Mercurial > repos > artbio > repenrich2
changeset 5:08e50af788f7 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit b1761de76fd068b86a06d88e70c1ba1d8644e7b5
| author | artbio |
|---|---|
| date | Sun, 21 Apr 2024 21:52:40 +0000 |
| parents | c5bb2f9af708 |
| children | 388a47ca4199 |
| files | RepEnrich2.py macros.xml repenrich2.xml test-data/Samp.fastq.gz test-data/Samp_L.fastq.gz test-data/Samp_R.fastq.gz test-data/chrY_paired_unique_mapper_counts.tab test-data/chrY_single_unique_mapper_counts.tab |
| diffstat | 8 files changed, 302 insertions(+), 1 deletions(-) [+] |
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--- a/RepEnrich2.py Sat Apr 20 23:23:40 2024 +0000 +++ b/RepEnrich2.py Sun Apr 21 21:52:40 2024 +0000 @@ -115,6 +115,12 @@ sumofrepeatreads += int(line[4]) print(f"Identified {sumofrepeatreads} unique reads that mapped to repeats.") +# print unique mapper counts +with open("unique_mapper_counts.tsv", 'w') as fout: + fout.write("#element\tcount\n") + for count in sorted(counts): + fout.write(f"{count}\t{counts[count]}\n") + # multimapper parsing if not paired_end: args_list = [(metagenome, fastqfile_1) for
--- a/macros.xml Sat Apr 20 23:23:40 2024 +0000 +++ b/macros.xml Sun Apr 21 21:52:40 2024 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.31.1</token> - <token name="@VERSION_SUFFIX@">4</token> + <token name="@VERSION_SUFFIX@">5</token> <token name="@PROFILE@">23.0</token> <xml name="repenrich_requirements">
--- a/repenrich2.xml Sat Apr 20 23:23:40 2024 +0000 +++ b/repenrich2.xml Sun Apr 21 21:52:40 2024 +0000 @@ -102,6 +102,7 @@ </inputs> <outputs> + <data format="tabular" name="unique_mapper_counts" label="RepEnrich on ${on_string}: unique mapper counts" from_work_dir="unique_mapper_counts.tsv" /> <data format="tabular" name="class_fraction_counts" label="RepEnrich on ${on_string}: class fraction counts" from_work_dir="class_fraction_counts.tsv" /> <data format="tabular" name="family_fraction_counts" label="RepEnrich on ${on_string}: family fraction counts" from_work_dir="family_fraction_counts.tsv" /> <data format="tabular" name="fraction_counts" label="RepEnrich on ${on_string}: fraction counts" from_work_dir="fraction_counts.tsv" /> @@ -114,6 +115,7 @@ <param name="genomeSource" value="history"/> <param name="genome" value="chrY-1-500k.fa" ftype="fasta"/> <param name="repeatmasker" value="chrY-1-500k.fa.out" ftype="txt"/> + <output name="unique_mapper_counts" file="chrY_single_unique_mapper_counts.tab" ftype="tabular"/> <output name="class_fraction_counts" file="chrY_single_class_fraction_counts.tab" ftype="tabular"/> <output name="family_fraction_counts" file="chrY_single_family_fraction_counts.tab" ftype="tabular"/> <output name="fraction_counts" file="chrY_single_fraction_counts.tab" ftype="tabular"/> @@ -125,6 +127,7 @@ <param name="genomeSource" value="history"/> <param name="genome" value="chrY-1-500k.fa" ftype="fasta"/> <param name="repeatmasker" value="chrY-1-500k.fa.out" ftype="txt"/> + <output name="unique_mapper_counts" file="chrY_paired_unique_mapper_counts.tab" ftype="tabular"/> <output name="class_fraction_counts" file="chrY_paired_class_fraction_counts.tab" ftype="tabular"/> <output name="family_fraction_counts" file="chrY_paired_family_fraction_counts.tab" ftype="tabular"/> <output name="fraction_counts" file="chrY_paired_fraction_counts.tab" ftype="tabular"/>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrY_paired_unique_mapper_counts.tab Sun Apr 21 21:52:40 2024 +0000 @@ -0,0 +1,146 @@ +#element count +A-rich 0 +ACCORD2_I-int 0 +ACCORD2_LTR 0 +ACCORD_I-int 0 +BARI1 0 +BATUMI_LTR 0 +BS 0 +BS2 58 +BURDOCK_I-int 0 +Baggins1 0 +Bica_I-int 38 +Bica_LTR 0 +CIRCE 0 +Chouto_I-int 0 +Copia1-I_DM 0 +Copia_I-int 25181 +Copia_LTR 647 +DIVER2_I-int 0 +DIVER2_LTR 0 +DM1731_I-int 6 +DM1731_LTR 0 +DM176_I-int 0 +DM412 0 +DM412B_LTR 0 +DMCR1A 4 +DMLTR5 0 +DMRT1A 0 +DMRT1B 86 +DMRT1C 0 +DNAREP1_DM 0 +DOC2_DM 0 +DOC3_DM 0 +FB4_DM 38 +FROGGER_I-int 0 +FW2_DM 0 +G3_DM 0 +G5A_DM 0 +G5_DM 0 +G6_DM 0 +GA-rich 0 +GTWIN_I-int 0 +G_DM 0 +Gypsy11_I-int 0 +Gypsy11_LTR 0 +Gypsy12_LTR 0 +Gypsy2-I_DM 2 +Gypsy2-LTR_DM 0 +Gypsy3_LTR 0 +Gypsy4_I-int 0 +Gypsy5_I-int 0 +Gypsy6A_LTR 0 +Gypsy6_I-int 26 +Gypsy8_I-int 0 +Gypsy8_LTR 0 +Gypsy9_I-int 0 +Gypsy_I-int 32 +Gypsy_LTR 1 +HELENA_RT 0 +HETA 24 +HMSBEAGLE_I-int 2 +IDEFIX_I-int 4 +IDEFIX_LTR 0 +Invader1_I-int 0 +Invader1_LTR 0 +Invader2_I-int 0 +Invader4_I-int 0 +Invader4_LTR 0 +Invader5_I-int 0 +Invader5_LTR 0 +Invader6_I-int 0 +Invader6_LTR 0 +MAX_I-int 49 +MAX_LTR 2 +MDG1_I-int 0 +MDG1_LTR 0 +MDG3_I-int 152 +MDG3_LTR 0 +MICROPIA_I-int 0 +MICROPIA_LTR 0 +Mariner2_DM 0 +NINJA_I-int 0 +NOMAD_I-int 0 +PROTOP_A 32 +PROTOP_B 0 +QUASIMODO2-I_DM 42 +QUASIMODO2-LTR_DM 0 +QUASIMODO_I-int 10 +QUASIMODO_LTR 2 +R1_DM 0 +ROOA_I-int 0 +ROOA_LTR 0 +ROVER-I_DM 381 +ROVER-LTR_DM 2 +S2_DM 0 +STALKER4_I-int 77 +STALKER4_LTR 4 +S_DM 48 +Stalker2_I-int 80 +Stalker2_LTR 2 +TART-A 4 +TART_B1 19 +TC1-2_DM 0 +TC1_DM 0 +TLD2 0 +TRANSIB1 0 +TRANSIB2 30 +ZAM_I-int 0 +_AACACA_n 0 +_AAT_n 0 +_ACAATAG_n 0 +_ACC_n 0 +_AGAGAAG_n 0 +_AGAGA_n 0 +_ATAAT_n 0 +_ATATATT_n 0 +_ATATTAT_n 0 +_ATTTTT_n 0 +_ATT_n 0 +_AT_n 0 +_A_n 0 +_CATA_n 0 +_CTTTT_n 0 +_GAGAA_n 0 +_GCCTTT_n 0 +_TAATAT_n 0 +_TAATA_n 0 +_TATAAAA_n 0 +_TATAA_n 0 +_TATCATG_n 0 +_TA_n 0 +_TGTTG_n 0 +_TTATATA_n 0 +_TTATAT_n 0 +_TTATA_n 0 +_TTA_n 0 +_TTCTT_n 0 +_TTC_n 0 +_TTTAT_n 0 +_TTTA_n 0 +_TTTC_n 0 +_TTTGA_n 0 +_TTTTAG_n 0 +_TTTTCTT_n 0 +_TTTTC_n 0 +_T_n 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrY_single_unique_mapper_counts.tab Sun Apr 21 21:52:40 2024 +0000 @@ -0,0 +1,146 @@ +#element count +A-rich 0 +ACCORD2_I-int 0 +ACCORD2_LTR 0 +ACCORD_I-int 0 +BARI1 0 +BATUMI_LTR 0 +BS 0 +BS2 29 +BURDOCK_I-int 0 +Baggins1 0 +Bica_I-int 19 +Bica_LTR 0 +CIRCE 0 +Chouto_I-int 0 +Copia1-I_DM 0 +Copia_I-int 12652 +Copia_LTR 134 +DIVER2_I-int 1 +DIVER2_LTR 0 +DM1731_I-int 3 +DM1731_LTR 0 +DM176_I-int 0 +DM412 0 +DM412B_LTR 0 +DMCR1A 2 +DMLTR5 0 +DMRT1A 0 +DMRT1B 35 +DMRT1C 0 +DNAREP1_DM 0 +DOC2_DM 0 +DOC3_DM 0 +FB4_DM 15 +FROGGER_I-int 0 +FW2_DM 0 +G3_DM 0 +G5A_DM 0 +G5_DM 0 +G6_DM 0 +GA-rich 0 +GTWIN_I-int 0 +G_DM 0 +Gypsy11_I-int 0 +Gypsy11_LTR 0 +Gypsy12_LTR 0 +Gypsy2-I_DM 1 +Gypsy2-LTR_DM 0 +Gypsy3_LTR 0 +Gypsy4_I-int 0 +Gypsy5_I-int 0 +Gypsy6A_LTR 0 +Gypsy6_I-int 12 +Gypsy8_I-int 0 +Gypsy8_LTR 0 +Gypsy9_I-int 0 +Gypsy_I-int 15 +Gypsy_LTR 0 +HELENA_RT 0 +HETA 12 +HMSBEAGLE_I-int 1 +IDEFIX_I-int 0 +IDEFIX_LTR 0 +Invader1_I-int 0 +Invader1_LTR 0 +Invader2_I-int 0 +Invader4_I-int 0 +Invader4_LTR 0 +Invader5_I-int 0 +Invader5_LTR 0 +Invader6_I-int 0 +Invader6_LTR 0 +MAX_I-int 27 +MAX_LTR 1 +MDG1_I-int 0 +MDG1_LTR 0 +MDG3_I-int 70 +MDG3_LTR 0 +MICROPIA_I-int 0 +MICROPIA_LTR 0 +Mariner2_DM 0 +NINJA_I-int 0 +NOMAD_I-int 0 +PROTOP_A 18 +PROTOP_B 0 +QUASIMODO2-I_DM 19 +QUASIMODO2-LTR_DM 0 +QUASIMODO_I-int 3 +QUASIMODO_LTR 1 +R1_DM 0 +ROOA_I-int 0 +ROOA_LTR 0 +ROVER-I_DM 188 +ROVER-LTR_DM 1 +S2_DM 0 +STALKER4_I-int 28 +STALKER4_LTR 0 +S_DM 25 +Stalker2_I-int 32 +Stalker2_LTR 2 +TART-A 2 +TART_B1 10 +TC1-2_DM 0 +TC1_DM 0 +TLD2 0 +TRANSIB1 0 +TRANSIB2 12 +ZAM_I-int 0 +_AACACA_n 0 +_AAT_n 0 +_ACAATAG_n 0 +_ACC_n 0 +_AGAGAAG_n 0 +_AGAGA_n 0 +_ATAAT_n 0 +_ATATATT_n 0 +_ATATTAT_n 0 +_ATTTTT_n 0 +_ATT_n 0 +_AT_n 0 +_A_n 0 +_CATA_n 0 +_CTTTT_n 0 +_GAGAA_n 0 +_GCCTTT_n 0 +_TAATAT_n 0 +_TAATA_n 0 +_TATAAAA_n 0 +_TATAA_n 0 +_TATCATG_n 0 +_TA_n 0 +_TGTTG_n 0 +_TTATATA_n 0 +_TTATAT_n 0 +_TTATA_n 0 +_TTA_n 0 +_TTCTT_n 0 +_TTC_n 0 +_TTTAT_n 0 +_TTTA_n 0 +_TTTC_n 0 +_TTTGA_n 0 +_TTTTAG_n 0 +_TTTTCTT_n 0 +_TTTTC_n 0 +_T_n 0