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Bio/SwissProt: PEP8 whitespace cleanup.
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@cbrueffer @peterjc
cbrueffer authored and peterjc committed Dec 27, 2012
1 parent 85777b8 commit dd4f8e1
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Showing 2 changed files with 40 additions and 40 deletions.
4 changes: 2 additions & 2 deletions Bio/SwissProt/KeyWList.py
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Expand Up @@ -63,12 +63,12 @@ def parse(handle):
# We have reached the footer
break
key = line[:2]
if key=="//":
if key == "//":
record["DE"] = " ".join(record["DE"])
record["SY"] = " ".join(record["SY"])
yield record
record = Record()
elif line[2:5]==" ":
elif line[2:5] == " ":
value = line[5:].strip()
if key in ("ID", "IC", "AC", "CA"):
record[key] = value
Expand Down
76 changes: 38 additions & 38 deletions Bio/SwissProt/__init__.py
View file
Expand Up @@ -144,94 +144,94 @@ def _read(handle):
if unread:
value = unread + " " + value
unread = ""
if key=='**':
if key == '**':
#See Bug 2353, some files from the EBI have extra lines
#starting "**" (two asterisks/stars). They appear
#to be unofficial automated annotations. e.g.
#**
#** ################# INTERNAL SECTION ##################
#**HA SAM; Annotated by PicoHamap 1.88; MF_01138.1; 09-NOV-2003.
pass
elif key=='ID':
elif key == 'ID':
record = Record()
_read_id(record, line)
_sequence_lines = []
elif key=='AC':
elif key == 'AC':
accessions = [word for word in value.rstrip(";").split("; ")]
record.accessions.extend(accessions)
elif key=='DT':
elif key == 'DT':
_read_dt(record, line)
elif key=='DE':
elif key == 'DE':
record.description.append(value.strip())
elif key=='GN':
elif key == 'GN':
if record.gene_name:
record.gene_name += " "
record.gene_name += value
elif key=='OS':
elif key == 'OS':
record.organism.append(value)
elif key=='OG':
elif key == 'OG':
record.organelle += line[5:]
elif key=='OC':
elif key == 'OC':
cols = [col for col in value.rstrip(";.").split("; ")]
record.organism_classification.extend(cols)
elif key=='OX':
elif key == 'OX':
_read_ox(record, line)
elif key=='OH':
elif key == 'OH':
_read_oh(record, line)
elif key=='RN':
elif key == 'RN':
reference = Reference()
_read_rn(reference, value)
record.references.append(reference)
elif key=='RP':
elif key == 'RP':
assert record.references, "RP: missing RN"
record.references[-1].positions.append(value)
elif key=='RC':
elif key == 'RC':
assert record.references, "RC: missing RN"
reference = record.references[-1]
unread = _read_rc(reference, value)
elif key=='RX':
elif key == 'RX':
assert record.references, "RX: missing RN"
reference = record.references[-1]
_read_rx(reference, value)
elif key=='RL':
elif key == 'RL':
assert record.references, "RL: missing RN"
reference = record.references[-1]
reference.location.append(value)
# In UniProt release 1.12 of 6/21/04, there is a new RG
# (Reference Group) line, which references a group instead of
# an author. Each block must have at least 1 RA or RG line.
elif key=='RA':
elif key == 'RA':
assert record.references, "RA: missing RN"
reference = record.references[-1]
reference.authors.append(value)
elif key=='RG':
elif key == 'RG':
assert record.references, "RG: missing RN"
reference = record.references[-1]
reference.authors.append(value)
elif key=="RT":
elif key == "RT":
assert record.references, "RT: missing RN"
reference = record.references[-1]
reference.title.append(value)
elif key=='CC':
elif key == 'CC':
_read_cc(record, line)
elif key=='DR':
elif key == 'DR':
_read_dr(record, value)
elif key=='PE':
elif key == 'PE':
#TODO - Record this information?
pass
elif key=='KW':
elif key == 'KW':
cols = value.rstrip(";.").split('; ')
record.keywords.extend(cols)
elif key=='FT':
elif key == 'FT':
_read_ft(record, line)
elif key=='SQ':
elif key == 'SQ':
cols = value.split()
assert len(cols) == 7, "I don't understand SQ line %s" % line
# Do more checking here?
record.seqinfo = int(cols[1]), int(cols[3]), cols[5]
elif key==' ':
elif key == ' ':
_sequence_lines.append(value.replace(" ", "").rstrip())
elif key=='//':
elif key == '//':
# Join multiline data into one string
record.description = " ".join(record.description)
record.organism = " ".join(record.organism)
Expand Down Expand Up @@ -268,7 +268,7 @@ def _read_id(record, line):
record.molecule_type = None
record.sequence_length = int(cols[2])
else:
raise ValueError("ID line has unrecognised format:\n"+line)
raise ValueError("ID line has unrecognised format:\n" + line)
# check if the data class is one of the allowed values
allowed = ('STANDARD', 'PRELIMINARY', 'IPI', 'Reviewed', 'Unreviewed')
if record.data_class not in allowed:
Expand Down Expand Up @@ -398,7 +398,7 @@ def _read_oh(record, line):
# Line type OH (Organism Host) for viral hosts
assert line[5:].startswith("NCBI_TaxID="), "Unexpected %s" % line
line = line[16:].rstrip()
assert line[-1]=="." and line.count(";")==1, line
assert line[-1] == "." and line.count(";") == 1, line
taxid, name = line[:-1].split(";")
record.host_taxonomy_id.append(taxid.strip())
record.host_organism.append(name.strip())
Expand All @@ -411,7 +411,7 @@ def _read_rn(reference, rn):

def _read_rc(reference, value):
cols = value.split(';')
if value[-1]==';':
if value[-1] == ';':
unread = ""
else:
cols, unread = cols[:-1], cols[-1]
Expand All @@ -420,7 +420,7 @@ def _read_rc(reference, value):
return
# The token is everything before the first '=' character.
i = col.find("=")
if i>=0:
if i >= 0:
token, text = col[:i], col[i+1:]
comment = token.lstrip(), text
reference.comments.append(comment)
Expand All @@ -440,7 +440,7 @@ def _read_rx(reference, value):
# have extraneous information in the RX line. Check for
# this and chop it out of the line.
# (noticed by katel@worldpath.net)
value = value.replace(' [NCBI, ExPASy, Israel, Japan]','')
value = value.replace(' [NCBI, ExPASy, Israel, Japan]', '')

# RX lines can also be used of the form
# RX PubMed=9603189;
Expand Down Expand Up @@ -478,9 +478,9 @@ def _read_rx(reference, value):

def _read_cc(record, line):
key, value = line[5:8], line[9:].rstrip()
if key=='-!-': # Make a new comment
if key == '-!-': # Make a new comment
record.comments.append(value)
elif key==' ': # add to the previous comment
elif key == ' ': # add to the previous comment
if not record.comments:
# TCMO_STRGA in Release 37 has comment with no topic
record.comments.append(value)
Expand Down Expand Up @@ -509,15 +509,15 @@ def _read_ft(record, line):
except ValueError:
to_res = line[16:22].lstrip()
#if there is a feature_id (FTId), store it away
if line[29:35]==r"/FTId=":
if line[29:35] == r"/FTId=":
ft_id = line[35:70].rstrip()[:-1]
description = ""
else:
ft_id =""
ft_id = ""
description = line[29:70].rstrip()
if not name: # is continuation of last one
assert not from_res and not to_res
name, from_res, to_res, old_description,old_ft_id = record.features[-1]
name, from_res, to_res, old_description, old_ft_id = record.features[-1]
del record.features[-1]
description = ("%s %s" % (old_description, description)).strip()

Expand All @@ -543,7 +543,7 @@ def _read_ft(record, line):
second_seq = second_seq.replace(" ", "")
# reassemble the description
description = first_seq + " -> " + second_seq + extra_info
record.features.append((name, from_res, to_res, description,ft_id))
record.features.append((name, from_res, to_res, description, ft_id))


if __name__ == "__main__":
Expand Down

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