Mercurial > repos > iuc > ivar_removereads
changeset 10:ee29337f905c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 8ce6fd9aee543d9e62db33a9c95f79d8dc4e6dea
| author | iuc |
|---|---|
| date | Wed, 13 Jul 2022 15:20:33 +0000 |
| parents | 8d36959b000d |
| children | 7f1cfa4c0e32 |
| files | ivar_removereads.xml prepare_amplicon_info.py sanitize_bed.py write_amplicon_info_file.py |
| diffstat | 4 files changed, 20 insertions(+), 10 deletions(-) [+] |
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--- a/ivar_removereads.xml Fri Aug 20 20:34:11 2021 +0000 +++ b/ivar_removereads.xml Wed Jul 13 15:20:33 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="ivar_removereads" name="ivar removereads" version="@VERSION@+galaxy2"> +<tool id="ivar_removereads" name="ivar removereads" version="@VERSION@+galaxy3" profile="21.01"> <description>Remove reads from trimmed BAM file</description> <macros> <import>macros.xml</import> @@ -22,7 +22,7 @@ ln -s '$input_bam' sorted.bam && ln -s '${input_bam.metadata.bam_index}' sorted.bam.bai && - ivar removereads + ivar removereads -i sorted.bam -b binding_sites.bed -p removed_reads.bam @@ -109,7 +109,7 @@ Preprocessing of the BAM input with ivar trim is essential for this tool to work because only ``ivar trim`` can add required primer information to the BAM auxillary data of every read. - + ivar documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`__. ]]></help> <expand macro="citations" />
--- a/prepare_amplicon_info.py Fri Aug 20 20:34:11 2021 +0000 +++ b/prepare_amplicon_info.py Wed Jul 13 15:20:33 2022 +0000 @@ -11,7 +11,10 @@ primer_starts = {} with open(sys.argv[1]) as i: for line in i: - f = line.strip().split('\t') + line = line.strip() + if not line: + continue + f = line.split('\t') try: if f[5] == '+': primer_starts[f[3]] = int(f[1]) @@ -32,8 +35,11 @@ with open(sys.argv[2]) as i: ret_lines = [] for line in i: + line = line.strip() + if not line: + continue first = last = None - for pname in line.strip().split('\t'): + for pname in line.split('\t'): try: primer_start = primer_starts[pname] except KeyError:
--- a/sanitize_bed.py Fri Aug 20 20:34:11 2021 +0000 +++ b/sanitize_bed.py Wed Jul 13 15:20:33 2022 +0000 @@ -9,10 +9,11 @@ sanitized_data = [] try: for record in bed_data: - fields = record.split('\t') - sanitized_data.append( - '\t'.join(fields[:4] + ['60'] + fields[5:]) - ) + if record.strip(): + fields = record.split('\t') + sanitized_data.append( + '\t'.join(fields[:4] + ['60'] + fields[5:]) + ) except IndexError: pass # leave column number issue to getmasked else:
--- a/write_amplicon_info_file.py Fri Aug 20 20:34:11 2021 +0000 +++ b/write_amplicon_info_file.py Wed Jul 13 15:20:33 2022 +0000 @@ -10,7 +10,10 @@ def write_amplicon_info_file(bed_file, amplicon_info_file): amplicon_sets = {} for line in bed_file: - fields = line.strip().split('\t') + line = line.strip() + if not line: + continue + fields = line.split('\t') start = int(fields[1]) name = fields[3] re_match = AMPLICON_PAT.match(name)