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Print error messages on stderr consistently #8

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Print error messages on stderr consistently #8

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73 changes: 45 additions & 28 deletions kcalign/__init__.py
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Original file line number Diff line number Diff line change
@@ -1,11 +1,8 @@
#!/usr/bin/env python

from Bio.Seq import Seq
from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
import os
import pty
import shlex
import sys
import subprocess
import warnings
Expand Down Expand Up @@ -46,14 +43,14 @@ def invoke_kalign(input_file, output_file):
just to be safe.
"""
if not os.path.exists(input_file):
print('Input file missing')
print('Input file missing', file=sys.stderr)
return 1
# If STDIN is not a tty, kalign3 assumes that STDIN is an input file
# and fails to detect its type.
# Pass in a fake pty to work around this behavior, which is appropriate
# for command-line usage but doesn't work in a headless environment.
fakepty, alsofakepty = pty.openpty()
command = shlex.split(f'kalign -i {input_file} -o {output_file}')
command = ['kalign', '-i', input_file, '-o' output_file]
kaligner = subprocess.Popen(command, stderr=subprocess.PIPE,
stdout=subprocess.PIPE, stdin=fakepty)
kaligner.wait()
Expand All @@ -63,13 +60,13 @@ def invoke_kalign(input_file, output_file):
# If Kalign fails try again with MAFFT (Kalign sometimes seg faults on some data)
if kaligner.returncode != 0:
with open(output_file, 'w') as out_fh:
command = shlex.split(f'mafft {input_file}')
command = ['mafft', input_file]
mafft = subprocess.Popen(command, stdout=out_fh)
mafft.wait()
_, stderr = mafft.communicate()
if mafft.returncode != 0:
sys.stderr.write('Error running mafft')
sys.stderr.write(stderr.decode('utf-8'))
print('Error running mafft', file=sys.stderr)
print(stderr.decode('utf-8'), file=sys.stderr)
return 1
else:
return 0
Expand Down Expand Up @@ -516,11 +513,7 @@ def compressor(seqs, names, ids, og_seqs):
else:
new_ids.append('MultiSeq'+str(count)+'_'+str(len(same)))
count += 1
name = ''
for s in same:
name += s
name += ','
new_names.append(name[:-1])
new_names.append(','.join(s for s in same))
new_seqs.append(seqs[ids.index(same[0])])
new_og_seqs[new_ids[-1]] = og_seqs[same[0]]
return new_seqs, new_names, new_ids, new_og_seqs
Expand All @@ -529,27 +522,36 @@ def compressor(seqs, names, ids, og_seqs):
def check_input(reference, reads):
"""Check input FASTA is occupied and doesn't use invalid characters"""
records = []
invalids = ['E', 'F', 'I', 'J', 'L', 'O', 'P', 'Q', 'X', 'Z']
invalids = {'E', 'F', 'I', 'J', 'L', 'O', 'P', 'Q', 'X', 'Z'}
try:
for record in SeqIO.parse(reference, 'fasta'):
if any(x in invalids for x in record.seq):
print(f'Input Error: Invalid characters detected in reference sequence')
print(
'Input Error: Invalid characters detected in reference sequence',
file=sys.stderr
)
return 1
records.append(records)
if len(records) != 1:
print('User Error: reference input should contain exactly one sequence')
print(
'User Error: reference input should contain exactly one sequence',
file=sys.stderr
)
return 1
records = []
for record in SeqIO.parse(reads, 'fasta'):
if any(x in invalids for x in record.seq):
print(f'Input Error: Invalid characters detected in sequence ID: {record.id}')
print(
f'Input Error: Invalid characters detected in sequence ID: {record.id}',
file=sys.stderr
)
return 1
records.append(record)
if len(records) == 0:
print('User Error: sequence FASTA file is empty')
print('User Error: sequence FASTA file is empty', file=sys.stderr)
return 1
except Exception:
print('User Error: improperly formatted FASTA')
print('User Error: improperly formatted FASTA', file=sys.stderr)
return 1


Expand All @@ -561,7 +563,10 @@ def check_tab(tab):
if int(tab) in [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33]:
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use a range here!

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and do the int conversion outside of the function to avoid the duplicated action

tab = int(tab)
else:
print('User Error: Chosen translation table number is invalid. See: https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for valid options')
print(
'User Error: Chosen translation table number is invalid. See: https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for valid options',
file=sys.stderr
)
return 1
return tab

Expand All @@ -575,23 +580,35 @@ def genome_mode(reference, reads, start, end, compress, para, tab):
try:
start = int(start)-1
end = int(end)
except Exception:
print('User Error: invalid start/end coordinate(s)')
except ValueError:
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Also note that the try/except won't catch negative values, if that's the intention.

print(
'User Error: invalid start/end coordinate(s)',
file=sys.stderr
)
return 1
join = 0
if start >= end:
print('User Error: start coordinate(s) must be less than the end coordinate(s)')
print(
'User Error: start coordinate(s) must be less than the end coordinate(s)',
file=sys.stderr
)
return 1
else:
try:
start = (int(start.split(',')[0])-1, int(start.split(',')[1])-1)
end = (int(end.split(',')[0]), int(end.split(',')[1]))
except Exception:
print('User Error: invalid start/end coordinate(s)')
except ValueError:
print(
'User Error: invalid start/end coordinate(s)',
file=sys.stderr
)
return 1
join = 1
if start[0] >= end[0] or start[1] >= end[1]:
print('User Error: start coordinate(s) must be less than the end coordinate(s)')
print(
'User Error: start coordinate(s) must be less than the end coordinate(s)',
file=sys.stderr
)
return 1

# Find protein sequence of gene of interest and extract the original DNA
Expand All @@ -618,7 +635,7 @@ def genome_mode(reference, reads, start, end, compress, para, tab):
og_seqs[idd] = og_seqs[idd][:-3]
records = [SeqRecord(seq, id=idd, description=name)]
if len(seqs) == 0:
print('No homologous sequences were found')
print('No homologous sequences were found', file=sys.stderr)
return 1
combine_align(records, ids, names, seqs)
names = dict(zip(ids, names))
Expand Down Expand Up @@ -695,7 +712,7 @@ def mixed_mode(reference, reads, compress, para, tab):
og_seqs[idd] = og_seqs[idd][:-3]
records = [SeqRecord(seq, id=idd, description=name)]
if len(seqs) == 0:
print('No homologous sequences were found')
print('No homologous sequences were found', file=sys.stderr)
return 1
combine_align(records, ids, names, seqs)
names = dict(zip(ids, names))
Expand Down