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Addjust script printing #31

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Addjust script printing #31

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20 changes: 14 additions & 6 deletions reform.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,11 @@ def main():

## Sequential processing
for index in range(iterations):
## Read the new fasta (to be inserted into the ref genome)
# Start interation
print("-------------------------------------------")
print(f"Begin modification from in{index+1}.fa")
print("-------------------------------------------")
## Read the new fasta (to be inserted into the ref genome)
try:
record = list(SeqIO.parse(in_arg.in_fasta[index], "fasta"))[0]
except IndexError:
Expand Down Expand Up @@ -91,16 +95,17 @@ def main():
SeqIO.write([new_record], f, "fasta")
else:
SeqIO.write([chrom_seqs[s]], f, "fasta")
print("New fasta file created: ", new_fasta)

print("Preparing to create new annotation file")
if (index == iterations-1):
print("------------------------------------------")
print("Reform Complete")
print("------------------------------------------")
print("New fasta file created: ", new_fasta)

## Read in new GFF features from in_gff
in_gff_lines = get_in_gff_lines(in_arg.in_gff[index])

## Create a temp file for gff, if index is not equal to last iteration
annotation_name, annotation_ext = get_ref_basename(in_arg.ref_gff)
print(in_arg.ref_gff)
if index < iterations - 1:
temp_gff = tempfile.NamedTemporaryFile(delete=False, mode='w', suffix=annotation_ext)
temp_gff_name = temp_gff.name
Expand All @@ -117,7 +122,9 @@ def main():
else:
new_gff_path = create_new_gff(new_gff_name, in_arg.ref_gff, in_gff_lines, position, down_position, seq.id, len(str(record.seq)))
prev_gff_path = new_gff_path
print("New {} file created: {} ".format(annotation_ext.upper(), prev_gff_path))
if (index == iterations-1):
print(f"New fasta file created: {new_gff_path}")
print(f"Original Annotation: {in_arg.ref_gff}")


def index_fasta(fasta_path):
Expand Down Expand Up @@ -394,6 +401,7 @@ def create_new_gff(new_gff_name, ref_gff, in_gff_lines, position, down_position,
# and ends after down_position
elif gff_feat_start <= position and gff_feat_end > down_position:
print("Feature split")
print(line)
# Which side of the feature depends on the strand (we add this as a comment)
(x, y) = ("5", "3") if gff_feat_strand == "+" else ("3", "5")

Expand Down