fixed write_tf_records for very short sequences

bin/write_tfrecord_species.py

@@ -47,18 +47,13 @@ def load_clamsa_data(clamsa_prefix, seq_names, seq_len=None):
         return np.concatenate([clamsa_chunks[::-1,::-1, [1,0,3,2]], clamsa_chunks], axis=0)
 
 def get_species_data_hmm(genome_path='', annot_path='', species='', seq_len=500004, overlap_size=0, transition=False):
-
-    if not genome_path:
-        genome_path = f'/home/gabriell/deepl_data/genomes/{species}.fa.combined.masked'
-    if not annot_path:
-        annot_path=f'/home/gabriell//deepl_data/annot_longest_fixed/{species}.gtf'
-
     fasta = GenomeSequences(fasta_file=genome_path,
             chunksize=seq_len,
             overlap=overlap_size)
     fasta.encode_sequences() 
     seqs = [len(s) for s in fasta.sequences]
-    seq_names = fasta.sequence_names
+    seq_names = [seq_n for seq, seq_n in zip(fasta.sequence, fasta.sequence_names) \
+                    if len(seq)>seq_len]
     f_chunk, _, _ = fasta.get_flat_chunks(strand='+', pad=False)
     del fasta
     print(f_chunk.shape)