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Merge pull request #291 from sanger-tol/galaxy_dev
1.1.0 - Ancient Aurora
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,30 +1,38 @@ | ||
| assembly: | ||
| assem_level: scaffold | ||
| assem_version: 1 | ||
| sample_id: OscheiusSUBSET | ||
| latin_name: to_provide_taxonomic_rank | ||
| defined_class: nematode | ||
| assem_version: 1 | ||
| project_id: DTOL | ||
| reference_file: /lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_SUBSET/assembly/draft/SUBSET_genome/Oscheius_SUBSET.fasta | ||
| #/lustre/scratch123/tol/resources/treeval/nextflow_test_data/Oscheius_DF5033/assembly/draft/DF5033.hifiasm.noTelos.20211120/DF5033.noTelos.hifiasm.purged.noCont.noMito.fasta | ||
| map_order: length | ||
| assem_reads: | ||
| pacbio: /lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_SUBSET/genomic_data/pacbio/ | ||
| hic: /lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_DF5033/genomic_data/nxOscSpes1/hic-arima2/subset/ | ||
| supplementary: path | ||
| read_type: hifi | ||
| read_data: /lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_SUBSET/genomic_data/pacbio/ | ||
| supplementary_data: path | ||
| hic_data: | ||
| hic_cram: /lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_DF5033/genomic_data/nxOscSpes1/hic-arima2/subset/ | ||
| hic_aligner: minimap2 | ||
| kmer_profile: | ||
| # kmer_length will act as input for kmer_read_cov fastk and as the name of folder in profile_dir | ||
| kmer_length: 31 | ||
| dir: /lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_DF5033/genomic_data/nxOscSpes1/pacbio/ | ||
| alignment: | ||
| data_dir: /lustre/scratch123/tol/resources/treeval/gene_alignment_data/ | ||
| common_name: "" # For future implementation (adding bee, wasp, ant etc) | ||
| geneset: "Gae_host.Gae" | ||
| geneset_id: "Gae_host.Gae" | ||
| #Path should end up looking like "{data_dir}{classT}/{common_name}/csv_data/{geneset}-data.csv" | ||
| self_comp: | ||
| motif_len: 0 | ||
| mummer_chunk: 4 | ||
| mummer_chunk: 10 | ||
| intron: | ||
| size: "50k" | ||
| telomere: | ||
| teloseq: TTAGGG | ||
| synteny: | ||
| synteny_genome_path: /lustre/scratch123/tol/resources/treeval/synteny/ | ||
| synteny_path: /nfs/treeoflife-01/teams/tola/users/dp24/treeval/TreeValTinyData/synteny/ | ||
| synteny_genomes: "" | ||
| busco: | ||
| lineages_path: /lustre/scratch123/tol/resources/busco/v5 | ||
| lineage: nematoda_odb10 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -2,8 +2,11 @@ | |
| import pandas as pd | ||
| import optparse | ||
|
|
||
|
|
||
| # Script originally developed by Yumi Sims ([email protected]) | ||
| # ------------------- | ||
| # Update for BUSCO 5.5.0 - by we3 (Will Eagles) | ||
| # Reorder start and end so smallest always second column. Also, trim range from scaffold name in first column. | ||
| # ------------------- | ||
|
|
||
| parser = optparse.OptionParser(version="%prog 1.0") | ||
| parser.add_option( | ||
|
|
@@ -65,4 +68,15 @@ | |
|
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| df_final = df_final.astype({"Gene End": "int", "Gene Start": "int"}) | ||
|
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| df_final["Sequence"] = df_final["Sequence"].str.replace(r":.*", "", regex=True) | ||
|
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||
| df_final[["Gene Start", "Gene End"]] = df_final.apply( | ||
| lambda row: ( | ||
| (row["Gene Start"], row["Gene End"]) | ||
| if row["Gene Start"] < row["Gene End"] | ||
| else (row["Gene End"], row["Gene Start"]) | ||
| ), | ||
| axis=1, | ||
| result_type="expand", | ||
| ) | ||
| df_final.to_csv(csvfile, index=False, header=False, sep="\t") | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| awk 'BEGIN{OFS="\t"}{if($1 ~ /^\@/) {print($0)} else {$2=and($2,compl(2048)); print(substr($0,2))}}' |
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