fix: remove new lines from input stream

2 files changed, 10 insertions, 15 deletions

diff --git a/pangraph/utils.py b/pangraph/utils.py
index 3e553a0..e4b63f3 100644
--- a/pangraph/utils.py
+++ b/pangraph/utils.py
@@ -174,7 +174,9 @@ def parse_fasta(fh):
             self.meta = meta
 
         def __str__(self):
-            return f">{self.name} {self.meta}\n{self.seq[:77]}...\n"
+            NL = '\n'
+            nc = 80
+            return f">{self.name} {self.meta}\n{NL.join([self.seq[i:(i+nc)] for i in range(0, len(self.seq), nc)])}"
 
         def __repr__(self):
             return str(self)
@@ -187,7 +189,7 @@ def parse_fasta(fh):
             line = as_str(line)
             if line == "" or line[0] == ">":
                 break
-            seq.write(line)
+            seq.write(line[:-1])
 
         header = as_str(line)
         yield Record(name=name[0], meta=" ".join(name[1:]), seq=seq.getvalue())
diff --git a/scripts/filter_plasmids.py b/scripts/filter_plasmids.py
index 9461451..4ef2670 100755
--- a/scripts/filter_plasmids.py
+++ b/scripts/filter_plasmids.py
@@ -13,8 +13,6 @@ from glob import glob
 sys.path.insert(0, os.path.abspath('.')) # gross hack
 from pangraph.utils import parse_fasta, breakpoint
 
-from Bio import SeqIO
-
 def open(path, *args, **kwargs):
     if path.endswith('.gz'):
         return gzip.open(path, *args, **kwargs)
@@ -26,18 +24,13 @@ def open(path, *args, **kwargs):
 
 from time import time
 if __name__ == "__main__":
-    t0 = time()
-    for path in glob("data/staph/assemblies/*.fna.gz"):
-        with open(path, 'rt') as fd:
-            seqs = [record for record in SeqIO.parse(fd, 'fasta')]
-    t1 = time()
-    print(f"bio parser took {t1 - t0} seconds")
-
-    t0 = time()
     for path in glob("data/staph/assemblies/*.fna.gz"):
-        with open(path, 'rt') as fd:
+        with open(path, 'rt') as fd, open("test.fa", 'w') as wtr:
+            for rec in parse_fasta(fd):
+                # print(str(rec))
+                wtr.write(str(rec))
+                wtr.write('\n')
             seqs = [record for record in parse_fasta(fd)]
-    t1 = time()
-    print(f"my parser took {t1 - t0} seconds")
+        break
 
     # main(sys.argv[1:])