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Add python requirement to CONVERTER_bed_to_gff_0

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mvdbeek
2020-02-09 16:44:20 +01:00
parent 113b01085a
commit d355b778c5
2 changed files with 50 additions and 48 deletions
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lib/galaxy/datatypes/converters/bed_to_gff_converter.xml
+4 -1
View File
@@ -1,6 +1,9 @@
<tool id="CONVERTER_bed_to_gff_0" name="Convert BED to GFF" version="2.0.0">
<tool id="CONVERTER_bed_to_gff_0" name="Convert BED to GFF" version="2.0.1" profile="16.04">
<!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
<!-- Used on the metadata edit page. -->
<requirements>
<requirement type="package" version="3.7">python</requirement>
</requirements>
<command>python '$__tool_directory__/bed_to_gff_converter.py' '$input1' '$output1'</command>
<inputs>
<param format="bed" name="input1" type="data" label="Choose BED file"/>
tools/filters/bed_to_gff_converter.py
+46 -47
View File
@@ -12,60 +12,59 @@ def __main__():
output_name = sys.argv[2]
skipped_lines = 0
first_skipped_line = 0
out = open(output_name, 'w')
i = 0
for i, line in enumerate(open(input_name)):
complete_bed = False
line = line.rstrip('\r\n')
if line and not line.startswith('#') and not line.startswith('track') and not line.startswith('browser'):
try:
elems = line.split('\t')
if len(elems) == 12:
complete_bed = True
chrom = elems[0]
if complete_bed:
feature = "mRNA"
else:
with open(output_name, 'w') as out, open(input_name) as fh_in:
for i, line in enumerate(fh_in):
complete_bed = False
line = line.rstrip('\r\n')
if line and not line.startswith('#') and not line.startswith('track') and not line.startswith('browser'):
try:
elems = line.split('\t')
if len(elems) == 12:
complete_bed = True
chrom = elems[0]
if complete_bed:
feature = "mRNA"
else:
try:
feature = elems[3]
except Exception:
feature = 'feature%d' % (i + 1)
start = int(elems[1]) + 1
end = int(elems[2])
try:
feature = elems[3]
score = elems[4]
except Exception:
feature = 'feature%d' % (i + 1)
start = int(elems[1]) + 1
end = int(elems[2])
try:
score = elems[4]
score = '0'
try:
strand = elems[5]
except Exception:
strand = '+'
try:
group = elems[3]
except Exception:
group = 'group%d' % (i + 1)
if complete_bed:
out.write('%s\tbed2gff\t%s\t%d\t%d\t%s\t%s\t.\t%s %s;\n' % (chrom, feature, start, end, score, strand, feature, group))
else:
out.write('%s\tbed2gff\t%s\t%d\t%d\t%s\t%s\t.\t%s;\n' % (chrom, feature, start, end, score, strand, group))
if complete_bed:
# We have all the info necessary to annotate exons for genes and mRNAs
block_count = int(elems[9])
block_sizes = elems[10].split(',')
block_starts = elems[11].split(',')
for j in range(block_count):
exon_start = int(start) + int(block_starts[j])
exon_end = exon_start + int(block_sizes[j]) - 1
out.write('%s\tbed2gff\texon\t%d\t%d\t%s\t%s\t.\texon %s;\n' % (chrom, exon_start, exon_end, score, strand, group))
except Exception:
score = '0'
try:
strand = elems[5]
except Exception:
strand = '+'
try:
group = elems[3]
except Exception:
group = 'group%d' % (i + 1)
if complete_bed:
out.write('%s\tbed2gff\t%s\t%d\t%d\t%s\t%s\t.\t%s %s;\n' % (chrom, feature, start, end, score, strand, feature, group))
else:
out.write('%s\tbed2gff\t%s\t%d\t%d\t%s\t%s\t.\t%s;\n' % (chrom, feature, start, end, score, strand, group))
if complete_bed:
# We have all the info necessary to annotate exons for genes and mRNAs
block_count = int(elems[9])
block_sizes = elems[10].split(',')
block_starts = elems[11].split(',')
for j in range(block_count):
exon_start = int(start) + int(block_starts[j])
exon_end = exon_start + int(block_sizes[j]) - 1
out.write('%s\tbed2gff\texon\t%d\t%d\t%s\t%s\t.\texon %s;\n' % (chrom, exon_start, exon_end, score, strand, group))
except Exception:
skipped_lines += 1
if not first_skipped_line:
first_skipped_line = i + 1
else:
skipped_lines += 1
if not first_skipped_line:
first_skipped_line = i + 1
else:
skipped_lines += 1
if not first_skipped_line:
first_skipped_line = i + 1
out.close()
info_msg = "%i lines converted to GFF version 2. " % (i + 1 - skipped_lines)
if skipped_lines > 0:
info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." % (skipped_lines, first_skipped_line)