Author: bugman
Date: Wed Jan 28 15:15:13 2015
New Revision: 27343
URL: http://svn.gna.org/viewcvs/relax?rev=27343&view=rev
Log:
Modified the lib.structure.internal.coordinates.common_residues() function.
It now accepts the seq argument which will caused the gapped sequence strings
to be returned. This
is to allow for checking in the unit tests.
Modified:
trunk/lib/structure/internal/coordinates.py
Modified: trunk/lib/structure/internal/coordinates.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/internal/coordinates.py?rev=27343&r1=27342&r2=27343&view=diff
==============================================================================
--- trunk/lib/structure/internal/coordinates.py (original)
+++ trunk/lib/structure/internal/coordinates.py Wed Jan 28 15:15:13 2015
@@ -24,7 +24,6 @@
# Python module imports.
from numpy import array, float64
-import sys
# relax module imports.
from lib.errors import RelaxFault
@@ -254,14 +253,16 @@
return coord, ids
-def common_residues(gap_matrices=None, one_letter_codes=None):
+def common_residues(gap_matrices=None, one_letter_codes=None, seq=False):
"""Determine the common residues between all the pairwise alignments.
@keyword gap_matrices: The list of gap matrices from the pairwise
alignments.
@type gap_matrices: list of numpy rank-2 arrays.
@keyword one_letter_codes: The list of strings of one letter residue
codes for each molecule.
@type one_letter_codes: list of str
- @return: The residue skipping data structure. The
first dimension corresponds to the molecule, the second to the residue. A one
means the residue should be skipped, whereas zero means keep the residue.
+ @keyword seq: A flag which if True will cause the gapped
sequence strings to be returned.
+ @type seq: bool
+ @return: The residue skipping data structure and the
optional gapped sequence strings. For the skipping structure, the first
dimension corresponds to the molecule and the second to the residue. A one
means the residue should be skipped, whereas zero means keep the residue.
@rtype: list of list of int
"""
@@ -292,40 +293,35 @@
if gap_matrices[mol_index][1, j]:
skip[0][seq_index] = 1
- # Printout.
- sys.stdout.write("Shared residues:\n")
- sys.stdout.write("Molecule %3i: " % 1)
+ # Initialise the gapped strings data structure for the first molecule.
+ gapped_strings = ['']
for j in range(max(res_counts)):
# No more residues.
if j >= res_counts[0]:
- sys.stdout.write("-")
+ gapped_strings[0] += "-"
continue
# A skip.
if skip[0][j]:
- sys.stdout.write("-")
+ gapped_strings[0] += "-"
# A gap, so skip the residue.
elif gap_matrices[0][0, j]:
- sys.stdout.write("-")
- sys.stdout.write(one_letter_codes[0][j])
+ gapped_strings[0] += "-" + one_letter_codes[0][j]
# Keep the residue.
else:
- sys.stdout.write(one_letter_codes[0][j])
- sys.stdout.write("\n")
+ gapped_strings[0] += one_letter_codes[0][j]
# Update the first molecule skip counts.
skip_counts[0] = sum(skip[0])
# Update the residue skipping structures for all other molecules.
for mol_index in range(1, num_mols):
- # Printout.
- sys.stdout.write("Molecule %3i: " % (mol_index+1))
-
# Loop over the residues of alignment mol_index.
seq1_index = -1
seq2_index = -1
+ gapped_strings.append('')
for j in range(len(gap_matrices[mol_index-1][0])):
# Increment the sequence indices.
if not gap_matrices[mol_index-1][0, j]:
@@ -339,7 +335,7 @@
for k in range(seq2_index, res_counts[mol_index]):
skip[mol_index][k] = 1
skip_counts[mol_index] += 1
- sys.stdout.write("-")
+ gapped_strings[mol_index] += "-"
# Terminate the loop.
break
@@ -348,24 +344,26 @@
if gap_matrices[mol_index-1][0, j]:
skip[mol_index][seq2_index] = 1
skip_counts[mol_index] += 1
- sys.stdout.write("-")
+ gapped_strings[mol_index] += "-"
# Already skipped in the first molecule.
elif skip[0][seq1_index] and not gap_matrices[mol_index-1][1, j]:
skip[mol_index][seq2_index] = 1
skip_counts[mol_index] += 1
- sys.stdout.write("-")
+ gapped_strings[mol_index] += "-"
# Skipped in the second molecule.
elif gap_matrices[mol_index-1][1, j]:
- sys.stdout.write("-")
+ gapped_strings[mol_index] += "-"
# Print out the one letter code.
else:
- sys.stdout.write(one_letter_codes[mol_index][seq2_index])
-
- # EOL.
- sys.stdout.write("\n")
+ gapped_strings[mol_index] +=
one_letter_codes[mol_index][seq2_index]
+
+ # Printout.
+ print("Shared residues:")
+ for mol_index in range(num_mols):
+ print("Molecule %3i: %s" % (mol_index, gapped_strings[mol_index]))
# Sanity checks.
total = res_counts[0] - skip_counts[0]
@@ -375,7 +373,10 @@
raise RelaxFault
# Return the skipping data structure.
- return skip
+ if seq:
+ return skip, gapped_strings
+ else:
+ return skip
def loop_coord_structures(objects=None, molecules=None, models=None,
atom_id=None):
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