amp['f3_pos']
p_3_DeltaG = amp['p_3_DeltaG']
p_qseq = amp['p_qseq']
p_aseq = amp['p_aseq']
p_sseq = amp['p_sseq']
p_tail = amp['p_tail']
p_Tm = amp['p_Tm']
p_DeltaG = amp['p_DeltaG']
p_sb = f_3_pos - len(p_aseq) + 1
m_qid = amp['mid']
r_len = amp['mlen']
mseq = amp['mseq']
r_3_pos = amp['r3_pos']
m_3_DeltaG = amp['m_3_DeltaG']
m_qseq = amp['m_qseq']
m_aseq = amp['m_aseq']
m_sseq = amp['m_sseq']
m_tail = amp['m_tail']
m_Tm = amp['m_Tm']
m_DeltaG = amp['m_DeltaG']
m_se = r_3_pos + len(m_aseq)
amp_graphic = amp['amp_graphic']
mid_seq = amp['mid_seq']
real_hid = amp['real_hid']
hdesc = amp['hdesc']
amp_seq = p_tail + p_qseq + mid_seq + m_qseq + m_tail
amp_GC = chilli.cal_GC_content(amp_seq, + amp_len)
if len(desc) > 42:
desc = desc[:42] + '...'
if p_qid == m_qid:
ppc = '-%.1f' % ppc
else:
ppc = '%.1f' % ppc
out.append(desc.ljust(42) + (str(amp_len)).rjust(11) + ppc.rjust(8) + ('%.1f' % p_Tm).rjust(8) + ('%.1f' % m_Tm).rjust(8) + ('%.1f' % p_DeltaG).rjust(8) + ('%.1f' % m_DeltaG).rjust(8) + ('%.1f' % p_3_DeltaG).rjust(8) + ('%.1f' % m_3_DeltaG).rjust(8))
if not hdesc:
detail_line.append('%s: %s + %s ==> %s%s' % (sn, p_qid, m_qid, hid, linesep))
fa_desc = '>%s %s + %s %s' % (sn, p_qid, m_qid, hid)
else:
detail_line.append('%s: %s + %s ==> %s %s%s' % (sn, p_qid, m_qid, hid, hdesc, linesep))
fa_desc = '>%s %s %s %s %s' % (sn, p_qid, m_qid, hid, hdesc)
detail_line.append(' ' + 'PPC = %s%%, Size = %s bp, GC content = %.1f%%' % (ppc, amp_len, amp_GC))
detail_line.append(' ' + 'FP: Tm = %.1f (%s), %sG = %.1f (kcal/mol), 3\'%sG = %.1f (kcal/mol)' % (p_Tm, u'\u2103', u'\u0394', p_DeltaG, u'\u0394', p_3_DeltaG))
detail_line.append(' ' + 'RP: Tm = %.1f (%s), %sG = %.1f (kcal/mol), 3\'%sG = %.1f (kcal/mol)' % (m_Tm, u'\u2103', u'\u0394', m_DeltaG, u'\u0394', m_3_DeltaG))
detail_line.append(' ' + 'Binding sites: %s(%s/%s) ... %s(%s/%s)' % (p_sb, len(p_aseq), f_len, m_se, len(m_aseq), r_len))
detail_line.append(linesep)
detail_line.append(amp_graphic + linesep)
fa_seq = chilli.print_seq(amp_seq, 80)
fa_file.append(fa_desc)
fa_file.append(fa_seq)
detail_line.append(fa_desc + linesep + fa_seq + linesep)
#out = []
out.append(linesep)
out.append('Details for the primers binding to the DNA template')
out.append('[Sorted by average Tm in descending order]' + linesep)
for i in xrange(len(detail_line)):
line = detail_line[i]
out.append(line)
out.append(linesep*2)
out = print_foot(out, options, start_time)
out = os.linesep.join(out)
options.outfile.write(out.encode('utf-8'))
if options.amplicon:
try:
out_file = options.outfile.name + '.fa'
fh = open(out_file, 'w')
except:
msg = 'Error: can not open %s for write' % out_file
print2stderr(msg)
fh.write(os.linesep.join(fa_file))
fh.close()
def format_output_primer(amp_list, oligos, options, start_time, session_dir):
'''Format output in primer task'''
linesep = os.linesep
out = []
out = print_head(out, options)
ID_list = []
for i in xrange(len(oligos)):
ID_list.append(oligos[i]['id'])
query_line = textwrap.fill('Query = %s' % ('; '.join(ID_list)), 80)
out.append(query_line)
out.append(' %s primer sequences' % (len(oligos)))
out.append(linesep)
out.append('Database = %s' % textwrap.fill(
', '.join([os.path.basename(db) for db in options.database]), 80))
#out.append(' %s sequences' % (len(fcdict)))
out.append(linesep)
out.append('Reports Beginning'.ljust(80, '.'))
out.append(linesep * 2)
amp_num = len(amp_list)
if amp_num > 1:
out.append(
'Distribution of %s potential PCR amplicons predicted by MFEprimer-2.0 on the query primers'
% amp_num)
else:
out.append(
'Distribution of %s potential PCR amplicon predicted by MFEprimer-2.0 on the query primers'
% amp_num)
out.append(linesep)
out.append('[Sorted by average Tm in descending order]')
out.append('FP '.rjust(69) + 'RP '.rjust(8) + 'FP '.rjust(8) +
'RP '.rjust(8) + 'FP '.rjust(8) + 'RP '.rjust(8))
# Δ takes two characters position
out.append('Size'.rjust(53) + 'PPC '.rjust(8) + 'Tm '.rjust(8) +
'Tm '.rjust(8) + ('%sG' % u'\u0394').rjust(7) +
('%sG' % u'\u0394').rjust(7) + ('3\'%sG' % u'\u0394').rjust(8) +
('3\'%sG' % u'\u0394').rjust(7))
out.append('Primers producing potential PCR products:'.ljust(42) +
'(bp)'.rjust(11) + '(%) '.rjust(8) + u'\u2103'.rjust(6) +
u'\u2103'.rjust(7) + '(kcal/mol)'.center(22) +
'(kcal/mol)'.center(14))
out.append(linesep)
detail_line = []
fa_file = []
sn = 0
#amp_list.append([amp_len, ave_Tm, p, m, ppc, amp_graphic, mid_seq, real_hid, hdesc])
amp_list.sort(key=itemgetter(1, 2), reverse=True)
for ave_Tm, ppc, amp_len, amp in amp_list:
sn = sn + 1
hid = amp['real_hid']
desc = '%s: %s' % (sn, hid)
amp_len = amp['size']
p_qid = amp['pid']
f_len = amp['plen']
pseq = amp['pseq']
f_3_pos = amp['f3_pos']
p_3_DeltaG = amp['p_3_DeltaG']
p_qseq = amp['p_qseq']
p_aseq = amp['p_aseq']
p_sseq = amp['p_sseq']
p_tail = amp['p_tail']
p_Tm = amp['p_Tm']
p_DeltaG = amp['p_DeltaG']
p_sb = f_3_pos - len(p_aseq) + 1
m_qid = amp['mid']
r_len = amp['mlen']
mseq = amp['mseq']
r_3_pos = amp['r3_pos']
m_3_DeltaG = amp['m_3_DeltaG']
m_qseq = amp['m_qseq']
m_aseq = amp['m_aseq']
m_sseq = amp['m_sseq']
m_tail = amp['m_tail']
m_Tm = amp['m_Tm']
m_DeltaG = amp['m_DeltaG']
m_se = r_3_pos + len(m_aseq)
amp_graphic = amp['amp_graphic']
mid_seq = amp['mid_seq']
real_hid = amp['real_hid']
hdesc = amp['hdesc']
amp_seq = p_tail + p_qseq + mid_seq + m_qseq + m_tail
amp_GC = chilli.cal_GC_content(amp_seq, +amp_len)
if len(desc) > 42:
desc = desc[:42] + '...'
if p_qid == m_qid:
ppc = '-%.1f' % ppc
else:
ppc = '%.1f' % ppc
out.append(
desc.ljust(42) + (str(amp_len)).rjust(11) + ppc.rjust(8) +
('%.1f' % p_Tm).rjust(8) + ('%.1f' % m_Tm).rjust(8) +
('%.1f' % p_DeltaG).rjust(8) + ('%.1f' % m_DeltaG).rjust(8) +
('%.1f' % p_3_DeltaG).rjust(8) + ('%.1f' % m_3_DeltaG).rjust(8))
if not hdesc:
detail_line.append('%s: %s + %s ==> %s%s' %
(sn, p_qid, m_qid, hid, linesep))
fa_desc = '>%s %s + %s %s' % (sn, p_qid, m_qid, hid)
else:
detail_line.append('%s: %s + %s ==> %s %s%s' %
(sn, p_qid, m_qid, hid, hdesc, linesep))
fa_desc = '>%s %s %s %s %s' % (sn, p_qid, m_qid, hid, hdesc)
detail_line.append(' ' +
'PPC = %s%%, Size = %s bp, GC content = %.1f%%' %
(ppc, amp_len, amp_GC))
detail_line.append(
' ' +
'FP: Tm = %.1f (%s), %sG = %.1f (kcal/mol), 3\'%sG = %.1f (kcal/mol)'
% (p_Tm, u'\u2103', u'\u0394', p_DeltaG, u'\u0394', p_3_DeltaG))
detail_line.append(
' ' +
'RP: Tm = %.1f (%s), %sG = %.1f (kcal/mol), 3\'%sG = %.1f (kcal/mol)'
% (m_Tm, u'\u2103', u'\u0394', m_DeltaG, u'\u0394', m_3_DeltaG))
detail_line.append(
' ' + 'Binding sites: %s(%s/%s) ... %s(%s/%s)' %
(p_sb, len(p_aseq), f_len, m_se, len(m_aseq), r_len))
detail_line.append(linesep)
detail_line.append(amp_graphic + linesep)
fa_seq = chilli.print_seq(amp_seq, 80)
fa_file.append(fa_desc)
fa_file.append(fa_seq)
detail_line.append(fa_desc + linesep + fa_seq + linesep)
#out = []
out.append(linesep)
out.append('Details for the primers binding to the DNA template')
out.append('[Sorted by average Tm in descending order]' + linesep)
for i in xrange(len(detail_line)):
line = detail_line[i]
out.append(line)
out.append(linesep * 2)
out = print_foot(out, options, start_time)
out = os.linesep.join(out)
options.outfile.write(out.encode('utf-8'))
if options.amplicon:
try:
out_file = options.outfile.name + '.fa'
fh = open(out_file, 'w')
except:
msg = 'Error: can not open %s for write' % out_file
print2stderr(msg)
fh.write(os.linesep.join(fa_file))
fh.close()
def format_output_primer(amp_list, oligos, options, start_time, session_dir):
'''Format output in primer task'''
linesep = os.linesep
detail = []
#fa_file = []
ID_list = []
for i in xrange(len(oligos)):
ID_list.append(oligos[i]['id'])
size_dict = {}
dg_dict = {}
tm_dict = {}
sn = 0
amp_list.sort(key=itemgetter(1, 2), reverse=True)
for ave_Tm, ppc, amp_len, amp in amp_list:
sn = sn + 1
hid = amp['real_hid']
try:
acc = hid.split('|')[3]
except:
acc = hid
desc = '%s: %s' % (sn, hid)
amp_len = amp['size']
p_qid = amp['pid']
f_len = amp['plen']
pseq = amp['pseq']
f_3_pos = amp['f3_pos']
#p_3_DeltaG = amp['p_3_DeltaG']
p_3_DeltaG = '%.1f' % amp['p_3_DeltaG']
p_qseq = amp['p_qseq']
p_aseq = amp['p_aseq']
p_sseq = amp['p_sseq']
p_tail = amp['p_tail']
#p_Tm = amp['p_Tm']
p_Tm = '%.1f' % amp['p_Tm']
#p_DeltaG = amp['p_DeltaG']
p_DeltaG = '%.1f' % amp['p_DeltaG']
p_sb = f_3_pos - len(pseq) + 1
m_qid = amp['mid']
r_len = amp['mlen']
mseq = amp['mseq']
r_3_pos = amp['r3_pos']
#m_3_DeltaG = amp['m_3_DeltaG']
m_3_DeltaG = '%.1f' % amp['m_3_DeltaG']
m_qseq = amp['m_qseq']
m_aseq = amp['m_aseq']
m_sseq = amp['m_sseq']
m_tail = amp['m_tail']
#m_Tm = amp['m_Tm']
m_Tm = '%.1f' % amp['m_Tm']
#m_DeltaG = amp['m_DeltaG']
m_DeltaG = '%.1f' % amp['m_DeltaG']
m_se = r_3_pos + len(mseq)
amp_graphic = amp['amp_graphic']
mid_seq = amp['mid_seq']
real_hid = amp['real_hid']
hdesc = amp['hdesc']
amp_seq = p_tail + p_qseq + mid_seq + m_qseq + m_tail
amp_GC = '%.1f' % chilli.cal_GC_content(amp_seq, + amp_len)
if len(desc) > 42:
desc = desc[:42] + '...'
if p_qid == m_qid:
ppc = '-%.1f' % ppc
else:
ppc = '%.1f' % ppc
if not hdesc:
amp_title = '%s: %s + %s ==> %s' % (sn, p_qid, m_qid, hid)
fa_desc = '>Amp_%s %s + %s ==> %s' % (sn, p_qid, m_qid, hid)
else:
amp_title = '%s: %s + %s ==> %s %s' % (sn, p_qid, m_qid, hid, hdesc)
fa_desc = '>Amp_%s %s + %s ==> %s %s' % (sn, p_qid, m_qid, hid, hdesc)
fa_seq = chilli.print_seq(amp_seq, 80)
fa_seq = fa_desc + linesep + fa_seq + linesep
#fa_file.append(fa_desc)
#fa_file.append(fa_seq)
size_dict[amp_len] = size_dict.setdefault(amp_len, 0) + 1
tm_dict[p_Tm] = tm_dict.setdefault(p_Tm, 0) + 1
tm_dict[m_Tm] = tm_dict.setdefault(m_Tm, 0) + 1
dg_dict[p_DeltaG] = dg_dict.setdefault(p_DeltaG, 0) + 1
dg_dict[m_DeltaG] = dg_dict.setdefault(m_DeltaG, 0) + 1
detail.append((sn, acc, p_qid, m_qid, amp_len, ppc, p_Tm, m_Tm, p_DeltaG, m_DeltaG, p_3_DeltaG, m_3_DeltaG, amp_GC, p_sb, len(p_aseq), f_len, m_se, len(m_aseq), r_len, amp_graphic, fa_seq, hid, hdesc))
return detail, size_dict, tm_dict, dg_dict