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pharokka annotation working phage map building not yet
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,106 @@ | ||
| process pharokka { | ||
| publishDir "${params.output}/${name}/pharokka", mode: 'copy' | ||
| label 'pharokka' | ||
| input: | ||
| tuple val(name), path(fasta) | ||
| output: | ||
| path("*_pharokka_out"), emit: pharokka_folder_ch optional true | ||
| script: | ||
| """ | ||
| pharokka.py -i ${fasta} -o ${name}_pharokka_out -t 10 -d /pharokka_v1.4.0_databases -f -p ${name} | ||
| """ | ||
| stub: | ||
| """ | ||
| mkdir stub_pharokka_out | ||
| """ | ||
| } | ||
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| process pharokka_plotter { | ||
| publishDir "${params.output}/${name}/pharokka", mode: 'copy' | ||
| label 'pharokka' | ||
| input: | ||
| tuple val(name), path(fasta) | ||
| path(pharokka_annotation_out) | ||
| tuple val(sec_name), path(checkv_results) | ||
| output: | ||
| tuple val(name), path("pharokka_plots"), emit: annotation_map_ch optional true | ||
| script: | ||
| """ | ||
| ## split fasta to single contigs needed | ||
| ## LC_ALL=C allow awk to use float numbers | ||
| LC_ALL=C awk '{if(\$9>75.00)print\$1}' < ${checkv_results} |tail -n+2 > tmp_contigs_to_plot.tsv | ||
| ## extract contigs based on list | ||
| mkdir fastas_to_plot | ||
| mkdir fastas_to_plot/sub | ||
| awk -F'>' 'NR==FNR{ids[\$0]; next} NF>1{f=(\$2 in ids)} f' tmp_contigs_to_plot.tsv ${fasta} > fastas_to_plot/sub/tmp_contigs_to_plot.fasta | ||
| ## split fasta into several files | ||
| cd fastas_to_plot/ && awk -F "|" '/^>/ {close(F); ID=\$1; gsub("^>", "", ID); F=ID".fasta"} {print >> F}' sub/tmp_contigs_to_plot.fasta && cd .. | ||
| for i in fastas_to_plot/*.fasta; do | ||
| contig_name=\$(echo \$i |cut -d"/" -f2 |cut -d"." -f1) | ||
| pharokka_multiplotter.py -g ${pharokka_annotation_out}/.gbk -o pharokka_plots | ||
| pharokka_plotter.py -i \$i -n "\$contig_name"_annotation_map -o ${pharokka_annotation_out} --interval 8000 --annotations 0.5 --plot_title "\$contig_name" -p ${name} -f | ||
| ## mv ${pharokka_annotation_out}/_annotation_map.png "\$contig_name"_annotation_map.png | ||
| ## mv ${pharokka_annotation_out}/_annotation_map.svg "\$contig_name"_annotation_map.svg | ||
| mv ${pharokka_annotation_out}/*_annotation_map.png . | ||
| mv ${pharokka_annotation_out}/*_annotation_map.svg . | ||
| done | ||
| """ | ||
| stub: | ||
| """ | ||
| touch stub.svg | ||
| touch stub.png | ||
| """ | ||
| } | ||
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| // pharokka_plotter.py -i all_pos_phage_filtered.fa -n all_pos_phage_annotation_map -o all_pos_phage_pharokka_out --interval 8000 --annotations 0.5 --plot_title 'test_Phage' -p all_pos_phage | ||
| // split fasta and keep contigname as a file name:awk 'BEGIN{RS=">";FS="\n"} NR>1{fnme=$1".fasta"; print ">" $0 > fnme; close(fnme);}' example.fasta | ||
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| // | ||
| LOCUS pos_phage_9 221908 bp DNA linear PHG 25-JUL-2024 | ||
| DEFINITION pos_phage_9. | ||
| ACCESSION pos_phage_9 | ||
| VERSION pos_phage_9 | ||
| KEYWORDS . | ||
| SOURCE . | ||
| ORGANISM . | ||
| . | ||
| FEATURES Location/Qualifiers | ||
| CDS 1..753 | ||
| /ID="EPQHBJFJ_CDS_0949" | ||
| /transl_table=11 | ||
| /phrog="246" | ||
| /top_hit="p216000 VI_03943" | ||
| /locus_tag="EPQHBJFJ_CDS_0949" | ||
| /function="other" | ||
| /product="NinI-like serine-threonine phosphatase" | ||
| /source="PHANOTATE_1.5.1" | ||
| /score="-139481.4743619502" | ||
| /phase="0" | ||
| /translation="MNKRLLVISDIHGEYDMFVRLLDKVKYNPQTCQLMLLGDFVDKGP | ||
| KSREVIELVMKLVAGGAKASLGNHELSFLRWLQGDRSRFHSSTSSTFRSYVYTSGNARR | ||
| KYTRFELDEGRRYILKRYKHHVNFLKSLPYYFEDDEHVYVHAGFDSSSDDWRKNTKTDD | ||
| FVWIRERFYNNPTNEEKITVFGHTKCRRLHDSDDPWFDGDKIGIDGGASEQGQLNCLEI | ||
| LGNKEYRIHKVFARNVRGGNQTYGKQAM" | ||
| ORIGIN | ||
| 1 atgaataagc gattattagt aatatcggac atacacggag agtacgatat gttcgttagg | ||
| 61 ttattagata aagtaaagta taatccccaa acttgccaac taatgttact cggtgacttc | ||
| 121 gtggataaag gtccaaagtc acgtgaggta atcgagcttg tgatgaagtt agtcgctggt | ||
| 181 ggtgcaaaag cgtcacttgg taatcacgag ttgtcgttct tacgttggtt gcaaggcgat | ||
| 241 cgatcccgat tccattccag tacatcttca acctttagga gttatgttta cacttcaggt | ||
| 301 aacgctagac gtaagtacac tcggtttgaa ttagatgagg gtagacgtta tatacttaag | ||
| 361 cgttataagc atcatgtcaa tttcttaaag tcattgcctt attactttga agacgatgag | ||
| 421 catgtatacg ttcatgctgg attcgattca tcatccgacg actggagaaa gaacacgaag | ||
| 481 acggatgact tcgtatggat tagagaacgt ttttataaca atccaactaa tgaagaaaag | ||
| // |
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