Merge pull request #718 from lldelisle/biopython

Make it compatiblle with last versions of Biopython

docs/conf.py

@@ -28,7 +28,7 @@
                 'matplotlib', 'matplotlib.pyplot', 'matplotlib.gridspec', 'matplotlib.ticker',
                 'matplotlib.textpath', 'matplotlib.patches', 'matplotlib.colors', 'matplotlib.cm',
                 'mpl_toolkits', 'mpl_toolkits.axisartist', 'mpl_toolkits.mplot3d', 'mpl_toolkits.axes_grid1',
-                'Bio', 'Bio.Seq', 'Bio.Alphabet', 'pyBigWig', 'tables', 'pytables', 'future', 'past', 'past.builtins',
+                'Bio', 'Bio.Seq', 'pyBigWig', 'tables', 'pytables', 'future', 'past', 'past.builtins',
                 'future.utils', 'cooler', 'logging', 'unidecode', 'hic2cool', 'hicmatrix', 'hicmatrix.HiCMatrix',
                 'hicmatrix.lib', 'krbalancing', 'fit_nbinom', 'pybedtools', 'graphviz', 'hyperopt', 'sklearn', 'sklearn.cluster']
 

docs/content/installation.rst

@@ -14,7 +14,7 @@ Requirements
 * ipykernel >= 5.3.0
 * pysam >= 0.16.*
 * intervaltree >= 3.1.*
-* biopython < 1.77
+* biopython
 * pytables >= 3.6.*
 * pandas >= 1.1.*
 * pybigwig >= 0.3.*

hicexplorer/hicBuildMatrix.py

@@ -21,7 +21,6 @@
 from intervaltree import IntervalTree, Interval
 
 from Bio.Seq import Seq
-from Bio.Alphabet import generic_dna
 
 # own tools
 from hicmatrix import HiCMatrix as hm
@@ -1204,7 +1203,7 @@ def main(args=None):
                 dangling_sequences[args.restrictionSequence[i]] = {}
                 dangling_sequences[args.restrictionSequence[i]]['pat_forw'] = args.danglingSequence[i]
                 dangling_sequences[args.restrictionSequence[i]]['pat_rev'] = str(
-                    Seq(args.danglingSequence[i], generic_dna).reverse_complement())
+                    Seq(args.danglingSequence[i]).reverse_complement())
 
         log.info("dangling sequences to check "
                  "are {}\n".format(dangling_sequences))

hicexplorer/hicFindRestSite.py

@@ -11,7 +11,6 @@
 from functools import partial
 from Bio import SeqIO
 from Bio.Seq import Seq
-from Bio.Alphabet import generic_dna
 from hicexplorer._version import __version__
 
 import logging
@@ -97,7 +96,7 @@ def find_pattern(pattern, fasta_file, out_file):
     """
 
     # get the reverse complement of the pattern
-    rev_compl = str(Seq(pattern, generic_dna).reverse_complement())
+    rev_compl = str(Seq(pattern).reverse_complement())
 
     temp = NamedTemporaryFile(suffix=".bed", delete=False, mode='wt')
     try:
@@ -109,7 +108,7 @@ def find_pattern(pattern, fasta_file, out_file):
     _open = partial(gzip.open, mode='rt') if encoding == 'gzip' else open
 
     with _open(fasta_file_name) as f:
-        for record in SeqIO.parse(f, 'fasta', generic_dna):
+        for record in SeqIO.parse(f, 'fasta'):
             # find all the occurrences of pattern
             for match in re.finditer(pattern, str(record.seq), re.IGNORECASE):
                 _ = temp.write('{}\t{}\t{}\t.\t0\t+\n'.format(record.name,

requirements.txt

@@ -5,7 +5,7 @@ matplotlib-base >= 3.1.*
 ipykernel >= 5.3.0
 pysam >= 0.16.*
 intervaltree >= 3.1.*
-biopython < 1.77
+biopython
 pytables >= 3.6.*
 pandas >= 1.1.*
 pybigwig >= 0.3.*

setup.py

@@ -98,7 +98,7 @@ def checkProgramIsInstalled(self, program, args, where_to_download,
                        "ipykernel >= 5.3.0",
                        "pysam >= 0.16",
                        "intervaltree >= 3.1.*",
-                       "biopython < 1.77",
+                       "biopython",
                        "tables >= 3.6.*",
                        "pandas >= 1.1.*",
                        "pyBigWig >= 0.3.*",